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329 results on '"Ciccarelli, Francesca D."'

3. A constitutive interferon-high immunophenotype defines response to immunotherapy in colorectal cancer

Author

Acha-Sagredo, Amelia, Andrei, Pietro, Clayton, Kalum, Taggart, Emma, Antoniotti, Carlotta, Woodman, Chloé A., Afrache, Hassnae, Fourny, Constance, Armero, Maria, Moinudeen, Hafsa Kaja, Green, Mary, Bhardwaj, Nisha, Mikolajczak, Anna, Rodriguez-Lopez, Maria, Crawford, Marg, Connick, Emma, Lim, Steven, Hobson, Philip, Linares, Josep, Ignatova, Ekaterina, Pelka, Diana, Smyth, Elizabeth C., Diamantis, Nikolaos, Sosnowska, Dominika, Carullo, Martina, Ciraci, Paolo, Bergamo, Francesca, Intini, Rossana, Nye, Emma, Barral, Patricia, Mishto, Michele, Arnold, James N., Lonardi, Sara, Cremolini, Chiara, Fontana, Elisa, Rodriguez-Justo, Manuel, and Ciccarelli, Francesca D.

Published
2025
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4. Multi-Omic Analysis of Esophageal Adenocarcinoma Uncovers Candidate Therapeutic Targets and Cancer-Selective Posttranscriptional Regulation

Author

Fitzgerald, Rebecca C., Edwards, Paul A.W., Grehan, Nicola, Nutzinger, Barbara, Loreno, Christine, Redmond, Aisling M., Abbas, Sujath, Freeman, Adam, Smyth, Elizabeth C., O'Donovan, Maria, Miremadi, Ahmad, Malhotra, Shalini, Tripathi, Monika, Cheah, Calvin, Coles, Hannah, Millington, Curtis, Devonshire, Ginny, Eldridge, Matthew, Secrier, Maria, Jammula, Sriganesh, Davies, Jim, Crichton, Charles, Carroll, Nick, Hardwick, Richard H., Safranek, Peter, Hindmarsh, Andrew, Sujendran, Vijayendran, Hayes, Stephen J., Ang, Yeng, Sharrocks, Andrew, Preston, Shaun R., Bagwan, Izhar, Save, Vicki, Skipworth, Richard J.E., Hupp, Ted R., O'Neill, J Robert, Tucker, Olga, Beggs, Andrew, Taniere, Philippe, Puig, Sonia, Contino, Gianmarco, Underwood, Timothy J., Walker, Robert C., Grace, Ben L., Lagergren, Jesper, Gossage, James, Davies, Andrew, Chang, Fuju, Mahadeva, Ula, Goh, Vicky, Ciccarelli, Francesca D., Sanders, Grant, Berrisford, Richard, Chan, David, Cheong, Ed, Kumar, Bhaskar, Sreedharan, L., Parsons, Simon L., Soomro, Irshad, Kaye, Philip, Saunders, John, Lovat, Laurence, Haidry, Rehan, Scott, Michael, Sothi, Sharmila, Lishman, Suzy, Hanna, George B., Peters, Christopher J., Moorthy, Krishna, Grabowska, Anna, Turkington, Richard, McManus, Damian, Coleman, Helen, Petty, Russell D., Bartlet, Freddie, O'Neill, J. Robert, Yébenes Mayordomo, Marcos, Mitulović, Goran, Al Shboul, Sofian, Bedran, Georges, Faktor, Jakub, Hernychova, Lenka, Uhrik, Lukas, Gómez-Herranz, Maria, Kocikowski, Mikołaj, Vojtěšek, Bořivoj, Arends, Mark J., Hupp, Ted, and Alfaro, Javier Antonio

Published
2024
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6. Molecular Biology and Evolution of Cancer: From Discovery to Action.

Author

Somarelli, Jason A, Gardner, Heather, Cannataro, Vincent L, Gunady, Ella F, Boddy, Amy M, Johnson, Norman A, Fisk, Jeffrey Nicholas, Gaffney, Stephen G, Chuang, Jeffrey H, Li, Sheng, Ciccarelli, Francesca D, Panchenko, Anna R, Megquier, Kate, Kumar, Sudhir, Dornburg, Alex, DeGregori, James, and Townsend, Jeffrey P

Subjects
cancer, comparative oncology, fitness landscapes, genomics, metastasis, tumor phylogenetics, Evolutionary Biology, Biochemistry and Cell Biology, Genetics
Abstract

Cancer progression is an evolutionary process. During this process, evolving cancer cell populations encounter restrictive ecological niches within the body, such as the primary tumor, circulatory system, and diverse metastatic sites. Efforts to prevent or delay cancer evolution-and progression-require a deep understanding of the underlying molecular evolutionary processes. Herein we discuss a suite of concepts and tools from evolutionary and ecological theory that can inform cancer biology in new and meaningful ways. We also highlight current challenges to applying these concepts, and propose ways in which incorporating these concepts could identify new therapeutic modes and vulnerabilities in cancer.

Published
2020

10. Immunogenomics of Colorectal Cancer Response to Checkpoint Blockade: Analysis of the KEYNOTE 177 Trial and Validation Cohorts

Author

Bortolomeazzi, Michele, Keddar, Mohamed Reda, Montorsi, Lucia, Acha-Sagredo, Amelia, Benedetti, Lorena, Temelkovski, Damjan, Choi, Subin, Petrov, Nedyalko, Todd, Katrina, Wai, Patty, Kohl, Johannes, Denner, Tamara, Nye, Emma, Goldstone, Robert, Ward, Sophia, Wilson, Gareth A., Al Bakir, Maise, Swanton, Charles, John, Susan, Miles, James, Larijani, Banafshe, Kunene, Victoria, Fontana, Elisa, Arkenau, Hendrik-Tobias, Parker, Peter J., Rodriguez-Justo, Manuel, Shiu, Kai-Keen, Spencer, Jo, and Ciccarelli, Francesca D.

Published
2021
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12. Identification of Subtypes of Barrett’s Esophagus and Esophageal Adenocarcinoma Based on DNA Methylation Profiles and Integration of Transcriptome and Genome Data

Author

Fitzgerald, Rebecca C., Noorani, Ayesha, Edwards, Paul A.W., Grehan, Nicola, Nutzinger, Barbara, Hughes, Caitriona, Fidziukiewicz, Elwira, Bornschein, Jan, MacRae, Shona, Crawte, Jason, Northrop, Alex, Contino, Gianmarco, Li, Xiaodun, de la Rue, Rachel, O’Donovan, Maria, Miremadi, Ahmad, Malhotra, Shalini, Tripathi, Monika, Tavaré, Simon, Lynch, Andy G., Eldridge, Matthew, Secrier, Maria, Bower, Lawrence, Devonshire, Ginny, Perner, Juliane, Jammula, Sriganesh, Davies, Jim, Crichton, Charles, Carroll, Nick, Safranek, Peter, Hindmarsh, Andrew, Sujendran, Vijayendran, Hayes, Stephen J., Ang, Yeng, Preston, Shaun R., Oakes, Sarah, Bagwan, Izhar, Save, Vicki, Skipworth, Richard J.E., Hupp, Ted R., O’Neill, J. Robert, Tucker, Olga, Beggs, Andrew, Taniere, Philippe, Puig, Sonia, Underwood, Timothy J., Noble, Fergus, Owsley, Jack, Barr, Hugh, Shepherd, Neil, Old, Oliver, Lagergren, Jesper, Gossage, James, Davies, Andrew, Chang, Fuju, Zylstra, Janine, Mahadeva, Ula, Goh, Vicky, Ciccarelli, Francesca D., Sanders, Grant, Berrisford, Richard, Harden, Catherine, Lewis, Mike, Cheong, Ed, Kumar, Bhaskar, Parsons, Simon L., Soomro, Irshad, Kaye, Philip, Saunders, John, Lovat, Laurence, Haidry, Rehan, Igali, Laszlo, Scott, Michael, Sothi, Sharmila, Suortamo, Sari, Lishman, Suzy, Hanna, George B., Moorthy, Krishna, Peters, Christopher J., Grabowska, Anna, Turkington, Richard, Jammula, SriGanesh, Katz-Summercorn, Annalise C., Linossi, Constanza, Smyth, Elizabeth, Killcoyne, Sarah, Biasci, Daniele, Subash, Vinod V., Abbas, Sujath, Blasko, Adrienn, Grantham, Amber, Wronowski, Filip, and Eldridge, Matthew D.

Published
2020
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15. Identification of Prognostic Phenotypes of Esophageal Adenocarcinoma in 2 Independent Cohorts

Author

Noorani, Ayesha, Edwards, Paul A.W., Grehan, Nicola, Nutzinger, Barbara, Hughes, Caitriona, Fidziukiewicz, Elwira, Bornschein, Jan, MacRae, Shona, Crawte, Jason, Contino, Gianmarco, Li, Xiaodun, Rue, Rachel de la, O’Donovan, Maria, Miremad, Ahmad, Malhotra, Shalini, Tripathi, Monika, Tavaré, Simon, Lynch, Andy G., Eldridge, Matthew, Secrier, Maria, Bower, Lawrence, Devonshire, Ginny, Perner, Juliane, Jammula, Sriganesh, Davies, Jim, Crichton, Charles, Carroll, Nick, Safranek, Peter, Hindmarsh, Andrew, Sujendran, Vijayendran, Hayes, Stephen J., Ang, Yeng, Preston, Shaun R., Oakes, Sarah, Bagwan, Izhar, Save, Vicki, Skipworth, Richard J.E., Hupp, Ted R., O’Neill, J. Robert, Tucker, Olga, Beggs, Andrew, Taniere, Philippe, Puig, Sonia, Underwood, Timothy J., Noble, Fergus, Owsley, Jack, Barr, Hugh, Shepherd, Neil, Old, Oliver, Lagergren, Jesper, Gossage, James, Davies, Andrew, Chang, Fuju, Zylstra, Janine, Mahadeva, Ula, Goh, Vicky, Ciccarelli, Francesca D., Sanders, Grant, Berrisford, Richard, Harden, Catherine, Bunting, David, Lewis, Mike, Cheong, Ed, Kumar, Bhaskar, Parsons, Simon L., Soomro, Irshad, Kaye, Philip, Saunders, John, Lovat, Laurence, Haidry, Rehan, Eneh, Victor, Igali, Laszlo, Scott, Michael, Sothi, Sharmila, Suortamo, Sari, Lishman, Suzy, Hanna, George B., Peters, Christopher J., Grabowska, Anna, Turkington, Richard, Sawas, Tarek, Killcoyne, Sarah, Iyer, Prasad G., Wang, Kenneth K., Smyrk, Thomas C., Kisiel, John B., Qin, Yi, Ahlquist, David A., Rustgi, Anil K., Costa, Rui J., Gerstung, Moritz, Fitzgerald, Rebecca C., and Katzka, David A.

Published
2018
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16. NCG 4.0: the network of cancer genes in the era of massive mutational screenings of cancer genomes

Author

An, Omer, Pendino, Vera, D’Antonio, Matteo, Ratti, Emanuele, Gentilini, Marco, and Ciccarelli, Francesca D

Subjects
Cancer, Biotechnology, Genetics, Databases, Genetic, Gene Expression Profiling, Gene Expression Regulation, Neoplastic, Gene Regulatory Networks, Genetic Association Studies, Genome, Human, Humans, Internet, MicroRNAs, Mutation, Neoplasms, Search Engine, Software, Data Format, Library and Information Studies
Abstract

NCG 4.0 is the latest update of the Network of Cancer Genes, a web-based repository of systems-level properties of cancer genes. In its current version, the database collects information on 537 known (i.e. experimentally supported) and 1463 candidate (i.e. inferred using statistical methods) cancer genes. Candidate cancer genes derive from the manual revision of 67 original publications describing the mutational screening of 3460 human exomes and genomes in 23 different cancer types. For all 2000 cancer genes, duplicability, evolutionary origin, expression, functional annotation, interaction network with other human proteins and with microRNAs are reported. In addition to providing a substantial update of cancer-related information, NCG 4.0 also introduces two new features. The first is the annotation of possible false-positive cancer drivers, defined as candidate cancer genes inferred from large-scale screenings whose association with cancer is likely to be spurious. The second is the description of the systems-level properties of 64 human microRNAs that are causally involved in cancer progression (oncomiRs). Owing to the manual revision of all information, NCG 4.0 constitutes a complete and reliable resource on human coding and non-coding genes whose deregulation drives cancer onset and/or progression. NCG 4.0 can also be downloaded as a free application for Android smart phones. Database URL: http://bio.ieo.eu/ncg/.

Published
2014

19. Unanticipated interacting features of human gut-associated lymphoid tissues link microbiota, intestinal immunity and autoimmunity

Author

Montorsi, Lucia, primary, Pitcher, Michael J, additional, Zhao, Yuan, additional, Demonti, Alicia, additional, Tull, Thomas J, additional, Dionisi, Chiara, additional, Dhami, Pawan, additional, Ellis, Richard J, additional, Bishop, Cynthia, additional, Sanderson, Jeremy, additional, Jain, Sahil, additional, D'Cruz, David, additional, Gibbons, Deena, additional, Winkler, Thomas H, additional, Bemark, Mats, additional, Ciccarelli, Francesca D, additional, and Spencer, Jo, additional

Published
2023
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23. Patient-specific cancer genes contribute to recurrently perturbed pathways and establish therapeutic vulnerabilities in esophageal adenocarcinoma

Author

Mourikis, Thanos P., Benedetti, Lorena, Foxall, Elizabeth, Temelkovski, Damjan, Nulsen, Joel, Perner, Juliane, Cereda, Matteo, Lagergren, Jesper, Howell, Michael, Yau, Christopher, Fitzgerald, Rebecca C., Scaffidi, Paola, The Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium, and Ciccarelli, Francesca D.

Published
2019
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25. Mechanistic insights into the interactions between cancer drivers and the tumour immune microenvironment

Author

Misetic, Hrvoje, Keddar, Mohamed Reda, Jeannon, Jean-Pierre, and Ciccarelli, Francesca D

Subjects
Genome Integrity & Repair, Gene Expression, Genetics & Genomics, Computational & Systems Biology
Abstract

BACKGROUND: The crosstalk between cancer and the tumour immune microenvironment (TIME) has attracted significant interest in the latest years because of its impact on cancer evolution and response to treatment. Despite this, cancer-specific tumour-TIME interactions and their mechanistic insights are still poorly understood. METHODS: Here, we compute the significant interactions occurring between cancer-specific genetic drivers and five anti- and pro-tumour TIME features in 32 cancer types using Lasso regularised ordinal regression. Focusing on head and neck squamous cancer (HNSC), we rebuild the functional networks linking specific TIME driver alterations to the TIME state they associate with. RESULTS: The 477 TIME drivers that we identify are multifunctional genes whose alterations are selected early in cancer evolution and recur across and within cancer types. Tumour suppressors and oncogenes have an opposite effect on the TIME and the overall anti-tumour TIME driver burden is predictive of response to immunotherapy. TIME driver alterations predict the immune profiles of HNSC molecular subtypes, and perturbations in keratinization, apoptosis and interferon signalling underpin specific driver-TIME interactions. CONCLUSIONS: Overall, our study delivers a comprehensive resource of TIME drivers, gives mechanistic insights into their immune-regulatory role, and provides an additional framework for patient prioritisation to immunotherapy. The full list of TIME drivers and associated properties are available at http://www.network-cancer-genes.org .

Published
2023
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28. Immunogenomics of Colorectal Cancer Response to Checkpoint Blockade: Analysis of the KEYNOTE 177 Trial and Validation Cohorts

Author

Cancer Research UK, Medical Research Council (UK), Wellcome Trust, Guy's & St Thomas' Foundation, European Commission, Kings College London, Ciccarelli, Francesca D. [0000-0002-9325-0900], Bortolomeazzi, Michele, Keddar, Mohamed Reda, Montorsi, Lucía, Acha-Sagredo, Amelia, Benedetti, Lorena, Temelkovski, Damjan, Choi, Subin, Petrov, Nedyalko, Todd, Katrina, Wai, Patty, Kohl, Johannes, Denner, Tamara, Nye, Emma, Goldstone, Robert, Ward, Sophia, Wilson, Gareth A., Al Bakir, Maise, Swanton, Charles, John, Susan, Miles, James, Larijani, Banafshé, Kunene, Victoria, Fontana, Elisa, Arkenau, Hendrik-Tobias, Parker, Peter J., Rodríguez-Justo, Manuel, Shiu, Kai-Keen, Spencer, Jo, Ciccarelli, Francesca D., Cancer Research UK, Medical Research Council (UK), Wellcome Trust, Guy's & St Thomas' Foundation, European Commission, Kings College London, Ciccarelli, Francesca D. [0000-0002-9325-0900], Bortolomeazzi, Michele, Keddar, Mohamed Reda, Montorsi, Lucía, Acha-Sagredo, Amelia, Benedetti, Lorena, Temelkovski, Damjan, Choi, Subin, Petrov, Nedyalko, Todd, Katrina, Wai, Patty, Kohl, Johannes, Denner, Tamara, Nye, Emma, Goldstone, Robert, Ward, Sophia, Wilson, Gareth A., Al Bakir, Maise, Swanton, Charles, John, Susan, Miles, James, Larijani, Banafshé, Kunene, Victoria, Fontana, Elisa, Arkenau, Hendrik-Tobias, Parker, Peter J., Rodríguez-Justo, Manuel, Shiu, Kai-Keen, Spencer, Jo, and Ciccarelli, Francesca D.

Abstract

Colorectal cancer (CRC) shows variable response to immune checkpoint blockade, which can only partially be explained by high tumor mutational burden (TMB). We conducted an integrated study of the cancer tissue and associated tumor microenvironment (TME) from patients treated with pembrolizumab (KEYNOTE 177 clinical trial) or nivolumab to dissect the cellular and molecular determinants of response to anti- programmed cell death 1 (PD1) immunotherapy.

Published
2021

29. Endogenous Retrotransposition Activates Oncogenic Pathways in Hepatocellular Carcinoma

Author

Shukla, Ruchi, Upton, Kyle R., Muñoz-Lopez, Martin, Gerhardt, Daniel J., Fisher, Malcolm E., Nguyen, Thu, Brennan, Paul M., Baillie, J. Kenneth, Collino, Agnese, Ghisletti, Serena, Sinha, Shruti, Iannelli, Fabio, Radaelli, Enrico, Dos Santos, Alexandre, Rapoud, Delphine, Guettier, Catherine, Samuel, Didier, Natoli, Gioacchino, Carninci, Piero, Ciccarelli, Francesca D., Garcia-Perez, Jose Luis, Faivre, Jamila, and Faulkner, Geoffrey J.

Published
2013
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30. Computational pan-genomics: status, promises and challenges

Author

Marschall, Tobias, Marz, Manja, Abeel, Thomas, Dijkstra, Louis, Dutilh, Bas E, Ghaffaari, Ali, Kersey, Paul, Kloosterman, Wigard P, Mäkinen, Veli, Novak, Adam M, Paten, Benedict, Porubsky, David, Rivals, Eric, Alkan, Can, Baaijens, Jasmijn A, De Bakker, Paul I W, Boeva, Valentina, Bonnal, Raoul J P, Chiaromonte, Francesca, Chikhi, Rayan, Ciccarelli, Francesca D, Cijvat, Robin, Datema, Erwin, Van Duijn, Cornelia M, Eichler, Evan E, Ernst, Corinna, Eskin, Eleazar, Garrison, Erik, El-Kebir, Mohammed, Klau, Gunnar W, Korbel, Jan O, Lameijer, Eric-Wubbo, Langmead, Benjamin, Martin, Marcel, Medvedev, Paul, Mu, John C, Neerincx, Pieter, Ouwens, Klaasjan, Peterlongo, Pierre, Pisanti, Nadia, Rahmann, Sven, Raphael, Ben, Reinert, Knut, de Ridder, Dick, de Ridder, Jeroen, Schlesner, Matthias, Schulz-Trieglaff, Ole, Sanders, Ashley D, Sheikhizadeh, Siavash, Shneider, Carl, Smit, Sandra, Valenzuela, Daniel, Wang, Jiayin, Wessels, Lodewyk, Zhang, Ying, Guryev, Victor, Vandin, Fabio, Ye, Kai, and Schönhuth, Alexander

Published
2018
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32. Additional file 2 of Comparative assessment of genes driving cancer and somatic evolution in non-cancer tissues: an update of the Network of Cancer Genes (NCG) resource

Author

Dressler, Lisa, Bortolomeazzi, Michele, Keddar, Mohamed Reda, Misetic, Hrvoje, Sartini, Giulia, Acha-Sagredo, Amelia, Montorsi, Lucia, Wijewardhane, Neshika, Repana, Dimitra, Nulsen, Joel, Goldman, Jacki, Pollitt, Marc, Davis, Patrick, Strange, Amy, Ambrose, Karen, and Ciccarelli, Francesca D.

Abstract

Additional file 2: Figure S1. Literature search, review and annotation workflow; Figure S2. Correlation between numbers of donors and cancer drivers in individual organ systems; Figure S3. Patterns of driver damaging alterations in TCGA samples.

Published
2022
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33. Additional file 10 of Comparative assessment of genes driving cancer and somatic evolution in non-cancer tissues: an update of the Network of Cancer Genes (NCG) resource

Author

Dressler, Lisa, Bortolomeazzi, Michele, Keddar, Mohamed Reda, Misetic, Hrvoje, Sartini, Giulia, Acha-Sagredo, Amelia, Montorsi, Lucia, Wijewardhane, Neshika, Repana, Dimitra, Nulsen, Joel, Goldman, Jacki, Pollitt, Marc, Davis, Patrick, Strange, Amy, Ambrose, Karen, and Ciccarelli, Francesca D.

Abstract

Additional file 10. Review history.

Published
2022
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34. Exome sequencing of hepatocellular carcinoma in lemurs identifies potential cancer drivers: A pilot study

Author

Gunady, Ella F, Ware, Kathryn E, Plumlee, Sarah Hoskinson, Devos, Nicolas, Corcoran, David, Prinz, Joseph, Misetic, Hrvoje, Ciccarelli, Francesca D, Harrison, Tara M, Thorne, Jeffrey L, Schopler, Robert, Everitt, Jeffrey I, Eward, William C, and Somarelli, Jason A

Subjects
Genome Integrity & Repair, Gene Expression, Genetics & Genomics, Computational & Systems Biology
Abstract

Background and objectives: Hepatocellular carcinoma occurs frequently in prosimians, but the cause of these liver cancers in this group is unknown. Characterizing the genetic changes associated with hepatocellular carcinoma in prosimians may point to possible causes, treatments and methods of prevention, aiding conservation efforts that are particularly crucial to the survival of endangered lemurs. Although genomic studies of cancer in non-human primates have been hampered by a lack of tools, recent studies have demonstrated the efficacy of using human exome capture reagents across primates. Methodology: In this proof-of-principle study, we applied human exome capture reagents to tumor-normal pairs from five lemurs with hepatocellular carcinoma to characterize the mutational landscape of this disease in lemurs. Results: Several genes implicated in human hepatocellular carcinoma, including ARID1A, TP53 and CTNNB1, were mutated in multiple lemurs, and analysis of cancer driver genes mutated in these samples identified enrichment of genes involved with TP53 degradation and regulation. In addition to these similarities with human hepatocellular carcinoma, we also noted unique features, including six genes that contain mutations in all five lemurs. Interestingly, these genes are infrequently mutated in human hepatocellular carcinoma, suggesting potential differences in the etiology and/or progression of this cancer in lemurs and humans. Conclusions and implications: Collectively, this pilot study suggests that human exome capture reagents are a promising tool for genomic studies of cancer in lemurs and other non-human primates. Lay Summary: Hepatocellular carcinoma occurs frequently in prosimians, but the cause of these liver cancers is unknown. In this proof-of-principle study, we applied human DNA sequencing tools to tumor-normal pairs from five lemurs with hepatocellular carcinoma and compared the lemur mutation profiles to those of human hepatocellular carcinomas.

Published
2022
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38. Additional file 1 of Pan-cancer detection of driver genes at the single-patient resolution

Author

Nulsen, Joel, Misetic, Hrvoje, Yau, Christopher, and Ciccarelli, Francesca D.

Abstract

Additional file 1: Supplementary Note, Supplementary Methods, Supplementary Figures. sysSVM2 rationale and algorithm description. Algorithm implementation and assessment. Figure S1. Comparison of simulated and TCGA samples. Figure S2. Selection of binary features derived for PPIN and tissue expression properties. Figure S3. Parameter convergence and feature selection. Figure S4. Patient-level comparison of driver detection methods. Figure S5. Setting comparison for sysSVM2 training on TCGA data.

Published
2021
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39. Serial circulating tumor DNA detection using a personalized, tumor-informed assay in esophageal adenocarcinoma patients following resection

Author

Ococks, Emma, Sharma, Shruti, Ng, Alvin Wei Tian, Consortium, OCCAMS, Aleshin, Alexey, Fitzgerald, Rebecca C, Smyth, Elizabeth, Edwards, Paul AW, Grehan, Nicola, Nutzinger, Barbara, Fidziukiewicz, Elwira, Redmond, Aisling M, Northrop, Alex, Abbas, Sujath, Smyth, Elizabeth C, O���Donovan, Maria, Miremadi, Ahmad, Malhotra, Shalini, Tripathi, Monika, Grantham, Amber, Cheah, Calvin, Coles, Hannah, Flint, Connor, Eldridge, Matthew, Secrier, Maria, Devonshire, Ginny, Jammula, Sriganesh, Davies, Jim, Crichton, Charles, Carroll, Nick, Hardwick, Richard H, Safranek, Peter, Hindmarsh, Andrew, Sujendran, Vijayendran, Hayes, Stephen J, Ang, Yeng, Sharrocks, Andrew, Preston, Shaun R, Bagwan, Izhar, Save, Vicki, Skipworth, Richard JE, Hupp, Ted R, O���Neill, J Robert, Tucker, Olga, Beggs, Andrew, Taniere, Philippe, Puig, Sonia, Contino, Gianmarco, Underwood, Timothy J, Walker, Robert C, Grace, Ben L, Lagergren, Jesper, Gossage, James, Mahadeva, Ula, Davies, Andrew, Chang, Fuju, Goh, Vicky, Ciccarelli, Francesca D, Sanders, Grant, Berrisford, Richard, Chan, David, Cheong, Ed, Kumar, Bhaskar, Sreedharan, L, Parsons, Simon L, Soomro, Irshad, Kaye, Philip, Saunders, John, Lovat, Laurence, Haidry, Rehan, Scott, Michael, Sothi, Sharmila, Lishman, Suzy, Hanna, George B, Moorthy, Krishna, Peters, Christopher J, Grabowska, Anna, Turkington, Richard, McManus, Damian, Coleman, Helen, and Petty, Russell D

Subjects
Genome Integrity & Repair, Gene Expression, Genetics & Genomics, Computational & Systems Biology
Abstract

No description supplied

Published
2021
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40. Synthetic lethal interaction between the tumour suppressor STAG2 and its paralog STAG1

Author

Benedetti, Lorena, Cereda, Matteo, Monteverde, LeeAnn, Desai, Nikita, and Ciccarelli, Francesca D

Subjects
Genome Integrity & Repair, Gene Expression, biological phenomena, cell phenomena, and immunity, Genetics & Genomics, Computational & Systems Biology
Abstract

Cohesin is a multi-protein complex that tethers sister chromatids during mitosis and mediates DNA repair, genome compartmentalisation and regulation of gene expression. Cohesin subunits frequently acquire cancer loss-of-function alterations and act as tumour suppressors in several tumour types. This has led to increased interest in cohesin as potential target in anti-cancer therapy. Here we show that the loss-of-function of STAG2, a core component of cohesin and an emerging tumour suppressor, leads to synthetic dependency of mutated cancer cells on its paralog STAG1. STAG1 and STAG2 share high sequence identity, encode mutually exclusive cohesin subunits and retain partially overlapping functions. We inhibited STAG1 and STAG2 in several cancer cell lines where the two genes have variable mutation and copy number status. In all cases, we observed that the simultaneous blocking of STAG1 and STAG2 significantly reduces cell proliferation. We further confirmed the synthetic lethal interaction developing a vector-free CRISPR system to induce STAG1/STAG2 double gene knockout. We provide strong evidence that STAG1 is a promising therapeutic target in cancers with inactivating alterations of STAG2.

Published
2021
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41. Comparative assessment of genes driving cancer and somatic evolution in noncancer tissues: an update of the NCG resource

Author

Dressler, Lisa, primary, Bortolomeazzi, Michele, additional, Keddar, Mohamed Reda, additional, Misetic, Hrvoje, additional, Sartini, Giulia, additional, Acha-Sagredo, Amelia, additional, Montorsi, Lucia, additional, Wijewardhane, Neshika, additional, Repana, Dimitra, additional, Nulsen, Joel, additional, Goldman, Jacki, additional, Pollit, Marc, additional, Davis, Patrick, additional, Strange, Amy, additional, Ambrose, Karen, additional, and Ciccarelli, Francesca D., additional

Published
2021
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42. Immunogenomics of colorectal cancer response to immune checkpoint blockade: TCRseq

Author

Bortolomeazzi, Michele, Keddar, Mohamed Reda, Montorsi, Lucia, Benedetti, Lorena, Temelkovski, Damjan, Choi, Subin, Nedyalko, Petrov, Katrina, Todd, Ward, Sophia, Wilson, Gareth A., Al Bakir, Maise, Swanton, Charles, John, Susan, Miles, James, Larijani, Banafshe, Parker, Peter, Rodriguez-Justo, Manuel, Shiu, Kai-Keen, Spencer, Jo, and Ciccarelli, Francesca D.

Subjects
Colorectal Cancer, Tumour Heterogeneity, WES, Tumour Microenvironment, DNA-seq
Abstract

VCF files from Strelka variant calling algorithm. For each sample, there is a *.indels.HighConfidence.vcf file for Indels and a *.snvs.HighConfidence.vcf file for SNVs. For some samples, there is one or two *.additional.*.vcf files that contain mutations that have been rescued manually.

Published
2020
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43. O-linked mucin-type glycosylation regulates the transcriptional programme downstream of EGFR

Author

Tajadura-Ortega, Virginia, Gambardella, Gennaro, Skinner, Alexandra, Halim, Adnan, Van Coillie, Julie, Schjoldager, Katrine Ter-Borch Gram, Beatson, Richard, Graham, Rosalind, Achkova, Daniela, Taylor-Papadimitriou, Joyce, Ciccarelli, Francesca D, Burchell, Joy M, Tajadura-Ortega, Virginia, Gambardella, Gennaro, Skinner, Alexandra, Halim, Adnan, Van Coillie, Julie, Schjoldager, Katrine Ter-Borch Gram, Beatson, Richard, Graham, Rosalind, Achkova, Daniela, Taylor-Papadimitriou, Joyce, Ciccarelli, Francesca D, and Burchell, Joy M

Published
2021

44. Immunogenomics of Colorectal Cancer Response to Checkpoint Blockade: Analysis of the KEYNOTE 177 Trial and Validation Cohorts

Author

Bioquímica y biología molecular, Biokimika eta biologia molekularra, Bortolomeazzi, Michele, Keddar, Mohamed Reda, Montorsi, Lucia, Acha-Sagredo, Amelia, Benedetti, Lorena, Temelkovski, Damjan, Choi, Subin, Petrov, Nedyalko, Todd, Katrina, Wai, Patty, Kohl, Johannes, Denner, Tamara, Nye, Emma, Goldstone, Robert, Ward, Sophia, Wilson, Gareth A., Al Bakir, Maise, Swanton, Charles, John, Susan, Miles, James, Larijani, Banafshé, Kunene, Victoria, Fontana, Elisa, Arkenau, Hendrik-Tobias, Parker, Peter J., Rodriguez-Justo, Manuel, Shiu, Kai-Keen, Spencer, Jo, Ciccarelli, Francesca D., Bioquímica y biología molecular, Biokimika eta biologia molekularra, Bortolomeazzi, Michele, Keddar, Mohamed Reda, Montorsi, Lucia, Acha-Sagredo, Amelia, Benedetti, Lorena, Temelkovski, Damjan, Choi, Subin, Petrov, Nedyalko, Todd, Katrina, Wai, Patty, Kohl, Johannes, Denner, Tamara, Nye, Emma, Goldstone, Robert, Ward, Sophia, Wilson, Gareth A., Al Bakir, Maise, Swanton, Charles, John, Susan, Miles, James, Larijani, Banafshé, Kunene, Victoria, Fontana, Elisa, Arkenau, Hendrik-Tobias, Parker, Peter J., Rodriguez-Justo, Manuel, Shiu, Kai-Keen, Spencer, Jo, and Ciccarelli, Francesca D.

Abstract

BACKGROUND & AIMS: Colorectal cancer (CRC) shows variable response to immune checkpoint blockade, which can only partially be explained by high tumor mutational burden (TMB). We conducted an integrated study of the cancer tissue and associated tumor microenvironment (TME) from patients treated with pembrolizumab (KEYNOTE 177 clinical trial) or nivolumab to dissect the cellular and molecular determinants of response to anti- programmed cell death 1 (PD1) immunotherapy. METHODS: We selected multiple regions per tumor showing variable T-cell infiltration for a total of 738 regions from 29 patients, divided into discovery and validation cohorts. We performed multiregional whole-exome and RNA sequencing of the tumor cells and integrated these with T-cell receptor sequencing, high-dimensional imaging mass cytometry, detection of programmed death-ligand 1 (PDL1) interaction in situ, multiplexed immunofluorescence, and computational spatial analysis of the TME. RESULTS: In hypermutated CRCs, response to anti-PD1 immunotherapy was not associated with TMB but with high clonality of immunogenic mutations, clonally expanded T cells, low activation of Wnt signaling, deregulation of the interferon gamma pathway, and active immune escape mechanisms. Responsive hypermutated CRCs were also rich in cytotoxic and proliferating PD1+CD8 T cells interacting with PDL1+ antigen-presenting macrophages. CONCLUSIONS: Our study clarified the limits of TMB as a predictor of response of CRC to anti-PD1 immunotherapy. It identified a population of antigen-presenting macrophages interacting with CD8 T cells that consistently segregate with response. We therefore concluded that anti-PD1 agents release the PD1-PDL1 interaction between CD8 T cells and macrophages to promote cytotoxic antitumor activity.

Published
2021

45. A SIMPLI (Single-cell Identification from MultiPLexed Images) approach for spatially resolved tissue phenotyping at single-cell resolution

Author

Bortolomeazzi, Michele, primary, Montorsi, Lucia, additional, Temelkovski, Damjan, additional, Keddar, Mohamed Reda, additional, Acha-Sagredo, Amelia, additional, Pitcher, Michael J., additional, Basso, Gianluca, additional, Laghi, Luigi, additional, Rodriguez-Justo, Manuel, additional, Spencer, Jo, additional, and Ciccarelli, Francesca D., additional

Published
2021
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46. Generation and annotation of the DNA sequences of human chromosomes 2 and 4

Author

Hillier, LaDeana W., Graves, Tina A., Fulton, Robert S., Fulton, Lucinda A., Pepin, Kymberlie H., Minx, Patrick, Wagner-McPherson, Caryn, Layman, Dan, Wylie, Kristine, Sekhon, Mandeep, Becker, Michael C., Fewell, Ginger A., Delehaunty, Kimberly D., Miner, Tracie L., Nash, William E., Kremitzki, Colin, Oddy, Lachlan, Du, Hui, Sun, Hui, Bradshaw-Cordum, Holland, Ali, Johar, Carter, Jason, Cordes, Matt, Harris, Anthony, Isak, Amber, van Brunt, Andrew, Nguyen, Christine, Du, Feiyu, Courtney, Laura, Kalicki, Joelle, Ozersky, Philip, Abbott, Scott, Armstrong, Jon, Belter, Edward A., Caruso, Lauren, Cedroni, Maria, Cotton, Marc, Davidson, Teresa, Desai, Anu, Elliott, Glendoria, Erb, Thomas, Fronick, Catrina, Gaige, Tony, Haakenson, William, Haglund, Krista, Holmes, Andrea, Harkins, Richard, Kim, Kyung, Kruchowski, Scott S., Strong, Cynthia Madsen, Grewal, Neenu, Goyea, Ernest, Hou, Shunfang, Levy, Andrew, Martinka, Scott, Mead, Kelly, McLellan, Michael D., Meyer, Rick, Randall-Maher, Jennifer, Tomlinson, Chad, Dauphin-Kohlberg, Sara, Kozlowicz-Reilly, Amy, Shah, Neha, Swearengen-Shahid, Sharhonda, Snider, Jacqueline, Strong, Joseph T., Thompson, Johanna, Yoakum, Martin, Leonard, Shawn, Pearman, Charlene, Trani, Lee, Radionenko, Maxim, Waligorski, Jason E., Wang, Chunyan, Rock, Susan M., Tin-Wollam, Aye-Mon, Maupin, Rachel, Latreille, Phil, Wendl, Michael C., Yang, Shiaw-Pyng, Pohl, Craig, Wallis, John W., Spieth, John, Bieri, Tamberlyn A., Berkowicz, Nicolas, Nelson, Joanne O., Osborne, John, Ding, Li, Meyer, Rekha, Sabo, Aniko, Shotland, Yoram, Sinha, Prashant, Wohldmann, Patricia E., Cook, Lisa L., Hickenbotham, Matthew T., Eldred, James, Williams, Donald, Jones, Thomas A., She, Xinwei, Ciccarelli, Francesca D., Izaurralde, Elisa, Taylor, James, Schmutz, Jeremy, Myers, Richard M., Cox, David R., Huang, Xiaoqiu, McPherson, John D., Mardis, Elaine R., Clifton, Sandra W., Warren, Wesley C., Chinwalla, Asif T., Eddy, Sean R., Marra, Marco A., Ovcharenko, Ivan, Furey, Terrence S., Miller, Webb, Eichler, Evan E., Bork, Peer, Suyama, Mikita, Torrents, David, Waterston, Robert H., and Wilson, Richard K.

Abstract

Author(s): LaDeana W. Hillier [1]; Tina A. Graves [1]; Robert S. Fulton [1]; Lucinda A. Fulton [1]; Kymberlie H. Pepin [1]; Patrick Minx [1]; Caryn Wagner-McPherson [1]; Dan Layman [1]; [...]

Published
2005
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49. The KIND module: a putative signalling domain evolved from the C lobe of the protein kinase fold

Author

Ciccarelli, Francesca D., Bork, Peer, and Kerkhoff, Eugen

Subjects
Protein kinases -- Research, Biological sciences, Chemistry
Abstract

A novel putative interaction domain--KIND (kinase non-catalytic C-lobe domain)--has been identified as being similar to the C-terminal protein kinase catalytic fold (C lobe). Its presence at the N terminus of signalling proteins and the absence of the active-site residues in the catalytic and activation loops suggest that it folds independently and is likely to be non-catalytic. The occurrence of the novel domain only in metazoa implies that it has evolved from the catalytic protein kinase domain into an interaction domain possibly by keeping the substrate-binding features.

Published
2003

50. CASH -- a [beta]-helix domain widespread among carbohydrate-binding proteins. (Protein Sequence Motif)

Author

Ciccarelli, Francesca D., Copley, Richard R., Doerks, Tobias, Russell, Robert B., and Bork, Peer

Subjects
Proteins -- Structure, Carrier proteins -- Research, Biological sciences, Chemistry
Abstract

In this article, we describe a novel, widespread domain (CASH) that is shared by many carbohydrate-binding proteins and sugar hydrolases. This domain occurs in more than 1000 proteins distributed among all three kingdoms of life. The CASH domain is characterized by internal repetitions of glycines and hydrophobic residues that correspond to the repetitive units of a predicted or observed right-handed [beta]-helix structure of the pectate lyase superfamily.

Published
2002

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