37 results on '"Puente, Xose S."'
Search Results
2. Molecular map of chronic lymphocytic leukemia and its impact on outcome
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Knisbacher, Binyamin A, Lin, Ziao, Hahn, Cynthia K, Nadeu, Ferran, Duran-Ferrer, Martí, Stevenson, Kristen E, Tausch, Eugen, Delgado, Julio, Barbera-Mourelle, Alex, Taylor-Weiner, Amaro, Bousquets-Muñoz, Pablo, Diaz-Navarro, Ander, Dunford, Andrew, Anand, Shankara, Kretzmer, Helene, Gutierrez-Abril, Jesus, López-Tamargo, Sara, Fernandes, Stacey M, Sun, Clare, Sivina, Mariela, Rassenti, Laura Z, Schneider, Christof, Li, Shuqiang, Parida, Laxmi, Meissner, Alexander, Aguet, François, Burger, Jan A, Wiestner, Adrian, Kipps, Thomas J, Brown, Jennifer R, Hallek, Michael, Stewart, Chip, Neuberg, Donna S, Martín-Subero, José I, Puente, Xose S, Stilgenbauer, Stephan, Wu, Catherine J, Campo, Elias, and Getz, Gad
- Subjects
Hematology ,Clinical Research ,Cancer ,Human Genome ,Rare Diseases ,Biotechnology ,Genetics ,Lymphoma ,Humans ,Leukemia ,Lymphocytic ,Chronic ,B-Cell ,Immunoglobulin Variable Region ,Mutation ,Prognosis ,Genomics ,Biological Sciences ,Medical and Health Sciences ,Developmental Biology - Abstract
Recent advances in cancer characterization have consistently revealed marked heterogeneity, impeding the completion of integrated molecular and clinical maps for each malignancy. Here, we focus on chronic lymphocytic leukemia (CLL), a B cell neoplasm with variable natural history that is conventionally categorized into two subtypes distinguished by extent of somatic mutations in the heavy-chain variable region of immunoglobulin genes (IGHV). To build the 'CLL map,' we integrated genomic, transcriptomic and epigenomic data from 1,148 patients. We identified 202 candidate genetic drivers of CLL (109 new) and refined the characterization of IGHV subtypes, which revealed distinct genomic landscapes and leukemogenic trajectories. Discovery of new gene expression subtypes further subcategorized this neoplasm and proved to be independent prognostic factors. Clinical outcomes were associated with a combination of genetic, epigenetic and gene expression features, further advancing our prognostic paradigm. Overall, this work reveals fresh insights into CLL oncogenesis and prognostication.
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- 2022
3. MALAT1 expression is associated with aggressive behavior in indolent B-cell neoplasms
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Fernández-Garnacho, Elena María, Nadeu, Ferran, Martín, Silvia, Mozas, Pablo, Rivero, Andrea, Delgado, Julio, Giné, Eva, López-Guillermo, Armando, Duran-Ferrer, Martí, Salaverria, Itziar, López, Cristina, Beà, Sílvia, Demajo, Santiago, Jares, Pedro, Puente, Xose S., Martín-Subero, José Ignacio, Campo, Elías, and Hernández, Lluís
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- 2023
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4. Detection of early seeding of Richter transformation in chronic lymphocytic leukemia
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Nadeu, Ferran, Royo, Romina, Massoni-Badosa, Ramon, Playa-Albinyana, Heribert, Garcia-Torre, Beatriz, Duran-Ferrer, Martí, Dawson, Kevin J., Kulis, Marta, Diaz-Navarro, Ander, Villamor, Neus, Melero, Juan L., Chapaprieta, Vicente, Dueso-Barroso, Ana, Delgado, Julio, Moia, Riccardo, Ruiz-Gil, Sara, Marchese, Domenica, Giró, Ariadna, Verdaguer-Dot, Núria, Romo, Mónica, Clot, Guillem, Rozman, Maria, Frigola, Gerard, Rivas-Delgado, Alfredo, Baumann, Tycho, Alcoceba, Miguel, González, Marcos, Climent, Fina, Abrisqueta, Pau, Castellví, Josep, Bosch, Francesc, Aymerich, Marta, Enjuanes, Anna, Ruiz-Gaspà, Sílvia, López-Guillermo, Armando, Jares, Pedro, Beà, Sílvia, Capella-Gutierrez, Salvador, Gelpí, Josep Ll., López-Bigas, Núria, Torrents, David, Campbell, Peter J., Gut, Ivo, Rossi, Davide, Gaidano, Gianluca, Puente, Xose S., Garcia-Roves, Pablo M., Colomer, Dolors, Heyn, Holger, Maura, Francesco, Martín-Subero, José I., and Campo, Elías
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- 2022
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5. PanCancer analysis of somatic mutations in repetitive regions reveals recurrent mutations in snRNA U2
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Bousquets-Muñoz, Pablo, Díaz-Navarro, Ander, Nadeu, Ferran, Sánchez-Pitiot, Ana, López-Tamargo, Sara, Shuai, Shimin, Balbín, Milagros, Tubio, Jose M. C., Beà, Sílvia, Martin-Subero, Jose I., Gutiérrez-Fernández, Ana, Stein, Lincoln D., Campo, Elías, and Puente, Xose S.
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- 2022
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6. Correction: ATM germline variants in a young adult with chronic lymphocytic leukemia: 8 years of genomic evolution
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Royo, Romina, Magnano, Laura, Delgado, Julio, Ruiz-Gil, Sara, Gelpí, Josep Ll., Heyn, Holger, Taylor, Malcom A., Stankovic, Tatjana, Puente, Xose S., Nadeu, Ferran, and Campo, Elías
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- 2022
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7. ATM germline variants in a young adult with chronic lymphocytic leukemia: 8 years of genomic evolution
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Royo, Romina, Magnano, Laura, Delgado, Julio, Ruiz-Gil, Sara, Gelpí, Josep Ll., Heyn, Holger, Taylor, Malcom A., Stankovic, Tatjana, Puente, Xose S., Nadeu, Ferran, and Campo, Elías
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- 2022
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8. mmsig: a fitting approach to accurately identify somatic mutational signatures in hematological malignancies
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Rustad, Even H., Nadeu, Ferran, Angelopoulos, Nicos, Ziccheddu, Bachisio, Bolli, Niccolò, Puente, Xose S., Campo, Elias, Landgren, Ola, and Maura, Francesco
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- 2021
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9. Author Correction: Comparative and demographic analysis of orang-utan genomes
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Locke, Devin P., Hillier, LaDeana W., Warren, Wesley C., Worley, Kim C., Nazareth, Lynne V., Muzny, Donna M., Yang, Shiaw-Pyng, Wang, Zhengyuan, Chinwalla, Asif T., Minx, Pat, Mitreva, Makedonka, Cook, Lisa, Delehaunty, Kim D., Fronick, Catrina, Schmidt, Heather, Fulton, Lucinda A., Fulton, Robert S., Nelson, Joanne O., Magrini, Vincent, Pohl, Craig, Graves, Tina A., Markovic, Chris, Cree, Andy, Dinh, Huyen H., Hume, Jennifer, Kovar, Christie L., Fowler, Gerald R., Lunter, Gerton, Meader, Stephen, Heger, Andreas, Ponting, Chris P., Marques-Bonet, Tomas, Alkan, Can, Chen, Lin, Cheng, Ze, Kidd, Jeffrey M., Eichler, Evan E., White, Simon, Searle, Stephen, Vilella, Albert J., Chen, Yuan, Flicek, Paul, Ma, Jian, Raney, Brian, Suh, Bernard, Burhans, Richard, Herrero, Javier, Haussler, David, Faria, Rui, Fernando, Olga, Darré, Fleur, Farré, Domènec, Gazave, Elodie, Oliva, Meritxell, Navarro, Arcadi, Roberto, Roberta, Capozzi, Oronzo, Archidiacono, Nicoletta, Della Valle, Giuliano, Purgato, Stefania, Rocchi, Mariano, Konkel, Miriam K., Walker, Jerilyn A., Ullmer, Brygg, Batzer, Mark A., Smit, Arian F. A., Hubley, Robert, Casola, Claudio, Schrider, Daniel R., Hahn, Matthew W., Quesada, Victor, Puente, Xose S., Ordoñez, Gonzalo R., López-Otín, Carlos, Vinar, Tomas, Brejova, Brona, Ratan, Aakrosh, Harris, Robert S., Miller, Webb, Kosiol, Carolin, Lawson, Heather A., Taliwal, Vikas, Martins, André L., Siepel, Adam, RoyChoudhury, Arindam, Ma, Xin, Degenhardt, Jeremiah, Bustamante, Carlos D., Gutenkunst, Ryan N., Mailund, Thomas, Dutheil, Julien Y., Hobolth, Asger, Schierup, Mikkel H., Ryder, Oliver A., Yoshinaga, Yuko, de Jong, Pieter J., Weinstock, George M., Rogers, Jeffrey, Mardis, Elaine R., Gibbs, Richard A., and Wilson, Richard K.
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- 2022
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10. Abstract 3814: In CLL the U1 snRNA driver mutation alters splicing in multiple genes and pathways
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Senff-Ribeiro, Andrea, primary, Almodaresi, Fatemeh, additional, Trinh, Quang, additional, Shuai, Shimin, additional, Spaner, David, additional, Puente, Xose S., additional, Campo, Elias, additional, and Stein, Lincoln D., additional
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- 2023
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11. Data from Clinical Response to a Lapatinib-Based Therapy for a Li-Fraumeni Syndrome Patient with a Novel HER2V659E Mutation
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Serra, Violeta, primary, Vivancos, Ana, primary, Puente, Xose S., primary, Felip, Enriqueta, primary, Silberschmidt, Daniel, primary, Caratù, Ginevra, primary, Parra, Josep-Lluís, primary, De Mattos-Arruda, Leticia, primary, Grueso, Judit, primary, Hernández-Losa, Javier, primary, Arribas, Joaquín, primary, Prudkin, Ludmila, primary, Nuciforo, Paolo, primary, Scaltriti, Maurizio, primary, Seoane, Joan, primary, and Baselga, José, primary
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- 2023
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12. Supplementary Data from Clinical Response to a Lapatinib-Based Therapy for a Li-Fraumeni Syndrome Patient with a Novel HER2V659E Mutation
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Serra, Violeta, primary, Vivancos, Ana, primary, Puente, Xose S., primary, Felip, Enriqueta, primary, Silberschmidt, Daniel, primary, Caratù, Ginevra, primary, Parra, Josep-Lluís, primary, De Mattos-Arruda, Leticia, primary, Grueso, Judit, primary, Hernández-Losa, Javier, primary, Arribas, Joaquín, primary, Prudkin, Ludmila, primary, Nuciforo, Paolo, primary, Scaltriti, Maurizio, primary, Seoane, Joan, primary, and Baselga, José, primary
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- 2023
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13. Supplementary Table 1 from Clinical Response to a Lapatinib-Based Therapy for a Li-Fraumeni Syndrome Patient with a Novel HER2V659E Mutation
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Serra, Violeta, primary, Vivancos, Ana, primary, Puente, Xose S., primary, Felip, Enriqueta, primary, Silberschmidt, Daniel, primary, Caratù, Ginevra, primary, Parra, Josep-Lluís, primary, De Mattos-Arruda, Leticia, primary, Grueso, Judit, primary, Hernández-Losa, Javier, primary, Arribas, Joaquín, primary, Prudkin, Ludmila, primary, Nuciforo, Paolo, primary, Scaltriti, Maurizio, primary, Seoane, Joan, primary, and Baselga, José, primary
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- 2023
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14. Supplementary Figures from Clinical Response to a Lapatinib-Based Therapy for a Li-Fraumeni Syndrome Patient with a Novel HER2V659E Mutation
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Serra, Violeta, primary, Vivancos, Ana, primary, Puente, Xose S., primary, Felip, Enriqueta, primary, Silberschmidt, Daniel, primary, Caratù, Ginevra, primary, Parra, Josep-Lluís, primary, De Mattos-Arruda, Leticia, primary, Grueso, Judit, primary, Hernández-Losa, Javier, primary, Arribas, Joaquín, primary, Prudkin, Ludmila, primary, Nuciforo, Paolo, primary, Scaltriti, Maurizio, primary, Seoane, Joan, primary, and Baselga, José, primary
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- 2023
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15. Backtracking NOM1::ETV6fusion to neonatal pathogenesis of t(7;12) (q36;p13) infant AML
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Bousquets-Muñoz, Pablo, Molina, Oscar, Varela, Ignacio, Álvarez-Eguiluz, Ángel, Fernández-Mateos, Javier, Gómez, Ana, Sánchez, Elena G., Balbín, Milagros, Ruano, David, Ramírez-Orellana, Manuel, Puente, Xose S., Menéndez, Pablo, and Velasco-Hernandez, Talia
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- 2024
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16. table s1 from The Oncogenic FOXL2 C134W Mutation Is a Key Driver of Granulosa Cell Tumors
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Llano, Elena, primary, Todeschini, Anne Laure, primary, Felipe-Medina, Natalia, primary, Corte-Torres, María D., primary, Condezo, Yazmine B., primary, Sanchez-Martin, Manuel, primary, López-Tamargo, Sara, primary, Astudillo, Aurora, primary, Puente, Xose S., primary, Pendas, Alberto M., primary, and Veitia, Reiner A., primary
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- 2023
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17. Supplementary Figure S1 from Chromosome 12p Amplification in Triple-Negative/BRCA1-Mutated Breast Cancer Associates with Emergence of Docetaxel Resistance and Carboplatin Sensitivity
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Gómez-Miragaya, Jorge, primary, Díaz-Navarro, Ander, primary, Tonda, Raul, primary, Beltran, Sergi, primary, Palomero, Luis, primary, Palafox, Marta, primary, Dobrolecki, Lacey E., primary, Huang, Chen, primary, Vasaikar, Suhas, primary, Zhang, Bing, primary, Wulf, Gerburg M., primary, Collado-Sole, Alejandro, primary, Trinidad, Eva M., primary, Muñoz, Purificación, primary, Paré, Laia, primary, Prat, Aleix, primary, Bruna, Alejandra, primary, Caldas, Carlos, primary, Arribas, Joaquín, primary, Soler-Monso, María Teresa, primary, Petit, Anna, primary, Balmaña, Judith, primary, Cruz, Cristina, primary, Serra, Violeta, primary, Pujana, Miguel Angel, primary, Lewis, Michael T., primary, Puente, Xose S., primary, and González-Suárez, Eva, primary
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- 2023
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18. Supplementary Data from The Oncogenic FOXL2 C134W Mutation Is a Key Driver of Granulosa Cell Tumors
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Llano, Elena, primary, Todeschini, Anne Laure, primary, Felipe-Medina, Natalia, primary, Corte-Torres, María D., primary, Condezo, Yazmine B., primary, Sanchez-Martin, Manuel, primary, López-Tamargo, Sara, primary, Astudillo, Aurora, primary, Puente, Xose S., primary, Pendas, Alberto M., primary, and Veitia, Reiner A., primary
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- 2023
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19. Data from Matrix Metalloproteinase-8 Functions as a Metastasis Suppressor through Modulation of Tumor Cell Adhesion and Invasion
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Gutiérrez-Fernández, Ana, primary, Fueyo, Antonio, primary, Folgueras, Alicia R., primary, Garabaya, Cecilia, primary, Pennington, Caroline J., primary, Pilgrim, Simon, primary, Edwards, Dylan R., primary, Holliday, Deborah L., primary, Jones, J. Louise, primary, Span, Paul N., primary, Sweep, Fred C.G.J., primary, Puente, Xose S., primary, and López-Otín, Carlos, primary
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- 2023
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20. Supplementary Figure 1 from Matrix Metalloproteinase-8 Functions as a Metastasis Suppressor through Modulation of Tumor Cell Adhesion and Invasion
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Gutiérrez-Fernández, Ana, primary, Fueyo, Antonio, primary, Folgueras, Alicia R., primary, Garabaya, Cecilia, primary, Pennington, Caroline J., primary, Pilgrim, Simon, primary, Edwards, Dylan R., primary, Holliday, Deborah L., primary, Jones, J. Louise, primary, Span, Paul N., primary, Sweep, Fred C.G.J., primary, Puente, Xose S., primary, and López-Otín, Carlos, primary
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- 2023
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21. MALAT1Expression is Associated with Aggressive Behavior in Indolent B-Cell Neoplasms
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María Fernández-Garnacho, Elena, primary, Nadeu, Ferran, additional, Martín, Silvia, additional, Mozas, Pablo, additional, Rivero, Andrea, additional, Delgado, Julio, additional, Giné, Eva, additional, López-Guillermo, Armando, additional, Duran-Ferrer, Martí, additional, Salaverria, Itziar, additional, López, Cristina, additional, Beà, Sílvia, additional, Demajo, Santiago, additional, Jares, Pedro, additional, Puente, Xose S, additional, Martín-Subero, José Ignacio, additional, Campo, Elias, additional, and Hernández, Lluís, additional
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- 2023
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22. A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns
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Jiao, Wei, Atwal, Gurnit, Polak, Paz, Karlic, Rosa, Cuppen, Edwin, Al-Shahrour, Fatima, Bailey, Peter J, Biankin, Andrew V, Boutros, Paul C, Campbell, Peter J, Chang, David K, Cooke, Susanna L, Deshpande, Vikram, Faltas, Bishoy M, Faquin, William C, Garraway, Levi, Getz, Gad, Grimmond, Sean M, Haider, Syed, Hoadley, Katherine A, Kaiser, Vera B, Kato, Mamoru, Kübler, Kirsten, Lazar, Alexander J, Li, Constance H, Louis, David N, Margolin, Adam, Martin, Sancha, Nahal-Bose, Hardeep K, Nielsen, G Petur, Nik-Zainal, Serena, Omberg, Larsson, P’ng, Christine, Perry, Marc D, Rheinbay, Esther, Rubin, Mark A, Semple, Colin A, Sgroi, Dennis C, Shibata, Tatsuhiro, Siebert, Reiner, Smith, Jaclyn, Stein, Lincoln D, Stobbe, Miranda D, Sun, Ren X, Thai, Kevin, Wright, Derek W, Wu, Chin-Lee, Yuan, Ke, Zhang, Junjun, Danyi, Alexandra, de Ridder, Jeroen, van Herpen, Carla, Lolkema, Martijn P, Steeghs, Neeltje, Morris, Quaid D, Aaltonen, Lauri A, Abascal, Federico, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J, Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, Akbani, Rehan, Akdemir, Kadir C, Al-Ahmadie, Hikmat, Al-Sedairy, Sultan T, Alawi, Malik, Albert, Monique, Aldape, Kenneth, Alexandrov, Ludmil B, Ally, Adrian, Alsop, Kathryn, Alvarez, Eva G, Amary, Fernanda, Amin, Samirkumar B, Aminou, Brice, Ammerpohl, Ole, Anderson, Matthew J, Ang, Yeng, Antonello, Davide, Anur, Pavana, Aparicio, Samuel, Appelbaum, Elizabeth L, Arai, Yasuhito, Aretz, Axel, Arihiro, Koji, Ariizumi, Shun-ichi, Armenia, Joshua, Arnould, Laurent, Asa, Sylvia, Assenov, Yassen, Aukema, Sietse, Auman, J Todd, Aure, Miriam RR, Awadalla, Philip, Aymerich, Marta, Bader, Gary D, Baez-Ortega, Adrian, Bailey, Matthew H, Balasundaram, Miruna, Balu, Saianand, Bandopadhayay, Pratiti, Banks, Rosamonde E, Barbi, Stefano, Barbour, Andrew P, Barenboim, Jonathan, Barnholtz-Sloan, Jill, Barr, Hugh, Barrera, Elisabet, Bartlett, John, Bartolome, Javier, Bassi, Claudio, Bathe, Oliver F, Baumhoer, Daniel, Bavi, Prashant, Baylin, Stephen B, Bazant, Wojciech, Beardsmore, Duncan, Beck, Timothy A, Behjati, Sam, Behren, Andreas, Niu, Beifang, Bell, Cindy, Beltran, Sergi, Benz, Christopher, Berchuck, Andrew, Bergmann, Anke K, Bergstrom, Erik N, Berman, Benjamin P, Berney, Daniel M, Bernhart, Stephan H, Beroukhim, Rameen, Berrios, Mario, Bersani, Samantha, Bertl, Johanna, Betancourt, Miguel, Bhandari, Vinayak, Bhosle, Shriram G, Bieg, Matthias, Bigner, Darell, Binder, Hans, Birney, Ewan, Birrer, Michael, Biswas, Nidhan K, Bjerkehagen, Bodil, Bodenheimer, Tom, Boice, Lori, Bonizzato, Giada, De Bono, Johann S, Boot, Arnoud, Bootwalla, Moiz S, Borg, Ake, Borkhardt, Arndt, Boroevich, Keith A, Borozan, Ivan, Borst, Christoph, Bosenberg, Marcus, Bosio, Mattia, Boultwood, Jacqueline, Bourque, Guillaume, Bova, G Steven, Bowen, David T, Bowlby, Reanne, Bowtell, David DL, Boyault, Sandrine, Boyce, Rich, Boyd, Jeffrey, Brazma, Alvis, Brennan, Paul, Brewer, Daniel S, Brinkman, Arie B, Bristow, Robert G, Broaddus, Russell R, Brock, Jane E, Brock, Malcolm, Broeks, Annegien, Brooks, Angela N, Brooks, Denise, Brors, Benedikt, Brunak, Søren, Bruxner, Timothy JC, Bruzos, Alicia L, Buchanan, Alex, Buchhalter, Ivo, Buchholz, Christiane, Bullman, Susan, Burke, Hazel, Burkhardt, Birgit, Burns, Kathleen H, Busanovich, John, Bustamante, Carlos D, Butler, Adam P, Butte, Atul J, Byrne, Niall J, Børresen-Dale, Anne-Lise, Caesar-Johnson, Samantha J, Cafferkey, Andy, Cahill, Declan, Calabrese, Claudia, Caldas, Carlos, Calvo, Fabien, Camacho, Niedzica, Campo, Elias, Cantù, Cinzia, Cao, Shaolong, Carey, Thomas E, Carlevaro-Fita, Joana, Carlsen, Rebecca, Cataldo, Ivana, Cazzola, Mario, Cebon, Jonathan, Cerfolio, Robert, Chadwick, Dianne E, Chakravarty, Dimple, Chalmers, Don, Chan, Calvin Wing Yiu, Chan, Kin, Chan-Seng-Yue, Michelle, Chandan, Vishal S, Chanock, Stephen J, Chantrill, Lorraine A, Chateigner, Aurélien, Chatterjee, Nilanjan, Chayama, Kazuaki, Chen, Hsiao-Wei, Chen, Jieming, Chen, Ken, Chen, Yiwen, Chen, Zhaohong, Cherniack, Andrew D, Chien, Jeremy, Chiew, Yoke-Eng, Chin, Suet-Feung, Cho, Juok, Cho, Sunghoon, Choi, Jung Kyoon, Choi, Wan, Chomienne, Christine, Chong, Zechen, Choo, Su Pin, Chou, Angela, Christ, Angelika N, Christie, Elizabeth L, Chuah, Eric, Cibulskis, Carrie, Cibulskis, Kristian, Cingarlini, Sara, Clapham, Peter, Claviez, Alexander, Cleary, Sean, Cloonan, Nicole, Cmero, Marek, Collins, Colin C, Connor, Ashton A, Cooper, Colin S, Cope, Leslie, Corbo, Vincenzo, Cordes, Matthew G, Cordner, Stephen M, Cortés-Ciriano, Isidro, Covington, Kyle, Cowin, Prue A, Craft, Brian, Craft, David, Creighton, Chad J, Cun, Yupeng, Curley, Erin, Cutcutache, Ioana, Czajka, Karolina, Czerniak, Bogdan, Dagg, Rebecca A, Danilova, Ludmila, Davi, Maria Vittoria, Davidson, Natalie R, Davies, Helen, Davis, Ian J, Davis-Dusenbery, Brandi N, Dawson, Kevin J, De La Vega, Francisco M, De Paoli-Iseppi, Ricardo, Defreitas, Timothy, Dei Tos, Angelo P, Delaneau, Olivier, Demchok, John A, Demeulemeester, Jonas, Demidov, German M, Demircioğlu, Deniz, Dennis, Nening M, Denroche, Robert E, Dentro, Stefan C, Desai, Nikita, Deshwar, Amit G, Desmedt, Christine, Deu-Pons, Jordi, Dhalla, Noreen, Dhani, Neesha C, Dhingra, Priyanka, Dhir, Rajiv, DiBiase, Anthony, Diamanti, Klev, Ding, Li, Ding, Shuai, Dinh, Huy Q, Dirix, Luc, Doddapaneni, HarshaVardhan, Donmez, Nilgun, Dow, Michelle T, Drapkin, Ronny, Drechsel, Oliver, Drews, Ruben M, Serge, Serge, Dudderidge, Tim, Dueso-Barroso, Ana, Dunford, Andrew J, Dunn, Michael, Dursi, Lewis Jonathan, Duthie, Fraser R, Dutton-Regester, Ken, Eagles, Jenna, Easton, Douglas F, Edmonds, Stuart, Edwards, Paul A, Edwards, Sandra E, Eeles, Rosalind A, Ehinger, Anna, Eils, Juergen, Eils, Roland, El-Naggar, Adel, Eldridge, Matthew, Ellrott, Kyle, Erkek, Serap, Escaramis, Georgia, Espiritu, Shadrielle MG, Estivill, Xavier, Etemadmoghadam, Dariush, Eyfjord, Jorunn E, Fan, Daiming, Fan, Yu, Farcas, Claudiu, Fassan, Matteo, Fatima, Aquila, Favero, Francesco, Fayzullaev, Nodirjon, Felau, Ina, Fereday, Sian, Ferguson, Martin L, Ferretti, Vincent, Feuerbach, Lars, Field, Matthew A, Fink, J Lynn, Finocchiaro, Gaetano, Fisher, Cyril, Fittall, Matthew W, Fitzgerald, Anna, Fitzgerald, Rebecca C, Flanagan, Adrienne M, Fleshner, Neil E, Flicek, Paul, Foekens, John A, Fong, Kwun M, Fonseca, Nuno A, Foster, Christopher S, Fox, Natalie S, Fraser, Michael, Frazer, Scott, Frenkel-Morgenstern, Milana, Friedman, William, Frigola, Joan, Fronick, Catrina C, Fujimoto, Akihiro, Fujita, Masashi, Fukayama, Masashi, Fulton, Lucinda A, Fulton, Robert S, Furuta, Mayuko, Futreal, P Andrew, Füllgrabe, Anja, Gabriel, Stacey B, Gallinger, Steven, Gambacorti-Passerini, Carlo, Gao, Jianjiong, Gao, Shengjie, Garred, Øystein, Garrison, Erik, Garsed, Dale W, Gehlenborg, Nils, Gelpi, Josep LL, George, Joshy, Gerhard, Daniela S, Gerhauser, Clarissa, Gershenwald, Jeffrey E, Gerstein, Mark, Gerstung, Moritz, Ghori, Mohammed, Ghossein, Ronald, Giama, Nasra H, Gibbs, Richard A, Gibson, Bob, Gill, Anthony J, Gill, Pelvender, Giri, Dilip D, Glodzik, Dominik, Gnanapragasam, Vincent J, Goebler, Maria Elisabeth, Goldman, Mary J, Gomez, Carmen, Gonzalez, Santiago, Gonzalez-Perez, Abel, Gordenin, Dmitry A, Gossage, James, Gotoh, Kunihito, Govindan, Ramaswamy, Grabau, Dorthe, Graham, Janet S, Grant, Robert C, Green, Anthony R, Green, Eric, Greger, Liliana, Grehan, Nicola, Grimaldi, Sonia, Grossman, Robert L, Grundhoff, Adam, Gundem, Gunes, Guo, Qianyun, Gupta, Manaswi, Gupta, Shailja, Gut, Ivo G, Gut, Marta, Göke, Jonathan, Ha, Gavin, Haake, Andrea, Haan, David, Haas, Siegfried, Haase, Kerstin, Haber, James E, Habermann, Nina, Hach, Faraz, Hama, Natsuko, Hamdy, Freddie C, Hamilton, Anne, Hamilton, Mark P, Han, Leng, Hanna, George B, Hansmann, Martin, Haradhvala, Nicholas J, Harismendy, Olivier, Harliwong, Ivon, Harmanci, Arif O, Harrington, Eoghan, Hasegawa, Takanori, Haussler, David, Hawkins, Steve, Hayami, Shinya, Hayashi, Shuto, Hayes, D Neil, Hayes, 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Deurzen, Carolien HM, van de Vijver, Marc J, Veer, L van’t, and von Mering, Christian
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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
In cancer, the primary tumour’s organ of origin and histopathology are the strongest determinants of its clinical behaviour, but in 3% of cases a patient presents with a metastatic tumour and no obvious primary. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we train a deep learning classifier to predict cancer type based on patterns of somatic passenger mutations detected in whole genome sequencing (WGS) of 2606 tumours representing 24 common cancer types produced by the PCAWG Consortium. Our classifier achieves an accuracy of 91% on held-out tumor samples and 88% and 83% respectively on independent primary and metastatic samples, roughly double the accuracy of trained pathologists when presented with a metastatic tumour without knowledge of the primary. Surprisingly, adding information on driver mutations reduced accuracy. Our results have clinical applicability, underscore how patterns of somatic passenger mutations encode the state of the cell of origin, and can inform future strategies to detect the source of circulating tumour DNA.
- Published
- 2023
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23. Combined burden and functional impact tests for cancer driver discovery using DriverPower
- Author
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Shuai, Shimin, Abascal, Federico, Amin, Samirkumar B, Bader, Gary D, Bandopadhayay, Pratiti, Barenboim, Jonathan, Beroukhim, Rameen, Bertl, Johanna, Boroevich, Keith A, Brunak, Søren, Campbell, Peter J, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Chen, Ken, Choi, Jung Kyoon, Deu-Pons, Jordi, Dhingra, Priyanka, Diamanti, Klev, Feuerbach, Lars, Fink, J Lynn, Fonseca, Nuno A, Frigola, Joan, Gambacorti-Passerini, Carlo, Garsed, Dale W, Gerstein, Mark, Getz, Gad, Guo, Qianyun, Gut, Ivo G, Haan, David, Hamilton, Mark P, Haradhvala, Nicholas J, Harmanci, Arif O, Helmy, Mohamed, Herrmann, Carl, Hess, Julian M, Hobolth, Asger, Hodzic, Ermin, Hong, Chen, Hornshøj, Henrik, Isaev, Keren, Izarzugaza, Jose MG, Johnson, Rory, Johnson, Todd A, Juul, Malene, Juul, Randi Istrup, Kahles, Andre, Kahraman, Abdullah, Kellis, Manolis, Khurana, Ekta, Kim, Jaegil, Kim, Jong K, Kim, Youngwook, Komorowski, Jan, Korbel, Jan O, Kumar, Sushant, Lanzós, Andrés, Larsson, Erik, Lawrence, Michael 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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
The discovery of driver mutations is one of the key motivations for cancer genome sequencing. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we describe DriverPower, a software package that uses mutational burden and functional impact evidence to identify driver mutations in coding and non-coding sites within cancer whole genomes. Using a total of 1373 genomic features derived from public sources, DriverPower’s background mutation model explains up to 93% of the regional variance in the mutation rate across multiple tumour types. By incorporating functional impact scores, we are able to further increase the accuracy of driver discovery. Testing across a collection of 2583 cancer genomes from the PCAWG project, DriverPower identifies 217 coding and 95 non-coding driver candidates. Comparing to six published methods used by the PCAWG Drivers and Functional Interpretation Working Group, DriverPower has the highest F1 score for both coding and non-coding driver discovery. This demonstrates that DriverPower is an effective framework for computational driver discovery.
- Published
- 2023
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24. Integrative pathway enrichment analysis of multivariate omics data
- Author
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Paczkowska, Marta, Barenboim, Jonathan, Sintupisut, Nardnisa, Fox, Natalie S, Zhu, Helen, Abd-Rabbo, Diala, Mee, Miles W, Boutros, Paul C, Abascal, Federico, Amin, Samirkumar B, Bader, Gary D, Beroukhim, Rameen, Bertl, Johanna, Boroevich, Keith A, Brunak, Søren, Campbell, Peter J, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Chen, Ken, Choi, Jung Kyoon, Deu-Pons, Jordi, Dhingra, Priyanka, Diamanti, Klev, Feuerbach, Lars, Fink, J Lynn, Fonseca, Nuno A, Frigola, Joan, Gambacorti-Passerini, Carlo, Garsed, Dale W, Gerstein, Mark, Getz, Gad, Gonzalez-Perez, Abel, Guo, Qianyun, Gut, Ivo G, Haan, David, Hamilton, Mark P, Haradhvala, Nicholas J, Harmanci, Arif O, Helmy, Mohamed, Herrmann, Carl, Hess, Julian M, Hobolth, Asger, Hodzic, Ermin, Hong, Chen, Hornshøj, Henrik, Isaev, Keren, Izarzugaza, Jose MG, Johnson, Rory, Johnson, Todd A, Juul, Malene, Juul, Randi Istrup, Kahles, Andre, Kahraman, Abdullah, Kellis, Manolis, Khurana, Ekta, Kim, Jaegil, Kim, Jong K, Kim, 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Vijver, Marc J, and Veer, L van’t
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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
Multi-omics datasets represent distinct aspects of the central dogma of molecular biology. Such high-dimensional molecular profiles pose challenges to data interpretation and hypothesis generation. ActivePathways is an integrative method that discovers significantly enriched pathways across multiple datasets using statistical data fusion, rationalizes contributing evidence and highlights associated genes. As part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumor types, we integrated genes with coding and non-coding mutations and revealed frequently mutated pathways and additional cancer genes with infrequent mutations. We also analyzed prognostic molecular pathways by integrating genomic and transcriptomic features of 1780 breast cancers and highlighted associations with immune response and anti-apoptotic signaling. Integration of ChIP-seq and RNA-seq data for master regulators of the Hippo pathway across normal human tissues identified processes of tissue regeneration and stem cell regulation. ActivePathways is a versatile method that improves systems-level understanding of cellular organization in health and disease through integration of multiple molecular datasets and pathway annotations.
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- 2023
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25. Pathway and network analysis of more than 2500 whole cancer genomes
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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
The catalog of cancer driver mutations in protein-coding genes has greatly expanded in the past decade. However, non-coding cancer driver mutations are less well-characterized and only a handful of recurrent non-coding mutations, most notably TERT promoter mutations, have been reported. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancer across 38 tumor types, we perform multi-faceted pathway and network analyses of non-coding mutations across 2583 whole cancer genomes from 27 tumor types compiled by the ICGC/TCGA PCAWG project that was motivated by the success of pathway and network analyses in prioritizing rare mutations in protein-coding genes. While few non-coding genomic elements are recurrently mutated in this cohort, we identify 93 genes harboring non-coding mutations that cluster into several modules of interacting proteins. Among these are promoter mutations associated with reduced mRNA expression in TP53, TLE4, and TCF4. We find that biological processes had variable proportions of coding and non-coding mutations, with chromatin remodeling and proliferation pathways altered primarily by coding mutations, while developmental pathways, including Wnt and Notch, altered by both coding and non-coding mutations. RNA splicing is primarily altered by non-coding mutations in this cohort, and samples containing non-coding mutations in well-known RNA splicing factors exhibit similar gene expression signatures as samples with coding mutations in these genes. These analyses contribute a new repertoire of possible cancer genes and mechanisms that are altered by non-coding mutations and offer insights into additional cancer vulnerabilities that can be investigated for potential therapeutic treatments.
- Published
- 2023
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26. Divergent mutational processes distinguish hypoxic and normoxic tumours
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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
Many primary tumours have low levels of molecular oxygen (hypoxia), and hypoxic tumours respond poorly to therapy. Pan-cancer molecular hallmarks of tumour hypoxia remain poorly understood, with limited comprehension of its associations with specific mutational processes, non-coding driver genes and evolutionary features. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we quantify hypoxia in 1188 tumours spanning 27 cancer types. Elevated hypoxia associates with increased mutational load across cancer types, irrespective of underlying mutational class. The proportion of mutations attributed to several mutational signatures of unknown aetiology directly associates with the level of hypoxia, suggesting underlying mutational processes for these signatures. At the gene level, driver mutations in TP53, MYC and PTEN are enriched in hypoxic tumours, and mutations in PTEN interact with hypoxia to direct tumour evolutionary trajectories. Overall, hypoxia plays a critical role in shaping the genomic and evolutionary landscapes of cancer.
- Published
- 2023
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27. Genomic footprints of activated telomere maintenance mechanisms in cancer
- Author
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Staaf, Johan, Stadler, Peter F, Staib, Peter, Stark, Stefan G, Stebbings, Lucy, Stefánsson, Ólafur Andri, Stegle, Oliver, Stein, Lincoln D, Stenhouse, Alasdair, Stilgenbauer, Stephan, Stobbe, Miranda D, Stratton, Michael R, Stretch, Jonathan R, Struck, Adam J, Stuart, Joshua M, Stunnenberg, Henk G, Su, Hong, Su, Xiaoping, Sun, Ren X, Sungalee, Stephanie, Susak, Hana, Suzuki, Akihiro, Sweep, Fred, Szczepanowski, Monika, Sültmann, Holger, Yugawa, Takashi, Tam, Angela, Tamborero, David, Tan, Benita Kiat Tee, Tan, Donghui, Tan, Patrick, Tanaka, Hiroko, Taniguchi, Hirokazu, Tanskanen, Tomas J, Tarabichi, Maxime, Tarnuzzer, Roy, Tarpey, Patrick, Taschuk, Morgan L, Tatsuno, Kenji, Tavaré, Simon, Taylor, Darrin F, Taylor-Weiner, Amaro, Teague, Jon W, Teh, Bin Tean, Tembe, Varsha, Temes, Javier, Thai, Kevin, Thayer, Sarah P, Thiessen, Nina, Thomas, Gilles, Thomas, Sarah, Thompson, Alan, Thompson, Alastair M, Thompson, John FF, Thompson, R Houston, Thorne, Heather, Thorne, Leigh B, Thorogood, Adrian, Tiao, Grace, Tijanic, Nebojsa, Timms, Lee E, Tirabosco, Roberto, Tojo, Marta, Tommasi, Stefania, Toon, Christopher W, Toprak, Umut H, Tortora, Giampaolo, Tost, Jörg, Totoki, Yasushi, Townend, David, Traficante, Nadia, Treilleux, Isabelle, Trotta, Jean-Rémi, Trümper, Lorenz HP, Tsao, Ming, Tsunoda, Tatsuhiko, Tucker, Olga, Turkington, Richard, Turner, Daniel J, Tutt, Andrew, Ueno, Masaki, Ueno, Naoto T, Umbricht, Christopher, Umer, Husen M, Underwood, Timothy J, Urban, Lara, Urushidate, Tomoko, Ushiku, Tetsuo, Uusküla-Reimand, Liis, Valencia, Alfonso, Van Den Berg, David J, Van Laere, Steven, Van Loo, Peter, Van Meir, Erwin G, Van den Eynden, Gert G, Van der Kwast, Theodorus, Vasudev, Naveen, Vazquez, Miguel, Vedururu, Ravikiran, Veluvolu, Umadevi, Vembu, Shankar, Verbeke, Lieven PC, Vermeulen, Peter, Verrill, Clare, Viari, Alain, Vicente, David, Vicentini, Caterina, VijayRaghavan, K, Viksna, Juris, Vilain, Ricardo E, Vincent-Salomon, Anne, Visakorpi, Tapio, Voet, Douglas, Vyas, Paresh, Vázquez-García, Ignacio, Waddell, Nick M, Wadelius, Claes, Wadi, Lina, Wagener, Rabea, Wang, Jian, Wang, Jiayin, Wang, Linghua, Wang, Qi, Wang, Wenyi, Wang, Yumeng, Wang, Zhining, Waring, Paul M, Warnatz, Hans-Jörg, Warrell, Jonathan, Warren, Anne Y, Waszak, Sebastian M, Wedge, David C, Weichenhan, Dieter, Weinberger, Paul, Weinstein, John N, Weisenberger, Daniel J, Welch, Ian, Wendl, Michael C, Werner, Johannes, Whalley, Justin P, Wheeler, David A, Whitaker, Hayley C, Wigle, Dennis, Wilkerson, Matthew D, Williams, Ashley, Wilmott, James S, Wilson, Gavin W, Wilson, Julie M, Wilson, Richard K, Winterhoff, Boris, Wintersinger, Jeffrey A, Wiznerowicz, Maciej, Wolf, Stephan, Wong, Bernice H, Wong, Tina, Wong, Winghing, Woo, Youngchoon, Wood, Scott, Wouters, Bradly G, Wright, Adam J, Wright, Derek W, Wright, Mark H, Wu, Chin-Lee, Wu, Dai-Ying, Wu, Guanming, Wu, Jianmin, Wu, Kui, Wu, Yang, Wu, Zhenggang, Xi, Liu, Xia, Tian, Xiang, Qian, Xiao, Xiao, Xing, Rui, Xiong, Heng, Xu, Qinying, Xu, Yanxun, Xue, Hong, Yachida, Shinichi, Yakneen, Sergei, Yamaguchi, Rui, Yamaguchi, Takafumi N, Yamamoto, Masakazu, Yamamoto, Shogo, Yamaue, Hiroki, Yang, Fan, Yang, Huanming, Yang, Jean Y, Yang, Liming, Yang, Shanlin, Yang, Tsun-Po, Yang, Yang, Yaspo, Marie-Laure, Yates, Lucy, Yau, Christina, Ye, Chen, Ye, Kai, Yellapantula, Venkata D, Yoon, Christopher J, Yousif, Fouad, Yu, Jun, Yu, Kaixian, Yu, Willie, Yu, Yingyan, Yuan, Ke, Yuan, Yuan, Yuen, Denis, Yung, Christina K, Zaikova, Olga, Zapatka, Marc, Zenklusen, Jean C, Zenz, Thorsten, Zeps, Nikolajs, Zhang, Fan, Zhang, Hailei, Zhang, Hongwei, Zhang, Hongxin, Zhang, Jiashan, Zhang, Jing, Zhang, Junjun, Zhang, Xiuqing, Zhang, Xuanping, Zhang, Yan, Zhang, Zemin, Zhao, Zhongming, Zheng, Liangtao, Zheng, Xiuqing, Zhou, Wanding, Zhou, Yong, Zhu, Bin, Zhu, Hongtu, Zhu, Jingchun, Zhu, Shida, Zou, Lihua, Zou, Xueqing, deFazio, Anna, van As, Nicholas, van Deurzen, Carolien HM, van de Vijver, Marc J, Veer, L van’t, and von Mering, Christian
- Subjects
Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
Cancers require telomere maintenance mechanisms for unlimited replicative potential. They achieve this through TERT activation or alternative telomere lengthening associated with ATRX or DAXX loss. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we dissect whole-genome sequencing data of over 2500 matched tumor-control samples from 36 different tumor types aggregated within the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium to characterize the genomic footprints of these mechanisms. While the telomere content of tumors with ATRX or DAXX mutations (ATRX/DAXXtrunc) is increased, tumors with TERT modifications show a moderate decrease of telomere content. One quarter of all tumor samples contain somatic integrations of telomeric sequences into non-telomeric DNA. This fraction is increased to 80% prevalence in ATRX/DAXXtrunc tumors, which carry an aberrant telomere variant repeat (TVR) distribution as another genomic marker. The latter feature includes enrichment or depletion of the previously undescribed singleton TVRs TTCGGG and TTTGGG, respectively. Our systematic analysis provides new insight into the recurrent genomic alterations associated with telomere maintenance mechanisms in cancer.
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- 2023
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28. The Oncogenic FOXL2 C134W Mutation Is a Key Driver of Granulosa Cell Tumors
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Llano, Elena, primary, Todeschini, Anne Laure, additional, Felipe-Medina, Natalia, additional, Corte-Torres, María D., additional, Condezo, Yazmine B., additional, Sanchez-Martin, Manuel, additional, López-Tamargo, Sara, additional, Astudillo, Aurora, additional, Puente, Xose S., additional, Pendas, Alberto M., additional, and Veitia, Reiner A., additional
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- 2022
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29. Molecular map of chronic lymphocytic leukemia and its impact on outcome
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Knisbacher, Binyamin A., Lin, Ziao, Hahn, Cynthia K., Nadeu, Ferran, Duran-Ferrer, Marti, Stevenson, Kristen E., Tausch, Eugen, Delgado, Julio, Barbera-Mourelle, Alex, Taylor-Weiner, Amaro, Bousquets-Munoz, Pablo, Diaz-Navarro, Ander, Dunford, Andrew, Anand, Shankara, Kretzmer, Helene, Gutierrez-Abril, Jesus, Lopez-Tamargo, Sara, Fernandes, Stacey M., Sun, Clare, Sivina, Mariela, Rassenti, Laura Z., Schneider, Christof, Li, Shuqiang, Parida, Laxmi, Meissner, Alexander, Aguet, Francois, Burger, Jan A., Wiestner, Adrian, Kipps, Thomas J., Brown, Jennifer R., Hallek, Michael, Stewart, Chip, Neuberg, Donna S., Martin-Subero, Jose, I, Puente, Xose S., Stilgenbauer, Stephan, Wu, Catherine J., Campo, Elias, Getz, Gad, Knisbacher, Binyamin A., Lin, Ziao, Hahn, Cynthia K., Nadeu, Ferran, Duran-Ferrer, Marti, Stevenson, Kristen E., Tausch, Eugen, Delgado, Julio, Barbera-Mourelle, Alex, Taylor-Weiner, Amaro, Bousquets-Munoz, Pablo, Diaz-Navarro, Ander, Dunford, Andrew, Anand, Shankara, Kretzmer, Helene, Gutierrez-Abril, Jesus, Lopez-Tamargo, Sara, Fernandes, Stacey M., Sun, Clare, Sivina, Mariela, Rassenti, Laura Z., Schneider, Christof, Li, Shuqiang, Parida, Laxmi, Meissner, Alexander, Aguet, Francois, Burger, Jan A., Wiestner, Adrian, Kipps, Thomas J., Brown, Jennifer R., Hallek, Michael, Stewart, Chip, Neuberg, Donna S., Martin-Subero, Jose, I, Puente, Xose S., Stilgenbauer, Stephan, Wu, Catherine J., Campo, Elias, and Getz, Gad
- Abstract
A genomic, transcriptomic and epigenomic analysis of chronic lymphocytic leukemia identifies genetic drivers and molecular subtypes associated with clinical outcomes. Recent advances in cancer characterization have consistently revealed marked heterogeneity, impeding the completion of integrated molecular and clinical maps for each malignancy. Here, we focus on chronic lymphocytic leukemia (CLL), a B cell neoplasm with variable natural history that is conventionally categorized into two subtypes distinguished by extent of somatic mutations in the heavy-chain variable region of immunoglobulin genes (IGHV). To build the 'CLL map,' we integrated genomic, transcriptomic and epigenomic data from 1,148 patients. We identified 202 candidate genetic drivers of CLL (109 new) and refined the characterization of IGHV subtypes, which revealed distinct genomic landscapes and leukemogenic trajectories. Discovery of new gene expression subtypes further subcategorized this neoplasm and proved to be independent prognostic factors. Clinical outcomes were associated with a combination of genetic, epigenetic and gene expression features, further advancing our prognostic paradigm. Overall, this work reveals fresh insights into CLL oncogenesis and prognostication.
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- 2022
30. Supplementary files of the article 'Detection of early seeding of Richter transformation in chronic lymphocytic leukemia' [Dataset]
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Nadeu, Ferran, Royo, Romina, Massoni-Badosa, Ramon, Playa-Albinyana, Heribert, Garcia-Torre, Beatriz, Duran-Ferrer, Martí, Dawson, Kevin J., Kulis, Marta, Diaz-Navarro, Ander, Villamor, Neus, Melero, Juan L., Chapaprieta, Vicente, Dueso-Barroso, Ana, Delgado, Julio, Moia, Riccardo, Ruiz-Gil, Sara, Marchese, Domenica, Giró, Ariadna, Verdaguer-Dot, Núria, Romo, Mónica, Clot, Guillem, Rozman, María, Frigola, Gerard, Rivas-Delgado, Alfredo, Baumann, Tycho, Alcoceba, Miguel, González, Marcos, Climent, Fina, Abrisqueta, Pau, Castellví, Josep, Bosch, Francesc, Aymerich, Marta, Enjuanes, Anna, Ruiz-Gaspà, Sílvia, López-Guillermo, Armando, Jares, Pedro, Beà, Silvia, Capella-Gutiérrez, Salvador, Gelpí, Josep Lluis, López-Bigas, Nuria, Torrents, David, Campbell, Peter J., Gut, Ivo, Rossi, Davide, Gaidano, Gianluca, Puente, Xose S., García-Roves, Pablo M., Colomer, Dolors, Heyn, Holger, Maura, Francesco, Martín-Subero, José Ignacio, Campo, Elías, Nadeu, Ferran, Royo, Romina, Massoni-Badosa, Ramon, Playa-Albinyana, Heribert, Garcia-Torre, Beatriz, Duran-Ferrer, Martí, Dawson, Kevin J., Kulis, Marta, Diaz-Navarro, Ander, Villamor, Neus, Melero, Juan L., Chapaprieta, Vicente, Dueso-Barroso, Ana, Delgado, Julio, Moia, Riccardo, Ruiz-Gil, Sara, Marchese, Domenica, Giró, Ariadna, Verdaguer-Dot, Núria, Romo, Mónica, Clot, Guillem, Rozman, María, Frigola, Gerard, Rivas-Delgado, Alfredo, Baumann, Tycho, Alcoceba, Miguel, González, Marcos, Climent, Fina, Abrisqueta, Pau, Castellví, Josep, Bosch, Francesc, Aymerich, Marta, Enjuanes, Anna, Ruiz-Gaspà, Sílvia, López-Guillermo, Armando, Jares, Pedro, Beà, Silvia, Capella-Gutiérrez, Salvador, Gelpí, Josep Lluis, López-Bigas, Nuria, Torrents, David, Campbell, Peter J., Gut, Ivo, Rossi, Davide, Gaidano, Gianluca, Puente, Xose S., García-Roves, Pablo M., Colomer, Dolors, Heyn, Holger, Maura, Francesco, Martín-Subero, José Ignacio, and Campo, Elías
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- 2022
31. Detection of early seeding of Richter transformation in chronic lymphocytic leukemia
- Author
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Fundación la Caixa, European Research Council, European Commission, Instituto de Salud Carlos III, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), American Association for Cancer Research, European Hematology Association, Lady Tata Memorial Trust, Generalitat de Catalunya, Asociación Española Contra el Cáncer, Fundació La Marató de TV3, Centro de Investigación Biomédica en Red Cáncer (España), Fundación Científica Asociación Española Contra el Cáncer, Associazione Italiana per la Ricerca sul Cancro, Eusko Jaurlaritza, Nadeu, Ferran, Royo, Romina, Massoni-Badosa, Ramon, Playa-Albinyana, Heribert, Garcia-Torre, Beatriz, Duran-Ferrer, Martí, Dawson, Kevin J., Kulis, Marta, Diaz-Navarro, Ander, Villamor, Neus, Melero, Juan L., Chapaprieta, Vicente, Dueso-Barroso, Ana, Delgado, Julio, Moia, Riccardo, Ruiz-Gil, Sara, Marchese, Domenica, Giró, Ariadna, Verdaguer-Dot, Núria, Romo, Mónica, Clot, Guillem, Rozman, María, Frigola, Gerard, Rivas-Delgado, Alfredo, Baumann, Tycho, Alcoceba, Miguel, González, Marcos, Climent, Fina, Abrisqueta, Pau, Castellví, Josep, Bosch, Francesc, Aymerich, Marta, Enjuanes, Anna, Ruiz-Gaspà, Sílvia, López-Guillermo, Armando, Jares, Pedro, Beà, Silvia, Capella-Gutiérrez, Salvador, Gelpí, Josep Lluis, López-Bigas, Nuria, Torrents, David, Campbell, Peter J., Gut, Ivo, Rossi, Davide, Gaidano, Gianluca, Puente, Xose S., García-Roves, Pablo M., Colomer, Dolors, Heyn, Holger, Maura, Francesco, Martín-Subero, José Ignacio, Campo, Elías, Fundación la Caixa, European Research Council, European Commission, Instituto de Salud Carlos III, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), American Association for Cancer Research, European Hematology Association, Lady Tata Memorial Trust, Generalitat de Catalunya, Asociación Española Contra el Cáncer, Fundació La Marató de TV3, Centro de Investigación Biomédica en Red Cáncer (España), Fundación Científica Asociación Española Contra el Cáncer, Associazione Italiana per la Ricerca sul Cancro, Eusko Jaurlaritza, Nadeu, Ferran, Royo, Romina, Massoni-Badosa, Ramon, Playa-Albinyana, Heribert, Garcia-Torre, Beatriz, Duran-Ferrer, Martí, Dawson, Kevin J., Kulis, Marta, Diaz-Navarro, Ander, Villamor, Neus, Melero, Juan L., Chapaprieta, Vicente, Dueso-Barroso, Ana, Delgado, Julio, Moia, Riccardo, Ruiz-Gil, Sara, Marchese, Domenica, Giró, Ariadna, Verdaguer-Dot, Núria, Romo, Mónica, Clot, Guillem, Rozman, María, Frigola, Gerard, Rivas-Delgado, Alfredo, Baumann, Tycho, Alcoceba, Miguel, González, Marcos, Climent, Fina, Abrisqueta, Pau, Castellví, Josep, Bosch, Francesc, Aymerich, Marta, Enjuanes, Anna, Ruiz-Gaspà, Sílvia, López-Guillermo, Armando, Jares, Pedro, Beà, Silvia, Capella-Gutiérrez, Salvador, Gelpí, Josep Lluis, López-Bigas, Nuria, Torrents, David, Campbell, Peter J., Gut, Ivo, Rossi, Davide, Gaidano, Gianluca, Puente, Xose S., García-Roves, Pablo M., Colomer, Dolors, Heyn, Holger, Maura, Francesco, Martín-Subero, José Ignacio, and Campo, Elías
- Abstract
Richter transformation (RT) is a paradigmatic evolution of chronic lymphocytic leukemia (CLL) into a very aggressive large B cell lymphoma conferring a dismal prognosis. The mechanisms driving RT remain largely unknown. We characterized the whole genome, epigenome and transcriptome, combined with single-cell DNA/RNA-sequencing analyses and functional experiments, of 19 cases of CLL developing RT. Studying 54 longitudinal samples covering up to 19 years of disease course, we uncovered minute subclones carrying genomic, immunogenetic and transcriptomic features of RT cells already at CLL diagnosis, which were dormant for up to 19 years before transformation. We also identified new driver alterations, discovered a new mutational signature (SBS-RT), recognized an oxidative phosphorylation (OXPHOS)high–B cell receptor (BCR)low-signaling transcriptional axis in RT and showed that OXPHOS inhibition reduces the proliferation of RT cells. These findings demonstrate the early seeding of subclones driving advanced stages of cancer evolution and uncover potential therapeutic targets for RT.
- Published
- 2022
32. Abstract 3795: Early seeding of Richter transformation in chronic lymphocytic leukemia
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Nadeu, Ferran, primary, Royo, Romina, additional, Massoni-Badosa, Ramon, additional, Garcia-Torre, Beatriz, additional, Duran-Ferrer, Martí, additional, Dawson, Kevin J., additional, Kulis, Marta, additional, Diaz-Navarro, Ander, additional, Villamor, Neus, additional, Melero, Juan L., additional, Chapaprieta, Vicente, additional, Dueso-Barroso, Ana, additional, Delgado, Julio, additional, Moia, Riccardo, additional, Ruiz-Gil, Sara, additional, Marchese, Domenica, additional, Verdaguer-Dot, Núria, additional, Romo, Mónica, additional, Rozman, Maria, additional, Frigola, Gerard, additional, Rivas-Delgado, Alfredo, additional, Baumann, Tycho, additional, Alcoceba, Miguel, additional, González, Marcos, additional, Climent, Fina, additional, Abrisqueta, Pau, additional, Castellví, Josep, additional, Bosch, Francesc, additional, Aymerich, Marta, additional, Enjuanes, Anna, additional, Ruiz-Gaspà, Sílvia, additional, López-Guillermo, Armando, additional, Jares, Pedro, additional, Beà, Sílvia, additional, Colomer, Dolors, additional, López-Bigas, Núria, additional, LlGelpí, Josep, additional, Torrents, David, additional, Campbell, Peter J., additional, Gut, Ivo, additional, Garcia-Roves, Pablo M., additional, Rossi, Davide, additional, Gaidano, Gianluca, additional, Puente, Xose S., additional, Heyn, Holger, additional, Maura, Francesco, additional, Martín-Subero, José I., additional, and Campo, Elías, additional
- Published
- 2022
- Full Text
- View/download PDF
33. RFcaller: a machine learning approach combined with read-level features to detect somatic mutations
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Díaz-Navarro, Ander, primary, Bousquets-Muñoz, Pablo, additional, Nadeu, Ferran, additional, López-Tamargo, Sara, additional, Beà, Silvia, additional, Campo, Elias, additional, and Puente, Xose S., additional
- Published
- 2022
- Full Text
- View/download PDF
34. Large B-cell lymphomas with CCND1 rearrangement have different immunoglobulin gene breakpoints and genomic profile than mantle cell lymphoma.
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Özoğul E, Montaner A, Pol M, Frigola G, Balagué O, Syrykh C, Bousquets-Muñoz P, Royo R, Fontaine J, Traverse-Glehen A, Bühler MM, Giudici L, Roncador M, Zenz T, Carras S, Valmary-Degano S, de Leval L, Bosch-Schips J, Climent F, Salmeron-Villalobos J, Bashiri M, Ruiz-Gaspà S, Costa D, Beà S, Salaverria I, Giné E, Quintanilla-Martinez L, Brousset P, Raffeld M, Jaffe ES, Puente XS, López C, Nadeu F, and Campo E
- Subjects
- Humans, Male, Female, Translocation, Genetic, Middle Aged, Aged, Chromosome Breakpoints, Genes, Immunoglobulin, Gene Rearrangement, V(D)J Recombination genetics, Lymphoma, Mantle-Cell genetics, Lymphoma, Mantle-Cell pathology, Cyclin D1 genetics, Lymphoma, Large B-Cell, Diffuse genetics
- Abstract
Mantle cell lymphoma (MCL) is genetically characterized by the IG::CCND1 translocation mediated by an aberrant V(D)J rearrangement. CCND1 translocations and overexpression have been identified in occasional aggressive B-cell lymphomas with unusual features for MCL. The mechanism generating CCND1 rearrangements in these tumors and their genomic profile are not known. We have reconstructed the IG::CCND1 translocations and the genomic profile of 13 SOX11-negative aggressive B-cell lymphomas using whole genome/exome and target sequencing. The mechanism behind the translocation was an aberrant V(D)J rearrangement in three tumors and by an anomalous IGH class-switch recombination (CSR) or somatic hypermutation (SHM) mechanism in ten. The tumors with a V(D)J-mediated translocation were two blastoid MCL and one high-grade B-cell lymphoma. None of them had a mutational profile suggestive of DLBCL. The ten tumors with CSR/SHM-mediated IGH::CCND1 were mainly large B-cell lymphomas, with mutated genes commonly seen in DLBCL and BCL6 rearrangements in 6. Two cases, which transformed from marginal zone lymphomas, carried mutations in KLF2, TNFAIP3 and KMT2D. These findings expand the spectrum of tumors carrying CCND1 rearrangement that may occur as a secondary event in DLBCL mediated by aberrant CSR/SHM and associated with a mutational profile different from that of MCL., (© 2024. The Author(s).)
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- 2024
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35. RFcaller: a machine learning approach combined with read-level features to detect somatic mutations.
- Author
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Díaz-Navarro A, Bousquets-Muñoz P, Nadeu F, López-Tamargo S, Beà S, Campo E, and Puente XS
- Abstract
The cost reduction in sequencing and the extensive genomic characterization of a wide variety of cancers are expanding tumor sequencing to a wide number of research groups and the clinical practice. Although specific pipelines have been generated for the identification of somatic mutations, their results usually differ considerably, and a common approach is to use several callers to achieve a more reliable set of mutations. This procedure is computationally expensive and time-consuming, and it suffers from the same limitations in sensitivity and specificity as other approaches. Expert revision of mutant calls is therefore required to verify calls that might be used for clinical diagnosis. This step could take advantage of machine learning techniques, as they provide a useful approach to incorporate expert-reviewed information for the identification of somatic mutations. Here we present RFcaller, a pipeline based on machine learning algorithms, for the detection of somatic mutations in tumor-normal paired samples that does not require large computing resources. RFcaller shows high accuracy for the detection of substitutions and insertions/deletions from whole genome or exome data. It allows the detection of mutations in driver genes missed by other approaches, and has been validated by comparison to deep and Sanger sequencing., (© The Author(s) 2023. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.)
- Published
- 2023
- Full Text
- View/download PDF
36. The Oncogenic FOXL2 C134W Mutation Is a Key Driver of Granulosa Cell Tumors.
- Author
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Llano E, Todeschini AL, Felipe-Medina N, Corte-Torres MD, Condezo YB, Sanchez-Martin M, López-Tamargo S, Astudillo A, Puente XS, Pendas AM, and Veitia RA
- Subjects
- Adult, Female, Humans, Animals, Mice, Forkhead Transcription Factors genetics, Forkhead Transcription Factors metabolism, Mutation, Forkhead Box Protein L2 genetics, Granulosa Cell Tumor genetics, Granulosa Cell Tumor metabolism, Skin Abnormalities, Ovarian Neoplasms genetics
- Abstract
Adult-type granulosa cell tumors (AGCT) are the most common type of malignant ovarian sex cord-stromal tumors. Most AGCTs carry the somatic variant c.402C>G (p.C134W) affecting the transcription factor FOXL2. Germline dominant variants in FOXL2 are responsible for blepharophimosis syndrome, which is characterized by underdevelopment of the eyelid. In this work, we generated a mouse model harboring the C134W variant of FOXL2 to evaluate in vivo the poorly understood oncogenic role of FOXL2. The mutation was dominant regarding eyelid hypoplasia, reminiscent of blepharophimosis syndrome. Interestingly, Foxl2+/C134W female mice had reduced fertility and developed AGCTs through a progression from abnormal ovaries with aberrant granulosa cells to ovaries with stromal hyperplasia and atypia and on to tumors in adut mice. The genes dysregulated in mouse AGCTs exhibited the hallmarks of cancer and were consistent with a gain-of-function of the mutated allele affecting TGFβ signaling. A comparison of these data with previous results on human AGCTs indicated similar deregulated pathways. Finally, a mutational analysis of mouse AGCT transcriptomic data suggested the absence of additional driver mutations apart from FOXL2-C134W. These results provide a clear in vivo example in which a single mutational hit triggers tumor development associated with profound transcriptomic alterations., Significance: A newly generated mouse model carrying a FOXL2 mutation characteristic of adult-type granulosa cell tumors shows that FOXL2 C134W shifts the transcriptome towards a signature of granulosa cell cancer and drives tumorigenesis., (©2022 American Association for Cancer Research.)
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- 2023
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37. Altered regulation of BRCA1 exon 11 splicing is associated with breast cancer risk in carriers of BRCA1 pathogenic variants.
- Author
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Ruiz de Garibay G, Fernandez-Garcia I, Mazoyer S, Leme de Calais F, Ameri P, Vijayakumar S, Martinez-Ruiz H, Damiola F, Barjhoux L, Thomassen M, Andersen LVB, Herranz C, Mateo F, Palomero L, Espín R, Gómez A, García N, Jimenez D, Bonifaci N, Extremera AI, Castaño J, Raya A, Eyras E, Puente XS, Brunet J, Lázaro C, Radice P, Barnes DR, Antoniou AC, Spurdle AB, de la Hoya M, Baralle D, Barcellos-Hoff MH, and Pujana MA
- Subjects
- Female, Humans, Introns, Breast Neoplasms genetics, Exons, Genes, BRCA1, Genetic Carrier Screening, Genetic Predisposition to Disease, RNA Splicing
- Abstract
Germline pathogenic variants in BRCA1 confer a high risk of developing breast and ovarian cancer. The BRCA1 exon 11 (formally exon 10) is one of the largest exons and codes for the nuclear localization signals of the corresponding gene product. This exon can be partially or entirely skipped during pre-mRNA splicing, leading to three major in-frame isoforms that are detectable in most cell types and tissue, and in normal and cancer settings. However, it is unclear whether the splicing imbalance of this exon is associated with cancer risk. Here we identify a common genetic variant in intron 10, rs5820483 (NC_000017.11:g.43095106_43095108dup), which is associated with exon 11 isoform expression and alternative splicing, and with the risk of breast cancer, but not ovarian cancer, in BRCA1 pathogenic variant carriers. The identification of this genetic effect was confirmed by analogous observations in mouse cells and tissue in which a loxP sequence was inserted in the syntenic intronic region. The prediction that the rs5820483 minor allele variant would create a binding site for the splicing silencer hnRNP A1 was confirmed by pull-down assays. Our data suggest that perturbation of BRCA1 exon 11 splicing modifies the breast cancer risk conferred by pathogenic variants of this gene., (© 2021 Wiley Periodicals LLC.)
- Published
- 2021
- Full Text
- View/download PDF
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