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4. Hepatitis B virus preS2Δ38–55 variants: A newly identified risk factor for hepatocellular carcinoma

Author

Cohen, Damien, Ghosh, Sumantra, Shimakawa, Yusuke, Ramou, Njie, Garcia, Pierre Simon, Dubois, Anaëlle, Guillot, Clément, Kakwata-Nkor Deluce, Nora, Tilloy, Valentin, Durand, Geoffroy, Voegele, Catherine, Ndow, Gibril, d'Alessandro, Umberto, Brochier-Armanet, Céline, Alain, Sophie, Le Calvez-Kelm, Florence, Hall, Janet, Zoulim, Fabien, Mendy, Maimuna, Thursz, Mark, Lemoine, Maud, and Chemin, Isabelle

Published
2020
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5. Circulating tumour-derived KRAS mutations in pancreatic cancer cases are predominantly carried by very short fragments of cell-free DNA

Author

Zvereva, Maria, Roberti, Gabriel, Durand, Geoffroy, Voegele, Catherine, Nguyen, Minh Dao, Delhomme, Tiffany M., Chopard, Priscilia, Fabianova, Eleonora, Adamcakova, Zora, Holcatova, Ivana, Foretova, Lenka, Janout, Vladimir, Brennan, Paul, Foll, Matthieu, Byrnes, Graham B., McKay, James D., Scelo, Ghislaine, and Le Calvez-Kelm, Florence

Published
2020
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6. No evidence that protein truncating variants in BRIP1 are associated with breast cancer risk: implications for gene panel testing.

Author

Easton, Douglas F, Lesueur, Fabienne, Decker, Brennan, Michailidou, Kyriaki, Li, Jun, Allen, Jamie, Luccarini, Craig, Pooley, Karen A, Shah, Mitul, Bolla, Manjeet K, Wang, Qin, Dennis, Joe, Ahmad, Jamil, Thompson, Ella R, Damiola, Francesca, Pertesi, Maroulio, Voegele, Catherine, Mebirouk, Noura, Robinot, Nivonirina, Durand, Geoffroy, Forey, Nathalie, Luben, Robert N, Ahmed, Shahana, Aittomäki, Kristiina, Anton-Culver, Hoda, Arndt, Volker, Australian Ovarian Cancer Study Group, Baynes, Caroline, Beckman, Matthias W, Benitez, Javier, Van Den Berg, David, Blot, William J, Bogdanova, Natalia V, Bojesen, Stig E, Brenner, Hermann, Chang-Claude, Jenny, Chia, Kee Seng, Choi, Ji-Yeob, Conroy, Don M, Cox, Angela, Cross, Simon S, Czene, Kamila, Darabi, Hatef, Devilee, Peter, Eriksson, Mikael, Fasching, Peter A, Figueroa, Jonine, Flyger, Henrik, Fostira, Florentia, García-Closas, Montserrat, Giles, Graham G, Glendon, Gord, González-Neira, Anna, Guénel, Pascal, Haiman, Christopher A, Hall, Per, Hart, Steven N, Hartman, Mikael, Hooning, Maartje J, Hsiung, Chia-Ni, Ito, Hidemi, Jakubowska, Anna, James, Paul A, John, Esther M, Johnson, Nichola, Jones, Michael, Kabisch, Maria, Kang, Daehee, kConFab Investigators, Kosma, Veli-Matti, Kristensen, Vessela, Lambrechts, Diether, Li, Na, Lifepool Investigators, Lindblom, Annika, Long, Jirong, Lophatananon, Artitaya, Lubinski, Jan, Mannermaa, Arto, Manoukian, Siranoush, Margolin, Sara, Matsuo, Keitaro, Meindl, Alfons, Mitchell, Gillian, Muir, Kenneth, NBCS Investigators, Nevelsteen, Ines, van den Ouweland, Ans, Peterlongo, Paolo, Phuah, Sze Yee, Pylkäs, Katri, Rowley, Simone M, Sangrajrang, Suleeporn, Schmutzler, Rita K, Shen, Chen-Yang, Shu, Xiao-Ou, Southey, Melissa C, Surowy, Harald, Swerdlow, Anthony, and Teo, Soo H

Subjects
Australian Ovarian Cancer Study Group, kConFab Investigators, Lifepool Investigators, NBCS Investigators, Humans, Breast Neoplasms, Genetic Predisposition to Disease, RNA Helicases, DNA-Binding Proteins, Risk, Cohort Studies, Mutation, Adult, Aged, Middle Aged, European Continental Ancestry Group, Female, Fanconi Anemia Complementation Group Proteins, Genetic Association Studies, Cancer: breast, Genetics & Heredity, Biological Sciences, Medical and Health Sciences
Abstract

BACKGROUND:BRCA1 interacting protein C-terminal helicase 1 (BRIP1) is one of the Fanconi Anaemia Complementation (FANC) group family of DNA repair proteins. Biallelic mutations in BRIP1 are responsible for FANC group J, and previous studies have also suggested that rare protein truncating variants in BRIP1 are associated with an increased risk of breast cancer. These studies have led to inclusion of BRIP1 on targeted sequencing panels for breast cancer risk prediction. METHODS:We evaluated a truncating variant, p.Arg798Ter (rs137852986), and 10 missense variants of BRIP1, in 48 144 cases and 43 607 controls of European origin, drawn from 41 studies participating in the Breast Cancer Association Consortium (BCAC). Additionally, we sequenced the coding regions of BRIP1 in 13 213 cases and 5242 controls from the UK, 1313 cases and 1123 controls from three population-based studies as part of the Breast Cancer Family Registry, and 1853 familial cases and 2001 controls from Australia. RESULTS:The rare truncating allele of rs137852986 was observed in 23 cases and 18 controls in Europeans in BCAC (OR 1.09, 95% CI 0.58 to 2.03, p=0.79). Truncating variants were found in the sequencing studies in 34 cases (0.21%) and 19 controls (0.23%) (combined OR 0.90, 95% CI 0.48 to 1.70, p=0.75). CONCLUSIONS:These results suggest that truncating variants in BRIP1, and in particular p.Arg798Ter, are not associated with a substantial increase in breast cancer risk. Such observations have important implications for the reporting of results from breast cancer screening panels.

Published
2016

7. Urinary TERT promoter mutations as non-invasive biomarkers for the comprehensive detection of urothelial cancer

Author

Avogbe, Patrice Hodonou, Manel, Arnaud, Vian, Emmanuel, Durand, Geoffroy, Forey, Nathalie, Voegele, Catherine, Zvereva, Maria, Hosen, Md Ismail, Meziani, Sonia, De Tilly, Berengere, Polo, Gilles, Lole, Olesia, Francois, Pauline, Delhomme, Tiffany Myriam, Carreira, Christine, Monteiro-Reis, Sara, Henrique, Rui, Abedi-Ardekani, Behnoush, Byrnes, Graham, Foll, Matthieu, Weiderpass, Elisabete, McKay, James, Jeronimo, Carmen, Scelo, Ghislaine, and Le Calvez-Kelm, Florence

Published
2019
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8. Gradual transition towards anaplasia in Wilms tumor through tolerance to genetic damage

Author

Uno, Kaname, primary, Rastegar, Bahar, additional, Jansson, Caroline, additional, Durand, Geoffroy, additional, Valind, Anders, additional, Chattopadhyay, Subhayan, additional, Bertolotti, Alessia, additional, Ciceri, Sara, additional, Spreafico, Filippo, additional, Collini, Paola, additional, Perotti, Daniela, additional, Holmquist Mengelbier, Linda, additional, and Gisselsson, David, additional

Published
2023
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9. Sex specific associations in genome wide association analysis of renal cell carcinoma

Author

Laskar, Ruhina S., Muller, David C., Li, Peng, Machiela, Mitchell J., Ye, Yuanqing, Gaborieau, Valerie, Foll, Matthieu, Hofmann, Jonathan N., Colli, Leandro, Sampson, Joshua N., Wang, Zhaoming, Bacq-Daian, Delphine, Boland, Anne, Abedi-Ardekani, Behnoush, Durand, Geoffroy, Le Calvez-Kelm, Florence, Robinot, Nivonirina, Blanche, Helene, Prokhortchouk, Egor, Skryabin, Konstantin G., Burdett, Laurie, Yeager, Meredith, Radojevic-Skodric, Sanja, Savic, Slavisa, Foretova, Lenka, Holcatova, Ivana, Janout, Vladimir, Mates, Dana, Rascu, Stefan, Mukeria, Anush, Zaridze, David, Bencko, Vladimir, Cybulski, Cezary, Fabianova, Eleonora, Jinga, Viorel, Lissowska, Jolanta, Lubinski, Jan, Navratilova, Marie, Rudnai, Peter, Świątkowska, Beata, Benhamou, Simone, Cancel-Tassin, Geraldine, Cussenot, Olivier, Trichopoulou, Antonia, Riboli, Elio, Overvad, Kim, Panico, Salvatore, Ljungberg, Borje, Sitaram, Raviprakash T., Giles, Graham G., Milne, Roger L, Severi, Gianluca, Bruinsma, Fiona, Fletcher, Tony, Koppova, Kvetoslava, Larsson, Susanna C., Wolk, Alicja, Banks, Rosamonde E., Selby, Peter J., Easton, Douglas F., Pharoah, Paul, Andreotti, Gabriella, Beane Freeman, Laura E, Koutros, Stella, Albanes, Demetrius, Männistö, Satu, Weinstein, Stephanie, Clark, Peter E., Edwards, Todd L., Lipworth, Loren, Carol, Hallie, Freedman, Matthew L., Pomerantz, Mark M., Cho, Eunyoung, Kraft, Peter, Preston, Mark A., Wilson, Kathryn M., Michael Gaziano, J., Sesso, Howard D., Black, Amanda, Freedman, Neal D., Huang, Wen-Yi, Anema, John G., Kahnoski, Richard J., Lane, Brian R., Noyes, Sabrina L., Petillo, David, Teh, Bin Tean, Peters, Ulrike, White, Emily, Anderson, Garnet L., Johnson, Lisa, Luo, Juhua, Chow, Wong-Ho, Moore, Lee E., Choueiri, Toni K., Wood, Christopher, Johansson, Mattias, McKay, James D., Brown, Kevin M., Rothman, Nathaniel, Lathrop, Mark G., Deleuze, Jean-Francois, Wu, Xifeng, Brennan, Paul, Chanock, Stephen J., Purdue, Mark P., and Scelo, Ghislaine

Published
2019
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11. Table S3 from Resolving the Pathogenesis of Anaplastic Wilms Tumors through Spatial Mapping of Cancer Cell Evolution

Author

Rastegar, Bahar, primary, Andersson, Natalie, primary, Petersson, Alexandra, primary, Karlsson, Jenny, primary, Chattopadhyay, Subhayan, primary, Valind, Anders, primary, Jansson, Caroline, primary, Durand, Geoffroy, primary, Romerius, Patrik, primary, Jirström, Karin, primary, Holmquist Mengelbier, Linda, primary, and Gisselsson, David, primary

Published
2023
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12. Figure S1 from Resolving the Pathogenesis of Anaplastic Wilms Tumors through Spatial Mapping of Cancer Cell Evolution

Author

Rastegar, Bahar, primary, Andersson, Natalie, primary, Petersson, Alexandra, primary, Karlsson, Jenny, primary, Chattopadhyay, Subhayan, primary, Valind, Anders, primary, Jansson, Caroline, primary, Durand, Geoffroy, primary, Romerius, Patrik, primary, Jirström, Karin, primary, Holmquist Mengelbier, Linda, primary, and Gisselsson, David, primary

Published
2023
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13. Data from Resolving the Pathogenesis of Anaplastic Wilms Tumors through Spatial Mapping of Cancer Cell Evolution

Author

Rastegar, Bahar, primary, Andersson, Natalie, primary, Petersson, Alexandra, primary, Karlsson, Jenny, primary, Chattopadhyay, Subhayan, primary, Valind, Anders, primary, Jansson, Caroline, primary, Durand, Geoffroy, primary, Romerius, Patrik, primary, Jirström, Karin, primary, Holmquist Mengelbier, Linda, primary, and Gisselsson, David, primary

Published
2023
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14. DNA methylome analysis identifies accelerated epigenetic ageing associated with postmenopausal breast cancer susceptibility

Author

Ambatipudi, Srikant, Horvath, Steve, Perrier, Flavie, Cuenin, Cyrille, Hernandez-Vargas, Hector, Le Calvez-Kelm, Florence, Durand, Geoffroy, Byrnes, Graham, Ferrari, Pietro, Bouaoun, Liacine, Sklias, Athena, Chajes, Véronique, Overvad, Kim, Severi, Gianluca, Baglietto, Laura, Clavel-Chapelon, Françoise, Kaaks, Rudolf, Barrdahl, Myrto, Boeing, Heiner, Trichopoulou, Antonia, Lagiou, Pagona, Naska, Androniki, Masala, Giovanna, Agnoli, Claudia, Polidoro, Silvia, Tumino, Rosario, Panico, Salvatore, Dollé, Martijn, Peeters, Petra H.M., Onland-Moret, N. Charlotte, Sandanger, Torkjel M., Nøst, Therese H., Weiderpass, Elisabete, Quirós, J. Ramón, Agudo, Antonio, Rodriguez-Barranco, Miguel, Huerta Castaño, José María, Barricarte, Aurelio, Fernández, Ander Matheu, Travis, Ruth C., Vineis, Paolo, Muller, David C., Riboli, Elio, Gunter, Marc, Romieu, Isabelle, and Herceg, Zdenko

Published
2017
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15. Resolving the Pathogenesis of Anaplastic Wilms Tumors through Spatial Mapping of Cancer Cell Evolution

Author

Rastegar, Bahar, primary, Andersson, Natalie, additional, Petersson, Alexandra, additional, Karlsson, Jenny, additional, Chattopadhyay, Subhayan, additional, Valind, Anders, additional, Jansson, Caroline, additional, Durand, Geoffroy, additional, Romerius, Patrik, additional, Jirström, Karin, additional, Holmquist Mengelbier, Linda, additional, and Gisselsson, David, additional

Published
2023
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16. Supplementary Figure S2 from Low-Coverage Exome Sequencing Screen in Formalin-Fixed Paraffin-Embedded Tumors Reveals Evidence of Exposure to Carcinogenic Aristolochic Acid

Author

Castells, Xavier, primary, Karanović, Sandra, primary, Ardin, Maude, primary, Tomić, Karla, primary, Xylinas, Evanguelos, primary, Durand, Geoffroy, primary, Villar, Stephanie, primary, Forey, Nathalie, primary, Le Calvez-Kelm, Florence, primary, Voegele, Catherine, primary, Karlović, Krešimir, primary, Mišić, Maja, primary, Dittrich, Damir, primary, Dolgalev, Igor, primary, McKay, James, primary, Shariat, Shahrokh F., primary, Sidorenko, Viktoria S., primary, Fernandes, Andrea, primary, Heguy, Adriana, primary, Dickman, Kathleen G., primary, Olivier, Magali, primary, Grollman, Arthur P., primary, Jelaković, Bojan, primary, and Zavadil, Jiri, primary

Published
2023
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17. Supplemental Material (for review only) File - Supplementary Tables 1-5. from Low-Coverage Exome Sequencing Screen in Formalin-Fixed Paraffin-Embedded Tumors Reveals Evidence of Exposure to Carcinogenic Aristolochic Acid

Author

Castells, Xavier, primary, Karanović, Sandra, primary, Ardin, Maude, primary, Tomić, Karla, primary, Xylinas, Evanguelos, primary, Durand, Geoffroy, primary, Villar, Stephanie, primary, Forey, Nathalie, primary, Le Calvez-Kelm, Florence, primary, Voegele, Catherine, primary, Karlović, Krešimir, primary, Mišić, Maja, primary, Dittrich, Damir, primary, Dolgalev, Igor, primary, McKay, James, primary, Shariat, Shahrokh F., primary, Sidorenko, Viktoria S., primary, Fernandes, Andrea, primary, Heguy, Adriana, primary, Dickman, Kathleen G., primary, Olivier, Magali, primary, Grollman, Arthur P., primary, Jelaković, Bojan, primary, and Zavadil, Jiri, primary

Published
2023
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18. Supplementary Methods from Low-Coverage Exome Sequencing Screen in Formalin-Fixed Paraffin-Embedded Tumors Reveals Evidence of Exposure to Carcinogenic Aristolochic Acid

Author

Castells, Xavier, primary, Karanović, Sandra, primary, Ardin, Maude, primary, Tomić, Karla, primary, Xylinas, Evanguelos, primary, Durand, Geoffroy, primary, Villar, Stephanie, primary, Forey, Nathalie, primary, Le Calvez-Kelm, Florence, primary, Voegele, Catherine, primary, Karlović, Krešimir, primary, Mišić, Maja, primary, Dittrich, Damir, primary, Dolgalev, Igor, primary, McKay, James, primary, Shariat, Shahrokh F., primary, Sidorenko, Viktoria S., primary, Fernandes, Andrea, primary, Heguy, Adriana, primary, Dickman, Kathleen G., primary, Olivier, Magali, primary, Grollman, Arthur P., primary, Jelaković, Bojan, primary, and Zavadil, Jiri, primary

Published
2023
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19. Supplementary Figure legends from Low-Coverage Exome Sequencing Screen in Formalin-Fixed Paraffin-Embedded Tumors Reveals Evidence of Exposure to Carcinogenic Aristolochic Acid

Author

Castells, Xavier, primary, Karanović, Sandra, primary, Ardin, Maude, primary, Tomić, Karla, primary, Xylinas, Evanguelos, primary, Durand, Geoffroy, primary, Villar, Stephanie, primary, Forey, Nathalie, primary, Le Calvez-Kelm, Florence, primary, Voegele, Catherine, primary, Karlović, Krešimir, primary, Mišić, Maja, primary, Dittrich, Damir, primary, Dolgalev, Igor, primary, McKay, James, primary, Shariat, Shahrokh F., primary, Sidorenko, Viktoria S., primary, Fernandes, Andrea, primary, Heguy, Adriana, primary, Dickman, Kathleen G., primary, Olivier, Magali, primary, Grollman, Arthur P., primary, Jelaković, Bojan, primary, and Zavadil, Jiri, primary

Published
2023
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20. Data from Low-Coverage Exome Sequencing Screen in Formalin-Fixed Paraffin-Embedded Tumors Reveals Evidence of Exposure to Carcinogenic Aristolochic Acid

Author

Castells, Xavier, primary, Karanović, Sandra, primary, Ardin, Maude, primary, Tomić, Karla, primary, Xylinas, Evanguelos, primary, Durand, Geoffroy, primary, Villar, Stephanie, primary, Forey, Nathalie, primary, Le Calvez-Kelm, Florence, primary, Voegele, Catherine, primary, Karlović, Krešimir, primary, Mišić, Maja, primary, Dittrich, Damir, primary, Dolgalev, Igor, primary, McKay, James, primary, Shariat, Shahrokh F., primary, Sidorenko, Viktoria S., primary, Fernandes, Andrea, primary, Heguy, Adriana, primary, Dickman, Kathleen G., primary, Olivier, Magali, primary, Grollman, Arthur P., primary, Jelaković, Bojan, primary, and Zavadil, Jiri, primary

Published
2023
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21. First Molecular Characterization of Chronic Hepatitis B Carriers in Timbuktu, Mali

Author

Lawrence, Philip, primary, Chabane, Mawlouda, additional, Abrouk, Lucie, additional, Thiesson, Adrien, additional, Berthé, Diakaridia, additional, Diarra, Amadou B., additional, Bengaly, Karim, additional, Traoré, Brehima, additional, Kassogué, Djibril, additional, Durand, Geoffroy, additional, Voegele, Catherine, additional, Le Calvez-Kelm, Florence, additional, Steenkeste, Nicolas, additional, Hainaut, Pierre, additional, Kouriba, Bourema, additional, and Gormally, Emmanuelle, additional

Published
2023
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22. Early evolutionary branching across spatial domains predisposes to clonal replacement under chemotherapy in neuroblastoma

Author

Gisselsson, David, primary, Karlsson, Jenny, additional, Yasui, Hiroaki, additional, Manas, Adriana, additional, Andersson, Natalie, additional, Hansson, Karin, additional, Aaltonen, Kristina, additional, Jansson, Caroline, additional, Durand, Geoffroy, additional, Yang, Minjun, additional, Chattopadhyay, Subhayan, additional, Paulsson, Kajsa, additional, Spierings, Diana, additional, Foijer, Floris, additional, Valind, Anders, additional, and Bexell, Daniel, additional

Published
2022
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23. CASP9 germline mutation in a family with multiple brain tumors

Author

Ronellenfitsch, Michael W., Oh, Ji‐Eun, Satomi, Kaishi, Sumi, Koichiro, Harter, Patrick N., Steinbach, Joachim P., Felsberg, Jörg, Capper, David, Voegele, Catherine, Durand, Geoffroy, McKay, James, Le Calvez‐Kelm, Florence, Schittenhelm, Jens, Klink, Barbara, Mittelbronn, Michel, and Ohgaki, Hiroko

Published
2018
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24. Sexual dimorphism in cancer: insights from transcriptional signatures in kidney tissue and renal cell carcinoma

Author

Laskar, Ruhina S, Li, Peng, Ecsedi, Szilvia, Abedi-Ardekani, Behnoush, Durand, Geoffroy, Robinot, Nivonirina, Hubert, Jean-Noël, Janout, Vladimir, Zaridze, David, Mukeria, Anush, Mates, Dana, Holcatova, Ivana, Foretova, Lenka, Swiatkowska, Beata, Dzamic, Zoran, Milosavljevic, Sasa, Olaso, Robert, Boland, Anne, Deleuze, Jean-François, Muller, David C, McKay, James D, Brennan, Paul, Le Calvez-Kelm, Florence, Scelo, Ghislaine, and Chanudet, Estelle

Subjects
AcademicSubjects/SCI01140, Male, Sex Characteristics, Gene Expression Profiling, Middle Aged, Prognosis, Kidney Neoplasms, Gene Expression Regulation, Neoplastic, Genes, X-Linked, Biomarkers, Tumor, Disease Progression, Humans, Female, Genes, Tumor Suppressor, Genetic Predisposition to Disease, General Article, Carcinoma, Renal Cell, Genetic Association Studies, Aged, Genome-Wide Association Study
Abstract

Sexual dimorphism in cancer incidence and outcome is widespread. Understanding the underlying mechanisms is fundamental to improve cancer prevention and clinical management. Sex disparities are particularly striking in kidney cancer: across diverse populations, men consistently show unexplained 2-fold increased incidence and worse prognosis. We have characterized genome-wide expression and regulatory networks of 609 renal tumors and 256 non-tumor renal tissues. Normal kidney displayed sex-specific transcriptional signatures, including higher expression of X-linked tumor suppressor genes in women. Sex-dependent genotype–phenotype associations unraveled women-specific immune regulation. Sex differences were markedly expanded in tumors, with male-biased expression of key genes implicated in metabolism, non-malignant diseases with male predominance and carcinogenesis, including markers of tumor infiltrating leukocytes. Analysis of sex-dependent RCC progression and survival uncovered prognostic markers involved in immune response and oxygen homeostasis. In summary, human kidney tissues display remarkable sexual dimorphism at the molecular level. Sex-specific transcriptional signatures further shape renal cancer, with relevance for clinical management.

Published
2021

26. Development of a custom next-generation sequencing panel for the determination of bladder cancer risk in a Tunisian cohort

Author

Hemissi, Imen, primary, Boussetta, Sami, additional, Dallali, Hamza, additional, Hellal, Faycel, additional, Durand, Geoffroy, additional, Voegele, Catherine, additional, Ayed, Haroun, additional, Zaghbib, Selim, additional, Naimi, Zeineb, additional, Ayadi, Mouna, additional, Chebil, Mohamed, additional, Mckay, James, additional, Le Calvez-Kelm, Florence, additional, and Ouerhani, Slah, additional

Published
2021
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28. Development of a Custom NGS Panel for the Determination of Bladder Cancer Risk

Author

Hemissi, Imen, primary, BOUSETTA, SAMI, additional, Dallali, Hamza, additional, Hellal, Faycel, additional, Durand, Geoffroy, additional, Voegele, Catherine, additional, AYED, Haroun, additional, Zaghbib, Selim, additional, Naimi, Zeineb, additional, Ayadi, Mouna, additional, Chebil, Mohamed, additional, Mckay, James, additional, Calvez-Klem, Florence Le, additional, and Ouerhani, Slah, additional

Published
2021
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29. Epigenetic remodelling of enhancers in response to estrogen deprivation and re-stimulation

Author

Sklias, Athena, primary, Halaburkova, Andrea, additional, Vanzan, Ludovica, additional, Jimenez, Nora Fernandez, additional, Cuenin, Cyrille, additional, Bouaoun, Liacine, additional, Cahais, Vincent, additional, Ythier, Victor, additional, Sallé, Aurélie, additional, Renard, Claire, additional, Durand, Geoffroy, additional, Le Calvez-Kelm, Florence, additional, Khoueiry, Rita, additional, Murr, Rabih, additional, and Herceg, Zdenko, additional

Published
2021
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30. Epigenetic remodelling of enhancers in response to estrogen deprivation and re-stimulation

Author

Genética, antropología física y fisiología animal, Genetika,antropologia fisikoa eta animalien fisiologia, Sklias, Athena, Halaburkova, Andrea, Vanzan, Ludovica, Fernández Jiménez, Nora, Cuenin, Cyrille, Bouaoun, Liacine, Cahais, Vincent, Ythier, Victor, Salle, Aurelie, Renard, Claire, Durand, Geoffroy, Le Calvez Kelm, Florence, Khoueiry, Rita, Murr, Rabih, Herceg, Zdenko, Genética, antropología física y fisiología animal, Genetika,antropologia fisikoa eta animalien fisiologia, Sklias, Athena, Halaburkova, Andrea, Vanzan, Ludovica, Fernández Jiménez, Nora, Cuenin, Cyrille, Bouaoun, Liacine, Cahais, Vincent, Ythier, Victor, Salle, Aurelie, Renard, Claire, Durand, Geoffroy, Le Calvez Kelm, Florence, Khoueiry, Rita, Murr, Rabih, and Herceg, Zdenko

Abstract

Estrogen hormones are implicated in a majority of breast cancers and estrogen receptor alpha (ER), the main nuclear factor mediating estrogen signaling, orchestrates a complex molecular circuitry that is not yet fully elucidated. Here, we investigated genome-wide DNA methylation, histone acetylation and transcription after estradiol (E2) deprivation and re-stimulation to better characterize the ability of ER to coordinate gene regulation. We found that E2 deprivation mostly resulted in DNA hypermethylation and histone deacetylation in enhancers. Transcriptome analysis revealed that E2 deprivation leads to a global down-regulation in gene expression, and more specifically of TET2 demethylase that may be involved in the DNA hypermethylation following short-term E2 deprivation. Further enrichment analysis of transcription factor (TF) binding and motif occurrence highlights the importance of ER connection mainly with two partner TF families, AP-1 and FOX. Theseinteractions takeplace in the proximity of E2 deprivation-mediated differentially methylated and histone acetylated enhancers. Finally, while most deprivation-dependent epigenetic changes were reversed following E2 re-stimulation, DNA hypermethylation and H3K27 deacetylation at certain enhancers were partially retained. Overall, these results show that inactivation of ER mediates rapid and mostly reversible epigenetic changes at enhancers, and bring new insight into early events, which may ultimately lead to endocrine resistance.

Published
2021

31. Development of Sensitive Droplet Digital PCR Assays for Detecting Urinary TERT Promoter Mutations as Non-Invasive Biomarkers for Detection of Urothelial Cancer

Author

Hosen, Md Ismail, primary, Forey, Nathalie, additional, Durand, Geoffroy, additional, Voegele, Catherine, additional, Bilici, Selin, additional, Avogbe, Patrice Hodonou, additional, Delhomme, Tiffany Myriam, additional, Foll, Matthieu, additional, Manel, Arnaud, additional, Vian, Emmanuel, additional, Meziani, Sonia, additional, De Tilly, Berengere, additional, Polo, Gilles, additional, Lole, Olesia, additional, Francois, Pauline, additional, Boureille, Antoine, additional, Pisarev, Eduard, additional, Salas, Andrei R. O. S. E., additional, Monteiro-Reis, Sara, additional, Henrique, Rui, additional, Byrnes, Graham, additional, Jeronimo, Carmen, additional, Scelo, Ghislaine, additional, McKay, James D., additional, Calvez-Kelm, Florence Le, additional, and Zvereva, Maria, additional

Published
2020
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32. Urinary TERT promoter mutations are detectable up to 10 years prior to clinical diagnosis of bladder cancer: Evidence from the Golestan Cohort Study

Author

Hosen, Md Ismail, primary, Sheikh, Mahdi, additional, Zvereva, Maria, additional, Scelo, Ghislaine, additional, Forey, Nathalie, additional, Durand, Geoffroy, additional, Voegele, Catherine, additional, Poustchi, Hossein, additional, Khoshnia, Masoud, additional, Roshandel, Gholamreza, additional, Sotoudeh, Masoud, additional, Nikmanesh, Arash, additional, Etemadi, Arash, additional, Avogbe, Patrice Hodonou, additional, Chopard, Priscilia, additional, Delhomme, Tiffany Myriam, additional, Foll, Matthieu, additional, Manel, Arnaud, additional, Vian, Emmanuel, additional, Weiderpass, Elisabete, additional, Kamangar, Farin, additional, Boffetta, Paolo, additional, Pharaoh, Paul D., additional, Dawsey, Sanford M., additional, Abnet, Christian C., additional, Brennan, Paul, additional, McKay, James, additional, Malekzadeh, Reza, additional, and Calvez-Kelm, Florence Le, additional

Published
2020
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33. Merkel Cell Polyomavirus Downregulates N-myc Downstream-Regulated Gene 1, Leading to Cellular Proliferation and Migration

Author

Gupta, Purnima, primary, Shahzad, Naveed, additional, Harold, Alexis, additional, Shuda, Masahiro, additional, Venuti, Assunta, additional, Romero-Medina, Maria Carmen, additional, Pacini, Laura, additional, Brault, Lise, additional, Robitaille, Alexis, additional, Taverniti, Valerio, additional, Hernandez-Vargas, Hector, additional, Durand, Geoffroy, additional, Le Calvez-Kelm, Florence, additional, Gheit, Tarik, additional, Accardi, Rosita, additional, and Tommasino, Massimo, additional

Published
2020
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34. Sex specific associations in genome wide association analysis of renal cell carcinoma

Author

Laskar, Ruhina S, Muller, David C, Li, Peng, Machiela, Mitchell J, Ye, Yuanqing, Gaborieau, Valerie, Foll, Matthieu, Hofmann, Jonathan N, Colli, Leandro, Sampson, Joshua N, Wang, Zhaoming, Bacq-Daian, Delphine, Boland, Anne, Abedi-Ardekani, Behnoush, Durand, Geoffroy, Le Calvez-Kelm, Florence, Robinot, Nivonirina, Blanche, Helene, Prokhortchouk, Egor, Skryabin, Konstantin G, Burdett, Laurie, Yeager, Meredith, Radojevic-Skodric, Sanja, Savic, Slavisa, Foretova, Lenka, Holcatova, Ivana, Janout, Vladimir, Mates, Dana, Rascu, Stefan, Mukeria, Anush, Zaridze, David, Bencko, Vladimir, Cybulski, Cezary, Fabianova, Eleonora, Jinga, Viorel, Lissowska, Jolanta, Lubinski, Jan, Navratilova, Marie, Rudnai, Peter, Świątkowska, Beata, Benhamou, Simone, Cancel-Tassin, Geraldine, Cussenot, Olivier, Trichopoulou, Antonia, Riboli, Elio, Overvad, Kim, Panico, Salvatore, Ljungberg, Börje, Tumkur Sitaram, Raviprakash, Giles, Graham G, Milne, Roger L, Severi, Gianluca, Bruinsma, Fiona, Fletcher, Tony, Koppova, Kvetoslava, Larsson, Susanna C, Wolk, Alicja, Banks, Rosamonde E, Selby, Peter J, Easton, Douglas F, Pharoah, Paul, Andreotti, Gabriella, Beane Freeman, Laura E, Koutros, Stella, Albanes, Demetrius, Männistö, Satu, Weinstein, Stephanie, Clark, Peter E, Edwards, Todd L, Lipworth, Loren, Carol, Hallie, Freedman, Matthew L, Pomerantz, Mark M, Cho, Eunyoung, Kraft, Peter, Preston, Mark A, Wilson, Kathryn M, Michael Gaziano, J, Sesso, Howard D, Black, Amanda, Freedman, Neal D, Huang, Wen-Yi, Anema, John G, Kahnoski, Richard J, Lane, Brian R, Noyes, Sabrina L, Petillo, David, Teh, Bin Tean, Peters, Ulrike, White, Emily, Anderson, Garnet L, Johnson, Lisa, Luo, Juhua, Chow, Wong-Ho, Moore, Lee E, Choueiri, Toni K, Wood, Christopher, Johansson, Mattias, McKay, James D, Brown, Kevin M, Rothman, Nathaniel, Lathrop, Mark G, Deleuze, Jean-Francois, Wu, Xifeng, Brennan, Paul, Chanock, Stephen J, Purdue, Mark P, Scelo, Ghislaine, Laskar, Ruhina S, Muller, David C, Li, Peng, Machiela, Mitchell J, Ye, Yuanqing, Gaborieau, Valerie, Foll, Matthieu, Hofmann, Jonathan N, Colli, Leandro, Sampson, Joshua N, Wang, Zhaoming, Bacq-Daian, Delphine, Boland, Anne, Abedi-Ardekani, Behnoush, Durand, Geoffroy, Le Calvez-Kelm, Florence, Robinot, Nivonirina, Blanche, Helene, Prokhortchouk, Egor, Skryabin, Konstantin G, Burdett, Laurie, Yeager, Meredith, Radojevic-Skodric, Sanja, Savic, Slavisa, Foretova, Lenka, Holcatova, Ivana, Janout, Vladimir, Mates, Dana, Rascu, Stefan, Mukeria, Anush, Zaridze, David, Bencko, Vladimir, Cybulski, Cezary, Fabianova, Eleonora, Jinga, Viorel, Lissowska, Jolanta, Lubinski, Jan, Navratilova, Marie, Rudnai, Peter, Świątkowska, Beata, Benhamou, Simone, Cancel-Tassin, Geraldine, Cussenot, Olivier, Trichopoulou, Antonia, Riboli, Elio, Overvad, Kim, Panico, Salvatore, Ljungberg, Börje, Tumkur Sitaram, Raviprakash, Giles, Graham G, Milne, Roger L, Severi, Gianluca, Bruinsma, Fiona, Fletcher, Tony, Koppova, Kvetoslava, Larsson, Susanna C, Wolk, Alicja, Banks, Rosamonde E, Selby, Peter J, Easton, Douglas F, Pharoah, Paul, Andreotti, Gabriella, Beane Freeman, Laura E, Koutros, Stella, Albanes, Demetrius, Männistö, Satu, Weinstein, Stephanie, Clark, Peter E, Edwards, Todd L, Lipworth, Loren, Carol, Hallie, Freedman, Matthew L, Pomerantz, Mark M, Cho, Eunyoung, Kraft, Peter, Preston, Mark A, Wilson, Kathryn M, Michael Gaziano, J, Sesso, Howard D, Black, Amanda, Freedman, Neal D, Huang, Wen-Yi, Anema, John G, Kahnoski, Richard J, Lane, Brian R, Noyes, Sabrina L, Petillo, David, Teh, Bin Tean, Peters, Ulrike, White, Emily, Anderson, Garnet L, Johnson, Lisa, Luo, Juhua, Chow, Wong-Ho, Moore, Lee E, Choueiri, Toni K, Wood, Christopher, Johansson, Mattias, McKay, James D, Brown, Kevin M, Rothman, Nathaniel, Lathrop, Mark G, Deleuze, Jean-Francois, Wu, Xifeng, Brennan, Paul, Chanock, Stephen J, Purdue, Mark P, and Scelo, Ghislaine

Abstract

Renal cell carcinoma (RCC) has an undisputed genetic component and a stable 2:1 male to female sex ratio in its incidence across populations, suggesting possible sexual dimorphism in its genetic susceptibility. We conducted the first sex-specific genome-wide association analysis of RCC for men (3227 cases, 4916 controls) and women (1992 cases, 3095 controls) of European ancestry from two RCC genome-wide scans and replicated the top findings using an additional series of men (2261 cases, 5852 controls) and women (1399 cases, 1575 controls) from two independent cohorts of European origin. Our study confirmed sex-specific associations for two known RCC risk loci at 14q24.2 (DPF3) and 2p21(EPAS1). We also identified two additional suggestive male-specific loci at 6q24.3 (SAMD5, male odds ratio (ORmale) = 0.83 [95% CI = 0.78-0.89], Pmale = 1.71 × 10-8 compared with female odds ratio (ORfemale) = 0.98 [95% CI = 0.90-1.07], Pfemale = 0.68) and 12q23.3 (intergenic, ORmale = 0.75 [95% CI = 0.68-0.83], Pmale = 1.59 × 10-8 compared with ORfemale = 0.93 [95% CI = 0.82-1.06], Pfemale = 0.21) that attained genome-wide significance in the joint meta-analysis. Herein, we provide evidence of sex-specific associations in RCC genetic susceptibility and advocate the necessity of larger genetic and genomic studies to unravel the endogenous causes of sex bias in sexually dimorphic traits and diseases like RCC.

Published
2019
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35. Genomic analysis of head and neck cancer cases from two high incidence regions

Author

Perdomo, Sandra Anantharaman, Devasena Foll, Matthieu and Abedi-Ardekani, Behnoush Durand, Geoffroy Rosa, Luciana Albina Reis Holmila, Reetta Le Calvez-Kelm, Florence Tajara, Eloiza H. Wunsch-Filho, Victor Levi, Jose Eduardo Vilensky, Marta and Polesel, Jerry Holcatova, Ivana Simonato, Lorenzo and Canova, Cristina Lagiou, Pagona McKay, James D. Brennan, Paul

Subjects
neoplasms
Abstract

We investigated how somatic changes in HNSCC interact with environmental and host risk factors and whether they influence the risk of HNSCC occurrence and outcome. 180-paired samples diagnosed as HNSCC in two high incidence regions of Europe and South America underwent targeted sequencing (14 genes) and evaluation of copy number alterations (SCNAs). TP53, PIK3CA, NOTCH1, TP63 and CDKN2A were the most frequently mutated genes. Cases were characterized by a low copy number burden with recurrent focal amplification in 11q13.3 and deletion in 15q22. Cases with low SCNAs showed an improved overall survival. We found significant correlations with decreased overall survival between focal amplified regions 4p16, 10q22 and 22q11, and losses in 12p12, 15814 and 15q22. The mutational landscape in our cases showed an association to both environmental exposures and clinical characteristics. We confirmed that somatic copy number alterations are an important predictor of HNSCC overall survival.

Published
2018

36. Interplay between the Epigenetic Enzyme Lysine (K)-Specific Demethylase 2B and Epstein-Barr Virus Infection

Author

Vargas-Ayala, Romina C., primary, Jay, Antonin, additional, Manara, Francesca, additional, Maroui, Mohamed Ali, additional, Hernandez-Vargas, Hector, additional, Diederichs, Audrey, additional, Robitaille, Alexis, additional, Sirand, Cecilia, additional, Ceraolo, Maria Grazia, additional, Romero-Medina, Maria Carmen, additional, Cros, Marie Pierre, additional, Cuenin, Cyrille, additional, Durand, Geoffroy, additional, Le Calvez-Kelm, Florence, additional, Mundo, Lucia, additional, Leoncini, Lorenzo, additional, Manet, Evelyne, additional, Herceg, Zdenko, additional, Gruffat, Henri, additional, and Accardi, Rosita, additional

Published
2019
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37. Multi-omics comparative analyses of pulmonary typical carcinoids, atypical carcinoids, and large-cell neuroendocrine carcinoma

Author

Leblay, Noemie, Alcala, Nicolas, Marin, David Hervas, Delhomme, Tiffany M., Giffon, Theo, Ghantous, Akram, Chabrier, Amelie, Cuenin, Cyrille, Altmueller, Janine, Durand, Geoffroy, Voegele, Catherine, Lorimier, Philippe, Toffart, Anne-Claire, Derks, Jules, Brustugun, Odd Terje, Clement, Joachim H., Saenger, Joerg, Field, John K., Soltermann, Alex, Wright, Gavin M., Roz, Luca, Muscarella, Lucia Anna, Graziano, Paolo, Herceg, Zdenko, Speel, Ernst-Jan, Nuernberg, Peter, McKay, James, Girard, Nicolas, Lantuejoul, Sylvie, Sandoval, Juan, Brambilla, Elisabeth, Foll, Matthieu, Fernandez-Cuesta, Lynnette, Leblay, Noemie, Alcala, Nicolas, Marin, David Hervas, Delhomme, Tiffany M., Giffon, Theo, Ghantous, Akram, Chabrier, Amelie, Cuenin, Cyrille, Altmueller, Janine, Durand, Geoffroy, Voegele, Catherine, Lorimier, Philippe, Toffart, Anne-Claire, Derks, Jules, Brustugun, Odd Terje, Clement, Joachim H., Saenger, Joerg, Field, John K., Soltermann, Alex, Wright, Gavin M., Roz, Luca, Muscarella, Lucia Anna, Graziano, Paolo, Herceg, Zdenko, Speel, Ernst-Jan, Nuernberg, Peter, McKay, James, Girard, Nicolas, Lantuejoul, Sylvie, Sandoval, Juan, Brambilla, Elisabeth, Foll, Matthieu, and Fernandez-Cuesta, Lynnette

Published
2018

38. Genome-wide association study identifies multiple risk loci for renal cell carcinoma

Author

Scelo, Ghislaine, Purdue, Mark P, Brown, Kevin M, Johansson, Mattias, Wang, Zhaoming, Eckel-Passow, Jeanette E, Ye, Yuanqing, Hofmann, Jonathan N, Choi, Jiyeon, Foll, Matthieu, Gaborieau, Valerie, Machiela, Mitchell J, Colli, Leandro M, Li, Peng, Sampson, Joshua N, Abedi-Ardekani, Behnoush, Besse, Celine, Blanche, Helene, Boland, Anne, Burdette, Laurie, Chabrier, Amelie, Durand, Geoffroy, Le Calvez-Kelm, Florence, Prokhortchouk, Egor, Robinot, Nivonirina, Skryabin, Konstantin G, Wozniak, Magdalena B, Yeager, Meredith, Basta-Jovanovic, Gordana, Dzamic, Zoran, Foretova, Lenka, Holcatova, Ivana, Janout, Vladimir, Mates, Dana, Mukeriya, Anush, Rascu, Stefan, Zaridze, David, Bencko, Vladimir, Cybulski, Cezary, Fabianova, Eleonora, Jinga, Viorel, Lissowska, Jolanta, Lubinski, Jan, Navratilova, Marie, Rudnai, Peter, Szeszenia-Dabrowska, Neonila, Benhamou, Simone, Cancel-Tassin, Geraldine, Cussenot, Olivier, Baglietto, Laura, Boeing, Heiner, Khaw, Kay-Tee, Weiderpass, Elisabete, Ljungberg, Borje, Sitaram, Raviprakash T, Bruinsma, Fiona, Jordan, Susan J, Severi, Gianluca, Winship, Ingrid, Hveem, Kristian, Vatten, Lars J, Fletcher, Tony, Koppova, Kvetoslava, Larsson, Susanna C, Wolk, Alicja, Banks, Rosamonde E, Selby, Peter J, Easton, Douglas F, Pharoah, Paul, Andreotti, Gabriella, Freeman, Laura E Beane, Koutros, Stella, Albanes, Demetrius, Männistö, Satu, Weinstein, Stephanie, Clark, Peter E, Edwards, Todd L, Lipworth, Loren, Gapstur, Susan M, Stevens, Victoria L, Carol, Hallie, Freedman, Matthew L, Pomerantz, Mark M, Cho, Eunyoung, Kraft, Peter, Preston, Mark A, Wilson, Kathryn M, Michael Gaziano, J, Sesso, Howard D, Black, Amanda, Freedman, Neal D, Huang, Wen-Yi, Anema, John G, Kahnoski, Richard J, Lane, Brian R, Noyes, Sabrina L, Petillo, David, Teh, Bin Tean, Peters, Ulrike, White, Emily, Anderson, Garnet L, Johnson, Lisa, Luo, Juhua, Buring, Julie, Lee, I-Min, Chow, Wong-Ho, Moore, Lee E, Wood, Christopher, Eisen, Timothy, Henrion, Marc, Larkin, James, Barman, Poulami, Leibovich, Bradley C, Choueiri, Toni K, Mark Lathrop, G, Rothman, Nathaniel, Deleuze, Jean-Francois, McKay, James D, Parker, Alexander S, Wu, Xifeng, Houlston, Richard S, Brennan, Paul, and Chanock, Stephen J

Abstract

Previous genome-wide association studies (GWAS) have identified six risk loci for renal cell carcinoma (RCC). We conducted a meta-analysis of two new scans of 5,198 cases and 7,331 controls together with four existing scans, totalling 10,784 cases and 20,406 controls of European ancestry. Twenty-four loci were tested in an additional 3,182 cases and 6,301 controls. We confirm the six known RCC risk loci and identify seven new loci at 1p32.3 (rs4381241, P=3.1 × 10-10), 3p22.1 (rs67311347, P=2.5 × 10-8), 3q26.2 (rs10936602, P=8.8 × 10-9), 8p21.3 (rs2241261, P=5.8 × 10-9), 10q24.33-q25.1 (rs11813268, P=3.9 × 10-8), 11q22.3 (rs74911261, P=2.1 × 10-10) and 14q24.2 (rs4903064, P=2.2 × 10-24). Expression quantitative trait analyses suggest plausible candidate genes at these regions that may contribute to RCC susceptibility.

Published
2017

39. CASP9 germline mutation in a family with multiple brain tumors

Author

Ronellenfitsch, Michael W., Oh, Ji‐Eun, Satomi, Kaishi, Sumi, Koichiro, Harter, Patrick N., Steinbach, Joachim P., Felsberg, Jörg, Capper, David, Voegele, Catherine, Durand, Geoffroy, McKay, James, Le Calvez‐Kelm, Florence, Schittenhelm, Jens, Klink, Barbara, Mittelbronn, Michel, and Ohgaki, Hiroko

Subjects
Adult, Brain Neoplasms, Brain, Humans, Family, Female, Genetic Predisposition to Disease, Astrocytoma, neoplasms, Research Articles, Caspase 9, Germ-Line Mutation
Abstract

We report a novel CASP9 germline mutation that may increase susceptibility to the development of brain tumors. We identified this mutation in a family in which three brain tumors had developed within three generations, including two anaplastic astrocytomas occurring in cousins. The cousins were diagnosed at similar ages (29 and 31 years), and their tumors showed similar histological features. Genetic analysis revealed somatic IDH1 and TP53 mutations in both tumors. However, no germline TP53 mutations were detected, despite the fact that this family fulfills the criteria of Li-Fraumeni-like syndrome. Whole exome sequencing revealed a germline stop-gain mutation (R65X) in the CASP9 gene, which encodes caspase-9, a key molecule for the p53-dependent mitochondrial death pathway. This mutation was also detected in DNA extracted from blood samples from the two siblings who were each a parent of one of the affected cousins. Caspase-9 immunohistochemistry showed the absence of caspase-9 immunoreactivity in the anaplastic astrocytomas and normal brain tissues of the cousins. These observations suggest that CASP9 germline mutations may have played a role at least in part to the susceptibility of development of gliomas in this Li-Fraumeni-like family lacking a TP53 germline mutation.

Published
2017

40. DNA methylome analysis identifies accelerated epigenetic ageing associated with postmenopausal breast cancer susceptibility

Author

Ambatipudi, Srikant Horvath, Steve Perrier, Flavie Cuenin, Cyrille Hernandez-Vargas, Hector Le Calvez-Kelm, Florence and Durand, Geoffroy Byrnes, Graham Ferrari, Pietro Bouaoun, Liacine Sklias, Athena Chajes, Veronique Overvad, Kim and Seven, Gianluca Baglietto, Laura Clavel-Chapelon, Francoise and Kaaks, Rudolf Barrdahl, Myrto Boeing, Heiner Trichopoulou, Antonia Lagiou, Pagona Naska, Androniki Masala, Giovanna and Agnoli, Claudia Polidoro, Silvia Tumino, Rosario Panico, Salvatore Dolle, Martijn Peeters, Petra H. M. Onland-Moret, N. Charlotte Sandanger, Torkjel M. Nost, Therese H. and Weiderpass, Elisabete Quiros, J. Ramon Agudo, Antonio and Rodriguez-Barranco, Miguel Castano, Jose Maria Huerta and Barricarte, Aurelio Fernandez, Ander Matheu Travis, Ruth C. and Vineis, Paolo Muller, David C. Riboli, Elio Gunter, Marc and Romieu, Isabelle Herceg, Zdenko

Abstract

Aim of the study: A vast majority of human malignancies are associated with ageing, and age is a strong predictor of cancer risk. Recently, DNA methylation-based marker of ageing, known as ‘epigenetic clock’, has been linked with cancer risk factors. This study aimed to evaluate whether the epigenetic clock is associated with breast cancer risk susceptibility and to identify potential epigenetics-based biomarkers for risk stratification. Methods: Here, we profiled DNA methylation changes in a nested case control study embedded in the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort (n = 960) using the Illumina HumanMethylation 450K BeadChip arrays and used the Horvath age estimation method to calculate epigenetic age for these samples. Intrinsic epigenetic age acceleration (IEAA) was estimated as the residuals by regressing epigenetic age on chronological age. Results: We observed an association between IEAA and breast cancer risk (OR, 1.04; 95% CI, 1.007-1.076, P = 0.016). One unit increase in IEAA was associated with a 4% increased odds of developing breast cancer (OR, 1.04; 95% CI, 1.007-1.076). Stratified analysis based on menopausal status revealed that IEAA was associated with development of postmenopausal breast cancers (OR, 1.07; 95% CI, 1.020-1.11, P = 0.003). In addition, methylome-wide analyses revealed that a higher mean DNA methylation at cytosine-phosphate-guanine (CpG) islands was associated with increased risk of breast cancer development (OR per 1 SD = 1.20; 95 %CI: 1.03-1.40, P = 0.02) whereas mean methylation levels at non-island CpGs were indistinguishable between cancer cases and controls. Conclusion: Epigenetic age acceleration and CpG island methylation have a weak, but statistically significant, association with breast cancer susceptibility. (C) 2017 Elsevier Ltd. All rights reserved.

Published
2017

41. Interplay between the epigenetic enzyme lysine (K)-specific demethylase 2B and Epstein-Barr virus infection

Author

Vargas-Ayala, Romina C., primary, Jay, Antonin, additional, Hernandez-Vargas, Hector, additional, Diederichs, Audrey, additional, Robitaille, Alexis, additional, Sirand, Cecilia, additional, Ceraolo, Maria Grazia, additional, Romero, Maria, additional, Cros, Marie Pierre, additional, Cuenin, Cyrille, additional, Durand, Geoffroy, additional, Calvez-Kelm, Florence Le, additional, Mundo, Lucia, additional, Maroui, Mohamed Ali, additional, Leoncini, Lorenzo, additional, Manet, Evelyne, additional, Herceg, Zdenko, additional, Gruffat, Henri, additional, and Accardi, Rosita, additional

Published
2018
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42. Abstract 5358: Multi-omics comparative analyses of pulmonary typical carcinoids, atypical carcinoids, and large-cell neuroendocrine carcinoma

Author

Leblay, Noémie, primary, Alcala, Nicolas, additional, Marin, David Hervás, additional, Delhomme, Tiffany M., additional, Giffon, Théo, additional, Ghantous, Akram, additional, Chabrier, Amélie, additional, Cuenin, Cyrille, additional, Altmueller, Janine, additional, Durand, Geoffroy, additional, Voegele, Catherine, additional, Lorimier, Philippe, additional, Toffart, Anne-Claire, additional, Derks, Jules, additional, Brustugun, Odd Terje, additional, Clement, Joachim H., additional, Saenger, Joerg, additional, Field, John K., additional, Soltermann, Alex, additional, Wright, Gavin M., additional, Roz, Luca, additional, Muscarella, Lucia Anna, additional, Graziano, Paolo, additional, Herceg, Zdenko, additional, Speel, Ernst-Jan, additional, Nuernberg, Peter, additional, McKay, James, additional, Girard, Nicolas, additional, Lantuejoul, Sylvie, additional, Sandoval, Juan, additional, Brambilla, Elisabeth, additional, Foll, Matthieu, additional, and Fernandez-Cuesta, Lynnette, additional

Published
2018
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43. Genomic analysis of head and neck cancer cases from two high incidence regions

Author

Perdomo, Sandra, primary, Anantharaman, Devasena, additional, Foll, Matthieu, additional, Abedi-Ardekani, Behnoush, additional, Durand, Geoffroy, additional, Reis Rosa, Luciana Albina, additional, Holmila, Reetta, additional, Le Calvez-Kelm, Florence, additional, Tajara, Eloiza H., additional, Wünsch-Filho, Victor, additional, Levi, José Eduardo, additional, Vilensky, Marta, additional, Polesel, Jerry, additional, Holcatova, Ivana, additional, Simonato, Lorenzo, additional, Canova, Cristina, additional, Lagiou, Pagona, additional, McKay, James D., additional, and Brennan, Paul, additional

Published
2018
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44. DNA methylome analysis identifies accelerated epigenetic ageing associated with postmenopausal breast cancer susceptibility

Author

Epidemiology & Health Economics, Epi Kanker Team 1, JC onderzoeksprogramma Kanker, Cancer, Cardiovasculaire Epi Team 3, Brain, Circulatory Health, JC onderzoeksprogramma Cardiovasculaire Epidemiologie, Ambatipudi, Srikant, Horvath, Steve, Perrier, Flavie, Cuenin, Cyrille, Hernandez-Vargas, Hector, Le Calvez-Kelm, Florence, Durand, Geoffroy, Byrnes, Graham, Ferrari, Pietro, Bouaoun, Liacine, Sklias, Athena, Chajes, Véronique, Overvad, Kim, Severi, Gianluca, Baglietto, Laura, Clavel-Chapelon, Françoise, Kaaks, Rudolf, Barrdahl, Myrto, Boeing, Heiner, Trichopoulou, Antonia, Lagiou, Pagona, Naska, Androniki, Masala, Giovanna, Agnoli, Claudia, Polidoro, Silvia, Tumino, Rosario, Panico, Salvatore, Dollé, Martijn, Peeters, Petra H M, Onland-Moret, N. Charlotte, Sandanger, Torkjel M., Nøst, Therese H., Weiderpass Vainio, Elisabete, Quirós, J. Ramón, Agudo, Antonio, Rodriguez-Barranco, Miguel, Huerta Castaño, José María, Barricarte, Aurelio, Fernández, Ander Matheu, Travis, Ruth C., Vineis, Paolo, Muller, David C., Riboli, Elio, Gunter, Marc, Romieu, Isabelle, Herceg, Zdenko, Epidemiology & Health Economics, Epi Kanker Team 1, JC onderzoeksprogramma Kanker, Cancer, Cardiovasculaire Epi Team 3, Brain, Circulatory Health, JC onderzoeksprogramma Cardiovasculaire Epidemiologie, Ambatipudi, Srikant, Horvath, Steve, Perrier, Flavie, Cuenin, Cyrille, Hernandez-Vargas, Hector, Le Calvez-Kelm, Florence, Durand, Geoffroy, Byrnes, Graham, Ferrari, Pietro, Bouaoun, Liacine, Sklias, Athena, Chajes, Véronique, Overvad, Kim, Severi, Gianluca, Baglietto, Laura, Clavel-Chapelon, Françoise, Kaaks, Rudolf, Barrdahl, Myrto, Boeing, Heiner, Trichopoulou, Antonia, Lagiou, Pagona, Naska, Androniki, Masala, Giovanna, Agnoli, Claudia, Polidoro, Silvia, Tumino, Rosario, Panico, Salvatore, Dollé, Martijn, Peeters, Petra H M, Onland-Moret, N. Charlotte, Sandanger, Torkjel M., Nøst, Therese H., Weiderpass Vainio, Elisabete, Quirós, J. Ramón, Agudo, Antonio, Rodriguez-Barranco, Miguel, Huerta Castaño, José María, Barricarte, Aurelio, Fernández, Ander Matheu, Travis, Ruth C., Vineis, Paolo, Muller, David C., Riboli, Elio, Gunter, Marc, Romieu, Isabelle, and Herceg, Zdenko

Published
2017

45. Viral driven epigenetic events alter the expression of cancer-related genes in Epstein-Barr-virus naturally infected Burkitt lymphoma cell lines

Author

Hernandez-Vargas, Hector, primary, Gruffat, Henri, additional, Cros, Marie Pierre, additional, Diederichs, Audrey, additional, Sirand, Cécilia, additional, Vargas-Ayala, Romina C., additional, Jay, Antonin, additional, Durand, Geoffroy, additional, Le Calvez-Kelm, Florence, additional, Herceg, Zdenko, additional, Manet, Evelyne, additional, Wild, Christopher P., additional, Tommasino, Massimo, additional, and Accardi, Rosita, additional

Published
2017
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46. Investigation of DNA repair-related SNPs underlying susceptibility to papillary thyroid carcinoma reveals MGMT as a novel candidate gene in Belarusian children exposed to radiation

Author

Lonjou, Christine, primary, Damiola, Francesca, additional, Moissonnier, Monika, additional, Durand, Geoffroy, additional, Malakhova, Irina, additional, Masyakin, Vladimir, additional, Le Calvez-Kelm, Florence, additional, Cardis, Elisabeth, additional, Byrnes, Graham, additional, Kesminiene, Ausrele, additional, and Lesueur, Fabienne, additional

Published
2017
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47. CASP9 germline mutation in a family with multiple brain tumors

Author

Ronellenfitsch, Michael W., primary, Oh, Ji-Eun, additional, Satomi, Kaishi, additional, Sumi, Koichiro, additional, Harter, Patrick N., additional, Steinbach, Joachim P., additional, Felsberg, Jörg, additional, Capper, David, additional, Voegele, Catherine, additional, Durand, Geoffroy, additional, McKay, James, additional, Le Calvez-Kelm, Florence, additional, Schittenhelm, Jens, additional, Klink, Barbara, additional, Mittelbronn, Michel, additional, and Ohgaki, Hiroko, additional

Published
2017
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48. Marine monitoring campaign in France and French overseas departments: more than 10 000 datasets from grab and passive sampling

Author

Botta, Fabrizio, Abarnou, A., Bocquene, G., Champin, M., Durand, Geoffroy, Gonzalez, J., Masson, J., Priou, P., Tixier, C., LEMOIGNE, M., Tapie, Nathalie, Lestremau, François, Andres, Sandrine, Devier, Marie-Hélène, Civs, Gestionnaire, and Institut National de l'Environnement Industriel et des Risques (INERIS)

Subjects
[SDE] Environmental Sciences, [SDV.TOX] Life Sciences [q-bio]/Toxicology, [SDV.TOX]Life Sciences [q-bio]/Toxicology, [SDE]Environmental Sciences
Abstract

A screening study of emerging contaminants was carried out in 2012 in coastal waters in both metropolitan France and overseas departments (Martinique, Guadeloupe, Reunion, Mayotte and French Guiana) as part of the National Action Plan against pollution of the aquatic environment, which requires the regular updating of the lists of substances to be included in monitoring programmes. The Action Plan stresses the need to set up a watch list of substances to be investigated at the national level in order to acquire missing information about the level of exposure to emerging contaminants in the aquatic environment and allow identification of substances for which specific actions need to be implemented. The Ministry of Ecology appointed ONEMA as principal contractor and INERIS as project leader. One of the main objectives of this screening study was to gain knowledge of the occurrence of substances of “emerging” concern in the marine environment. Different data were collected, such as the presence/absence of each investigated compound and the level of concentration observed in the aquatic environment (water and sediment). Moreover, the performance of different sampling techniques was assessed. This study contributes to increased knowledge of emerging pollutants in French waters and to the wider considerations for updating the list of relevant substances to be included in the new monitoring programmes to be established. Triplicate sampling of water at the same site followed by SBSE extraction displayed a high results variability, which limits the exploitation of the quantified results. Neverthless, the testing of in situ systems integrators – POCIS – and extraction by SBSE bars has proven the added value of these two complementary techniques for monitoring hydrophobic and hydrophilic compounds in marine water. Finally, analyses of sediment allowed a more complete assessment of the quality of the waterbodies.

Published
2015

50. No evidence that protein truncating variants in BRIP1 are associated with breast cancer risk: implications for gene panel testing

Author

Easton, Douglas F., Lesueur, Fabienne, Decker, Brennan, Michailidou, Kyriaki, Li, Jun, Allen, Jamie, Luccarini, Craig, Pooley, Karen A., Shah, Mitul, Bolla, Manjeet K., Wang, Qin, Dennis, Joe, Ahmad, Jamil, Thompson, Ella R., Damiola, Francesca, Pertesi, Maroulio, Voegele, Catherine, Mebirouk, Noura, Robinot, Nivonirina, Durand, Geoffroy, Forey, Nathalie, Luben, Robert N., Ahmed, Shahana, Aittomaki, Kristiina, Anton-Culver, Hoda, Arndt, Volker, Baynes, Caroline, Beckman, Matthias W., Benitez, Javier, Van Den Berg, David, Blot, William J., Bogdanova, Natalia V., Bojesen, Stig E., Brenner, Hermann, Chang-Claude, Jenny, Chia, Kee Seng, Choi, Ji-Yeob, Conroy, Don M., Cox, Angela, Cross, Simon S., Czene, Kamila, Darabi, Hatef, Devilee, Peter, Eriksson, Mikael, Fasching, Peter A., Figueroa, Jonine, Flyger, Henrik, Fostira, Florentia, Garcia-Closas, Montserrat, Giles, Graham G., Glendon, Gord, Gonzalez-Neira, Anna, Guenel, Pascal, Haiman, Christopher A., Hall, Per, Hart, Steven N., Hartman, Mikael, Hooning, Maartje J., Hsiung, Chia-Ni, Ito, Hidemi, Jakubowska, Anna, James, Paul A., John, Esther M., Johnson, Nichola, Jones, Michael, Kabisch, Maria, Kang, Daehee, Kosma, Veli-Matti, Kristensen, Vessela, Lambrechts, Diether, Li, Na, Lindblom, Annika, Long, Jirong, Lophatananon, Artitaya, Lubinski, Jan, Mannermaa, Arto, Manoukian, Siranoush, Margolin, Sara, Matsuo, Keitaro, Meindl, Alfons, Mitchell, Gillian, Muir, Kenneth, Nevelsteen, Ines, van den Ouweland, Ans, Peterlongo, Paolo, Phuah, Sze Yee, Pylkas, Katri, Rowley, Simone M., Sangrajrang, Suleeporn, Schmutzler, Rita K., Shen, Chen-Yang, Shu, Xiao-Ou, Southey, Melissa C., Surowy, Harald, Swerdlow, Anthony, Teo, Soo H., Tollenaar, Rob A. E. M., Tomlinson, Ian, Torres, Diana, Truong, Therese, Vachon, Celine, Verhoef, Senno, Wong-Brown, Michelle, Zheng, Wei, Zheng, Ying, Nevanlinna, Heli, Scott, Rodney J., Andrulis, Irene L., Wu, Anna H., Hopper, John L., Couch, Fergus J., Winqvist, Robert, Burwinkel, Barbara, Sawyer, Elinor J., Schmidt, Marjanka K., Rudolph, Anja, Doerk, Thilo, Brauch, Hiltrud, Hamann, Ute, Neuhausen, Susan L., Milne, Roger L., Fletcher, Olivia, Pharoah, Paul D. P., Campbell, Ian G., Dunning, Alison M., Le Calvez-Kelm, Florence, Goldgar, David E., Tavtigian, Sean V., Chenevix-Trench, Georgia, Easton, Douglas F., Lesueur, Fabienne, Decker, Brennan, Michailidou, Kyriaki, Li, Jun, Allen, Jamie, Luccarini, Craig, Pooley, Karen A., Shah, Mitul, Bolla, Manjeet K., Wang, Qin, Dennis, Joe, Ahmad, Jamil, Thompson, Ella R., Damiola, Francesca, Pertesi, Maroulio, Voegele, Catherine, Mebirouk, Noura, Robinot, Nivonirina, Durand, Geoffroy, Forey, Nathalie, Luben, Robert N., Ahmed, Shahana, Aittomaki, Kristiina, Anton-Culver, Hoda, Arndt, Volker, Baynes, Caroline, Beckman, Matthias W., Benitez, Javier, Van Den Berg, David, Blot, William J., Bogdanova, Natalia V., Bojesen, Stig E., Brenner, Hermann, Chang-Claude, Jenny, Chia, Kee Seng, Choi, Ji-Yeob, Conroy, Don M., Cox, Angela, Cross, Simon S., Czene, Kamila, Darabi, Hatef, Devilee, Peter, Eriksson, Mikael, Fasching, Peter A., Figueroa, Jonine, Flyger, Henrik, Fostira, Florentia, Garcia-Closas, Montserrat, Giles, Graham G., Glendon, Gord, Gonzalez-Neira, Anna, Guenel, Pascal, Haiman, Christopher A., Hall, Per, Hart, Steven N., Hartman, Mikael, Hooning, Maartje J., Hsiung, Chia-Ni, Ito, Hidemi, Jakubowska, Anna, James, Paul A., John, Esther M., Johnson, Nichola, Jones, Michael, Kabisch, Maria, Kang, Daehee, Kosma, Veli-Matti, Kristensen, Vessela, Lambrechts, Diether, Li, Na, Lindblom, Annika, Long, Jirong, Lophatananon, Artitaya, Lubinski, Jan, Mannermaa, Arto, Manoukian, Siranoush, Margolin, Sara, Matsuo, Keitaro, Meindl, Alfons, Mitchell, Gillian, Muir, Kenneth, Nevelsteen, Ines, van den Ouweland, Ans, Peterlongo, Paolo, Phuah, Sze Yee, Pylkas, Katri, Rowley, Simone M., Sangrajrang, Suleeporn, Schmutzler, Rita K., Shen, Chen-Yang, Shu, Xiao-Ou, Southey, Melissa C., Surowy, Harald, Swerdlow, Anthony, Teo, Soo H., Tollenaar, Rob A. E. M., Tomlinson, Ian, Torres, Diana, Truong, Therese, Vachon, Celine, Verhoef, Senno, Wong-Brown, Michelle, Zheng, Wei, Zheng, Ying, Nevanlinna, Heli, Scott, Rodney J., Andrulis, Irene L., Wu, Anna H., Hopper, John L., Couch, Fergus J., Winqvist, Robert, Burwinkel, Barbara, Sawyer, Elinor J., Schmidt, Marjanka K., Rudolph, Anja, Doerk, Thilo, Brauch, Hiltrud, Hamann, Ute, Neuhausen, Susan L., Milne, Roger L., Fletcher, Olivia, Pharoah, Paul D. P., Campbell, Ian G., Dunning, Alison M., Le Calvez-Kelm, Florence, Goldgar, David E., Tavtigian, Sean V., and Chenevix-Trench, Georgia

Abstract

Background BRCA1 interacting protein C-terminal helicase 1 (BRIP1) is one of the Fanconi Anaemia Complementation (FANC) group family of DNA repair proteins. Biallelic mutations in BRIP1 are responsible for FANC group J, and previous studies have also suggested that rare protein truncating variants in BRIP1 are associated with an increased risk of breast cancer. These studies have led to inclusion of BRIP1 on targeted sequencing panels for breast cancer risk prediction. Methods We evaluated a truncating variant, p.Arg798Ter (rs137852986), and 10 missense variants of BRIP1, in 48144 cases and 43607 controls of European origin, drawn from 41 studies participating in the Breast Cancer Association Consortium (BCAC). Additionally, we sequenced the coding regions of BRIP1 in 13213 cases and 5242 controls from the UK, 1313 cases and 1123 controls from three population-based studies as part of the Breast Cancer Family Registry, and 1853 familial cases and 2001 controls from Australia. Results The rare truncating allele of rs137852986 was observed in 23 cases and 18 controls in Europeans in BCAC (OR 1.09, 95% CI 0.58 to 2.03, p=0.79). Truncating variants were found in the sequencing studies in 34 cases (0.21%) and 19 controls (0.23%) (combined OR 0.90, 95% CI 0.48 to 1.70, p=0.75). Conclusions These results suggest that truncating variants in BRIP1, and in particular p.Arg798Ter, are not associated with a substantial increase in breast cancer risk. Such observations have important implications for the reporting of results from breast cancer screening panels.

Published
2016

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