Publications

Fraunhoffer, N. A., Moreno Vega, A. I., Abuelafia, A. M., Morvan, M., Lebarbier, E., Mary-Huard, T., Zimmermann, M., Lomberk, G., Urrutia, R., Dusetti, N., Blum, Y., Nicolle, R.# & Iovanna, J. Priming therapy by targeting enhancer-initiated pathways in patient-derived pancreatic cancer cells. eBioMedicine 92, 104602 (2023).

Mas, L., Cros, J., Svrcek, M., Van Laethem, J. L., Emile, J. F., Rebours, V., Nicolle, R. & Bachet, J. B. Trop-2 is a ubiquitous and promising target in pancreatic adenocarcinoma. Clinics and Research in Hepatology and Gastroenterology 47, 102108 (2023).

Hilmi, M., Kamal, M., Vacher, S., Dupain, C., Ibadioune, S., Halladjian, M., Sablin, M. P., Marret, G., Ajgal, Z. C., Nijnikoff, M., Salomon, A., El Beaino, Z., Servant, N., Dureau, S., Sokol, H., Nicolle, R., Le Tourneau, C., Bieche, I. & Neuzillet, C. Intratumoral microbiome is driven by metastatic site and associated with immune histopathological parameters: an ancillary study of the SHIVA clinical trial. European Journal of Cancer S0959804923000485 (2023).

Turpin, A., Neuzillet, C., Colle, E., Dusetti, N., Nicolle, R., Cros, J., de Mestier, L., Bachet, J.-B. & Hammel, P. Therapeutic advances in metastatic pancreatic cancer: a focus on targeted therapies. Therapeutic Advances in Medical Oncology 14, 175883592211180 (2022).

Ponzo, M., Debesset, A., Cossutta, M., Chalabi-Dchar, M., Houppe, C., Pilon, C., Nicolas-Boluda, A., Meunier, S., Raineri, F., Thiolat, A., Nicolle, R., Maione, F., Brundu, S., Cojocaru, C. F., Bouvet, P., Bousquet, C., Gazeau, F., Tournigand, C., Courty, J., Giraudo, E., Cohen, J. L. & Cascone, I. Nucleolin Therapeutic Targeting Decreases Pancreatic Cancer Immunosuppression. Cancers 14, 4265 (2022).

Nicolle, R., Gayet, O., Bigonnet, M., Roques, J., Chanez, B., Puleo, F., Augustin, J., Emile, J. F., Svrcek, M., Arsenijevic, T., Hammel, P., Rebours, V., Giovannini, M., Grandval, P., Dahan, L., Moutardier, V., Mitry, E., Van Laethem, J. L., Bachet, J. B., Cros, J., Iovanna, J. & Dusetti, N. J. Relevance of biopsy-derived pancreatic organoids in the development of efficient transcriptomic signatures to predict adjuvant chemosensitivity in pancreatic cancer. Translational Oncology 16, 101315 (2022).

Neuzillet, C., Nicolle, R., Raffenne, J., Tijeras-Raballand, A., Brunel, A., Astorgues-Xerri, L., Vacher, S., Arbateraz, F., Fanjul, M., Hilmi, M., Samain, R., Klein, C., Perraud, A., Rebours, V., Mathonnet, M., Bièche, I., Kocher, H., Cros, J. & Bousquet, C. Periostin- and podoplanin-positive cancer-associated fibroblast subtypes cooperate to shape the inflamed tumor microenvironment in aggressive pancreatic adenocarcinoma. The Journal of Pathology 258, 408–425 (2022).

Hilmi, M., Armenoult, L., Ayadi, M. & Nicolle, R. Whole-Transcriptome Profiling on Small FFPE Samples: Which Sequencing Kit Should Be Used? Current Issues in Molecular Biology 44, 2186–2193 (2022).

Fraunhoffer, N. A., Abuelafia, A. M., Bigonnet, M., Gayet, O., Roques, J., Nicolle, R., Lomberk, G., Urrutia, R., Dusetti, N. & Iovanna, J. Multi-omics data integration and modeling unravels new mechanisms for pancreatic cancer and improves prognostic prediction. npj Precision Oncology 6, 57 (2022).

Depoilly, T., Leroux, R., Andrade, D., Nicolle, R., Dioguardi Burgio, M., Marinoni, I., Dokmak, S., Ruszniewski, P., Hentic, O., Paradis, V., De Mestier, L., Perren, A., Couvelard, A. & Cros, J. Immunophenotypic and molecular characterization of pancreatic neuroendocrine tumors producing serotonin. Modern Pathology 35, 1713–1722 (2022).

de Mestier, L., Nicolle, R., Poté, N., Rebours, V., Cauchy, F., Hentic, O., Maire, F., Ronot, M., Lebtahi, R., Sauvanet, A., Paradis, V., Ruszniewski, P., Couvelard, A. & Cros, J. Molecular deciphering of primary liver neuroendocrine neoplasms confirms their distinct existence with foregut-like profile. The Journal of Pathology 258, 58–68 (2022).

Zhao, S., Nicolle, R., Augustin, J., Svrcek, M., de Mestier, L., Le Corre, D., Pietrasz, D., Caliez, O., Cros, J., Laurent-Puig, P. & Bachet, J.-B. Prognostic Relevance of Pancreatic Adenocarcinoma Whole-Tumor Transcriptomic Subtypes and Components. Clinical Cancer Research 27, 6491–6499 (2021).

Tijeras-Raballand, A., Hilmi, M., Astorgues-Xerri, L., Nicolle, R., Bièche, I. & Neuzillet, C. Microbiome and pancreatic ductal adenocarcinoma. Clinics and Research in Hepatology and Gastroenterology 45, 101589 (2021).

Samain, R., Brunel, A., Douché, T., Fanjul, M., Cassant-Sourdy, S., Rochotte, J., Cros, J., Neuzillet, C., Raffenne, J., Duluc, C., Perraud, A., Nigri, J., Gigoux, V., Bieche, I., Ponzo, M., Carpentier, G., Cascone, I., Tomasini, R., Schmid, H. A., Mathonnet, M., Nicolle, R., Bousquet, M.-P., Martineau, Y., Pyronnet, S., Jean, C. & Bousquet, C. Pharmacologic Normalization of Pancreatic Cancer-Associated Fibroblast Secretome Impairs Prometastatic Cross-Talk With Macrophages. Cellular and Molecular Gastroenterology and Hepatology 11, 1405–1436 (2021).

Ratovomanana, T., Cohen, R., Svrcek, M., Renaud, F., Cervera, P., Siret, A., Letourneur, Q., Buhard, O., Bourgoin, P., Guillerm, E., Dorard, C., Nicolle, R., Ayadi, M., Touat, M., Bielle, F., Sanson, M., Le Rouzic, P., Buisine, M.-P., Piessen, G., Collura, A., Fléjou, J.-F., de Reyniès, A., Coulet, F., Ghiringhelli, F., André, T., Jonchère, V. & Duval, A. Performance of Next-Generation Sequencing for the Detection of Microsatellite Instability in Colorectal Cancer With Deficient DNA Mismatch Repair. Gastroenterology 161, 814-826.e7 (2021).

Raffenne, J., Martin, F. A., Nicolle, R., Konta, M., Blum, Y., Torrisani, J., Puleo, F., Bachet, J. B., Svrcek, M., Bardier-Dupas, A., Emile, J. F., Demetter, P., Radman, M., Van Laethem, J. L., Hammel, P., Rebours, V., Paradis, V., Couvelard, A. & Cros, J. Pancreatic Ductal Adenocarcinoma Arising in Young and Old Patients Displays Similar Molecular Features. Cancers 13, (2021).

Nicolle, R., Gayet, O., Duconseil, P., Vanbrugghe, C., Roques, J., Bigonnet, M., Blum, Y., Elarouci, N., Armenoult, L., Ayadi, M., de Reyniès, A., Puleo, F., Augustin, J., Emile, J. F., Svrcek, M., Arsenijevic, T., Hammel, P., Giovannini, M., Grandval, P., Dahan, L., Moutardier, V., Gilabert, M., Van Laethem, J. L., Bachet, J. B., Cros, J., Iovanna, J. & Dusetti, N. J. A transcriptomic signature to predict adjuvant gemcitabine sensitivity in pancreatic adenocarcinoma. Annals of Oncology 32, 250–260 (2021).

Mohamed Abd-El-Halim, Y., El Kaoutari, A., Silvy, F., Rubis, M., Bigonnet, M., Roques, J., Cros, J., Nicolle, R., Iovanna, J., Dusetti, N. & Mas, E. A glycosyltransferase gene signature to detect pancreatic ductal adenocarcinoma patients with poor prognosis. EBioMedicine 71, 103541 (2021).

Hoare, O., Fraunhoffer, N., Elkaoutari, A., Gayet, O., Bigonnet, M., Roques, J., Nicolle, R., McGuckin, C., Forraz, N., Sohier, E., Tonon, L., Wajda, P., Boyault, S., Attignon, V., Tabone-Eglinger, S., Barbier, S., Mignard, C., Duchamp, O., Iovanna, J. & Dusetti, N. J. Exploring the Complementarity of Pancreatic Ductal Adenocarcinoma Preclinical Models. Cancers 13, 2473 (2021).

Hilmi, M., Cros, J., Puleo, F., Augustin, J., Emile, J.-F., Svrcek, M., Hammel, P., Arsenijevic, T., Van Laethem, J.-L., Bachet, J.-B. & Nicolle, R. Tumour and stroma RNA signatures predict more accurately distant recurrence than clinicopathological factors in resected pancreatic adenocarcinoma. European Journal of Cancer 148, 171–180 (2021).

Fraunhoffer, N. A., Abuelafia, A. M., Teyssedou, C., Chuluyan, E., Bigonnet, M., Palazzo, L., Gayet, O., Nicolle, R., Cros, J., Iovanna, J. & Dusetti, N. Squamousness gain defines pancreatic ductal adenocarcinoma hepatic metastases phenotype, and gemcitabine response. European Journal of Cancer 155, 42–53 (2021).

Dhara, S., Chhangawala, S., Chintalapudi, H., Askan, G., Aveson, V., Massa, A. L., Zhang, L., Torres, D., Makohon-Moore, A. P., Lecomte, N., Melchor, J. P., Bermeo, J., Cardenas, A., Sinha, S., Glassman, D., Nicolle, R., Moffitt, R., Yu, K. H., Leppanen, S., Laderman, S., Curry, B., Gui, J., Balachandran, V. P., Iacobuzio-Donahue, C., Chandwani, R., Leslie, C. S. & Leach, S. D. Pancreatic cancer prognosis is predicted by an ATAC-array technology for assessing chromatin accessibility. Nature Communications 12, 3044 (2021).

Decamps, C., Arnaud, A., Petitprez, F., Ayadi, M., Baurès, A., Armenoult, L., HADACA consortium, Escalera, S., Guyon, I., Nicolle, R., Tomasini, R., de Reyniès, A., Cros, J., Blum, Y. & Richard, M. DECONbench: a benchmarking platform dedicated to deconvolution methods for tumor heterogeneity quantification. BMC Bioinformatics 22, 473 (2021).

Cros, J., Théou-Anton, N., Gounant, V., Nicolle, R., Reyes, C., Humez, S., Hescot, S., Thomas de Montpréville, V., Guyétant, S., Scoazec, J.-Y., Guyard, A., de Mestier, L., Brosseau, S., Mordant, P., Castier, Y., Gentien, D., Ruszniewski, P., Zalcman, G., Couvelard, A. & Cazes, A. Specific Genomic Alterations in High-Grade Pulmonary Neuroendocrine Tumours with Carcinoid Morphology. Neuroendocrinology 111, 158–169 (2021).

Arsenijevic, T., Nicolle, R., Bouchart, C., D’Haene, N., Demetter, P., Puleo, F. & Van Laethem, J.-L. Pancreatic Cancer Meets Human Microbiota: Close Encounters of the Third Kind. Cancers 13, (2021).

Nicolle, R., Blum, Y., Duconseil, P., Vanbrugghe, C., Brandone, N., Poizat, F., Roques, J., Bigonnet, M., Gayet, O., Rubis, M., Elarouci, N., Armenoult, L., Ayadi, M., de Reyniès, A., Giovannini, M., Grandval, P., Garcia, S., Canivet, C., Cros, J., Bournet, B., Moutardier, V., Gilabert, M., Iovanna, J., Dusetti, N. & Buscail, L. Establishment of a pancreatic adenocarcinoma molecular gradient (PAMG) that predicts the clinical outcome of pancreatic cancer. EBioMedicine 57, 102858 (2020).

Juiz, N., Elkaoutari, A., Bigonnet, M., Gayet, O., Roques, J., Nicolle, R., Iovanna, J. & Dusetti, N. Basal-like and classical cells coexist in pancreatic cancer revealed by single-cell analysis on biopsy-derived pancreatic cancer organoids from the classical subtype. FASEB journal 34, 12214–12228 (2020).

Hilmi, M., Nicolle, R., Bousquet, C. & Neuzillet, C. Cancer-Associated Fibroblasts: Accomplices in the Tumor Immune Evasion. Cancers 12, 2969 (2020).

Raffenne, J., Nicolle, R., Puleo, F., Le Corre, D., Boyez, C., Marechal, R., Emile, J. F., Demetter, P., Bardier, A., Laurent-Puig, P., de Mestier, L., Paradis, V., Couvelard, A., VanLathem, J. L., MacKey, J. R., Bachet, J.-B., Svrcek, M. & Cros, J. hENT1 Testing in Pancreatic Ductal Adenocarcinoma: Are We Ready? A Multimodal Evaluation of hENT1 Status. Cancers 11, 1808 (2019).

Nicolle, R., Raffenne, J., Paradis, V., Couvelard, A., de Reynies, A., Blum, Y. & Cros, J. Prognostic Biomarkers in Pancreatic Cancer: Avoiding Errata When Using the TCGA Dataset. Cancers 11, 126 (2019).

Nicolle, R., Ayadi, M., Gomez-Brouchet, A., Armenoult, L., Banneau, G., Elarouci, N., Tallegas, M., Decouvelaere, A.-V., Aubert, S., Rédini, F., Marie, B., Labit-Bouvier, C., Reina, N., Karanian, M., le Nail, L.-R., Anract, P., Gouin, F., Larousserie, F., de Reyniès, A. & de Pinieux, G. Integrated molecular characterization of chondrosarcoma reveals critical determinants of disease progression. Nature Communications 10, 4622 (2019).

Martens, S., Lefesvre, P., Nicolle, R., Biankin, A. V., Puleo, F., Van Laethem, J. L. & Rooman, I. Different shades of pancreatic ductal adenocarcinoma, different paths towards precision therapeutic applications. Annals of Oncology 30, 1428–1436 (2019).

Puleo, F., Nicolle, R., Blum, Y., Cros, J., Marisa, L., Demetter, P., Quertinmont, E., Svrcek, M., Elarouci, N., Iovanna, J., Franchimont, D., Verset, L., Galdon, M. G., Devière, J., de Reyniès, A., Laurent-Puig, P., Van Laethem, J.-L., Bachet, J.-B. & Maréchal, R. Stratification of Pancreatic Ductal Adenocarcinomas Based on Tumor and Microenvironment Features. Gastroenterology 155, 1999-2013.e3 (2018).

Mahe, M., Dufour, F., Neyret-Kahn, H., Moreno-Vega, A., Beraud, C., Shi, M., Hamaidi, I., Sanchez-Quiles, V., Krucker, C., Dorland-Galliot, M., Chapeaublanc, E., Nicolle, R., Lang, H., Pouponnot, C., Massfelder, T., Radvanyi, F. & Bernard-Pierrot, I. An FGFR3/MYC positive feedback loop provides new opportunities for targeted therapies in bladder cancers. EMBO Molecular Medicine 10, (2018).

Lomberk, G., Blum, Y., Nicolle, R., Nair, A., Gaonkar, K. S., Marisa, L., Mathison, A., Sun, Z., Yan, H., Elarouci, N., Armenoult, L., Ayadi, M., Ordog, T., Lee, J.-H., Oliver, G., Klee, E., Moutardier, V., Gayet, O., Bian, B., Duconseil, P., Gilabert, M., Bigonnet, M., Garcia, S., Turrini, O., Delpero, J.-R., Giovannini, M., Grandval, P., Gasmi, M., Secq, V., De Reyniès, A., Dusetti, N., Iovanna, J. & Urrutia, R. Distinct epigenetic landscapes underlie the pathobiology of pancreatic cancer subtypes. Nature Communications 9, 1978 (2018).

Nicolle, R., Blum, Y., Marisa, L., Loncle, C., Gayet, O., Moutardier, V., Turrini, O., Giovannini, M., Bian, B., Bigonnet, M., Rubis, M., Elarouci, N., Armenoult, L., Ayadi, M., Duconseil, P., Gasmi, M., Ouaissi, M., Maignan, A., Lomberk, G., Boher, J.-M., Ewald, J., Bories, E., Garnier, J., Goncalves, A., Poizat, F., Raoul, J.-L., Secq, V., Garcia, S., Grandval, P., Barraud-Blanc, M., Norguet, E., Gilabert, M., Delpero, J.-R., Roques, J., Calvo, E., Guillaumond, F., Vasseur, S., Urrutia, R., de Reyniès, A., Dusetti, N. & Iovanna, J. Pancreatic Adenocarcinoma Therapeutic Targets Revealed by Tumor-Stroma Cross-Talk Analyses in Patient-Derived Xenografts. Cell Reports 21, 2458–2470 (2017).

Bian, B., Bigonnet, M., Gayet, O., Loncle, C., Maignan, A., Gilabert, M., Moutardier, V., Garcia, S., Turrini, O., Delpero, J., Giovannini, M., Grandval, P., Gasmi, M., Ouaissi, M., Secq, V., Poizat, F., Nicolle, R., Blum, Y., Marisa, L., Rubis, M., Raoul, J., Bradner, J. E., Qi, J., Lomberk, G., Urrutia, R., Saul, A., Dusetti, N. & Iovanna, J. Gene expression profiling of patient-derived pancreatic cancer xenografts predicts sensitivity to the BET bromodomain inhibitor JQ 1: implications for individualized medicine efforts. EMBO Molecular Medicine 9, 482–497 (2017).

Picchetti, T., Chiquet, J., Elati, M., Neuvial, P., Nicolle, R. & Birmelé, E. A model for gene deregulation detection using expression data. BMC systems biology 9, S6 (2015).

Nicolle, R., Radvanyi, F. & Elati, M. CoRegNet: reconstruction and integrated analysis of co-regulatory networks. Bioinformatics 31, 3066–3068 (2015).

Winterhalter, C., Nicolle, R., Louis, A., To, C., Radvanyi, F. & Elati, M. Pepper: cytoscape app for protein complex expansion using protein–protein interaction networks. Bioinformatics 30, 3419–3420 (2014).

Mahmood, S. F., Gruel, N., Nicolle, R., Chapeaublanc, E., Delattre, O., Radvanyi, F. & Bernard-Pierrot, I. PPAPDC1B and WHSC1L1 are common drivers of the 8p11-12 amplicon, not only in breast tumors but also in pancreatic adenocarcinomas and lung tumors. The American journal of pathology 183, 1634–1644 (2013).

Elati, M., Nicolle, R., Junier, I., Fernández, D., Fekih, R., Font, J. & Képès, F. PreCisIon: PREdiction of CIS-regulatory elements improved by gene’s positION. Nucleic acids research 41, 1406–1415 (2013).

Ho, J. R., Chapeaublanc, E., Kirkwood, L., Nicolle, R., Benhamou, S., Lebret, T., Allory, Y., Southgate, J., Radvanyi, F. & Goud, B. Deregulation of Rab and Rab Effector Genes in Bladder Cancer. PLoS ONE 7, e39469 (2012).