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CATALOGO DEI PRODOTTI DELLA RICERCA
Viral pathogen load in cancer genomes is estimated through analysis of sequencing data from 2,656 tumors across 35 cancer types using multiple pathogen-detection pipelines, identifying viruses in 382 genomic and 68 transcriptome datasets.Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, for which whole-genome and-for a subset-whole-transcriptome sequencing data from 2,658 cancers across 38 tumor types was aggregated, we systematically investigated potential viral pathogens using a consensus approach that integrated three independent pipelines. Viruses were detected in 382 genome and 68 transcriptome datasets. We found a high prevalence of known tumor-associated viruses such as Epstein-Barr virus (EBV), hepatitis B virus (HBV) and human papilloma virus (HPV; for example, HPV16 or HPV18). The study revealed significant exclusivity of HPV and driver mutations in head-and-neck cancer and the association of HPV with APOBEC mutational signatures, which suggests that impaired antiviral defense is a driving force in cervical, bladder and head-and-neck carcinoma. For HBV, HPV16, HPV18 and adeno-associated virus-2 (AAV2), viral integration was associated with local variations in genomic copy numbers. Integrations at the TERT promoter were associated with high telomerase expression evidently activating this tumor-driving process. High levels of endogenous retrovirus (ERV1) expression were linked to a worse survival outcome in patients with kidney cancer.
The landscape of viral associations in human cancers
Zapatka, Marc;Borozan, Ivan;Brewer, Daniel S.;Iskar, Murat;Grundhoff, Adam;Alawi, Malik;Desai, Nikita;Sültmann, Holger;Moch, Holger;Alawi, Malik;Borozan, Ivan;Brewer, Daniel S.;Cooper, Colin S.;Desai, Nikita;Eils, Roland;Ferretti, Vincent;Grundhoff, Adam;Iskar, Murat;Kleinheinz, Kortine;Lichter, Peter;Nakagawa, Hidewaki;Ojesina, Akinyemi I.;Pedamallu, Chandra Sekhar;Schlesner, Matthias;Su, Xiaoping;Zapatka, Marc;Cooper, Colin S.;Eils, Roland;Ferretti, Vincent;Lichter, Peter;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.;Al-Shahrour, Fatima;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;Atwal, Gurnit;Aukema, Sietse;Auman, J. 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Kimryn;Rausch, Tobias;Reifenberger, Guido;Reimand, Jüri;Reis-Filho, Jorge;Reuter, Victor;Reyes-Salazar, Iker;Reyna, Matthew A.;Reynolds, Sheila M.;Rheinbay, Esther;Riazalhosseini, Yasser;Richardson, Andrea L.;Richter, Julia;Ringel, Matthew;Ringnér, Markus;Rino, Yasushi;Rippe, Karsten;Roach, Jeffrey;Roberts, Lewis R.;Roberts, Nicola D.;Roberts, Steven A.;Robertson, A. Gordon;Robertson, Alan J.;Rodriguez, Javier Bartolomé;Rodriguez-Martin, Bernardo;Rodríguez-González, F. Germán;Roehrl, Michael H. A.;Rohde, Marius;Rokutan, Hirofumi;Romieu, Gilles;Rooman, Ilse;Roques, Tom;Rosebrock, Daniel;Rosenberg, Mara;Rosenstiel, Philip C.;Rosenwald, Andreas;Rowe, Edward W.;Royo, Romina;Rozen, Steven G.;Rubanova, Yulia;Rubin, Mark A.;Rubio-Perez, Carlota;Rudneva, Vasilisa A.;Rusev, Borislav C.;Ruzzenente, Andrea;Rätsch, Gunnar;Sabarinathan, Radhakrishnan;Sabelnykova, Veronica Y.;Sadeghi, Sara;Sahinalp, S. 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M.;Scardoni, Maria;Scarlett, Christopher J.;Scarpa, Aldo;Scelo, Ghislaine;Schadendorf, Dirk;Schein, Jacqueline E.;Schilhabel, Markus B.;Schlesner, Matthias;Schlomm, Thorsten;Schmidt, Heather K.;Schramm, Sarah-Jane;Schreiber, Stefan;Schultz, Nikolaus;Schumacher, Steven E.;Schwarz, Roland F.;Scolyer, Richard A.;Scott, David;Scully, Ralph;Seethala, Raja;Segre, Ayellet V.;Selander, Iris;Semple, Colin A.;Senbabaoglu, Yasin;Sengupta, Subhajit;Sereni, Elisabetta;Serra, Stefano;Sgroi, Dennis C.;Shackleton, Mark;Shah, Nimish C.;Shahabi, Sagedeh;Shang, Catherine A.;Shang, Ping;Shapira, Ofer;Shelton, Troy;Shen, Ciyue;Shen, Hui;Shepherd, Rebecca;Shi, Ruian;Shi, Yan;Shiah, Yu-Jia;Shibata, Tatsuhiro;Shih, Juliann;Shimizu, Eigo;Shimizu, Kiyo;Shin, Seung Jun;Shiraishi, Yuichi;Shmaya, Tal;Shmulevich, Ilya;Shorser, Solomon I.;Short, Charles;Shrestha, Raunak;Shringarpure, Suyash S.;Shriver, Craig;Shuai, Shimin;Sidiropoulos, Nikos;Siebert, Reiner;Sieuwerts, Anieta M.;Sieverling, Lina;Signoretti, Sabina;Sikora, Katarzyna O.;Simbolo, Michele;Simon, Ronald;Simons, Janae V.;Simpson, Jared T.;Simpson, Peter T.;Singer, Samuel;Sinnott-Armstrong, Nasa;Sipahimalani, Payal;Skelly, Tara J.;Smid, Marcel;Smith, Jaclyn;Smith-McCune, Karen;Socci, Nicholas D.;Sofia, Heidi J.;Soloway, Matthew G.;Song, Lei;Sood, Anil K.;Sothi, Sharmila;Sotiriou, Christos;Soulette, Cameron M.;Span, Paul N.;Spellman, Paul T.;Sperandio, Nicola;Spillane, Andrew J.;Spiro, Oliver;Spring, Jonathan;Staaf, Johan;Stadler, Peter F.;Staib, Peter;Stark, Stefan G.;Stebbings, Lucy;Stefánsson, Ólafur Andri;Stegle, Oliver;Stein, Lincoln D.;Stenhouse, Alasdair;Stewart, Chip;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 F. F.;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.;Torrents, David;Tortora, Giampaolo;Tost, Jörg;Totoki, Yasushi;Townend, David;Traficante, Nadia;Treilleux, Isabelle;Trotta, Jean-Rémi;Trümper, Lorenz H. P.;Tsao, Ming;Tsunoda, Tatsuhiko;Tubio, Jose M. C.;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 P. C.;Vermeulen, Peter;Verrill, Clare;Viari, Alain;Vicente, David;Vicentini, Caterina;VijayRaghavan, K.;Viksna, Juris;Vilain, Ricardo E.;Villasante, Izar;Vincent-Salomon, Anne;Visakorpi, Tapio;Voet, Douglas;Vyas, Paresh;Vázquez-García, Ignacio;Waddell, Nick M.;Waddell, Nicola;Wadelius, Claes;Wadi, Lina;Wagener, Rabea;Wala, Jeremiah A.;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.;Weischenfeldt, Joachim;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, Lixing;Yang, Shanlin;Yang, Tsun-Po;Yang, Yang;Yao, Xiaotong;Yaspo, Marie-Laure;Yates, Lucy;Yau, Christina;Ye, Chen;Ye, Kai;Yellapantula, Venkata D.;Yoon, Christopher J.;Yoon, Sung-Soo;Yousif, Fouad;Yu, Jun;Yu, Kaixian;Yu, Willie;Yu, Yingyan;Yuan, Ke;Yuan, Yuan;Yuen, Denis;Yung, Christina K.;Zaikova, Olga;Zamora, Jorge;Zapatka, Marc;Zenklusen, Jean C.;Zenz, Thorsten;Zeps, Nikolajs;Zhang, Cheng-Zhong;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 H. M.;van de Vijver, Marc J.;van’t Veer, L.;von Mering, Christian;null, null;null, null
2020-01-01
Abstract
Viral pathogen load in cancer genomes is estimated through analysis of sequencing data from 2,656 tumors across 35 cancer types using multiple pathogen-detection pipelines, identifying viruses in 382 genomic and 68 transcriptome datasets.Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, for which whole-genome and-for a subset-whole-transcriptome sequencing data from 2,658 cancers across 38 tumor types was aggregated, we systematically investigated potential viral pathogens using a consensus approach that integrated three independent pipelines. Viruses were detected in 382 genome and 68 transcriptome datasets. We found a high prevalence of known tumor-associated viruses such as Epstein-Barr virus (EBV), hepatitis B virus (HBV) and human papilloma virus (HPV; for example, HPV16 or HPV18). The study revealed significant exclusivity of HPV and driver mutations in head-and-neck cancer and the association of HPV with APOBEC mutational signatures, which suggests that impaired antiviral defense is a driving force in cervical, bladder and head-and-neck carcinoma. For HBV, HPV16, HPV18 and adeno-associated virus-2 (AAV2), viral integration was associated with local variations in genomic copy numbers. Integrations at the TERT promoter were associated with high telomerase expression evidently activating this tumor-driving process. High levels of endogenous retrovirus (ERV1) expression were linked to a worse survival outcome in patients with kidney cancer.
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11562/1120006
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simulazione ASN
Il report seguente simula gli indicatori relativi alla propria produzione scientifica in relazione alle soglie ASN 2023-2025 del proprio SC/SSD. Si ricorda che il superamento dei valori soglia (almeno 2 su 3) è requisito necessario ma non sufficiente al conseguimento dell'abilitazione. La simulazione si basa sui dati IRIS e sugli indicatori bibliometrici alla data indicata e non tiene conto di eventuali periodi di congedo obbligatorio, che in sede di domanda ASN danno diritto a incrementi percentuali dei valori. La simulazione può differire dall'esito di un’eventuale domanda ASN sia per errori di catalogazione e/o dati mancanti in IRIS, sia per la variabilità dei dati bibliometrici nel tempo. Si consideri che Anvur calcola i valori degli indicatori all'ultima data utile per la presentazione delle domande.
La presente simulazione è stata realizzata sulla base delle specifiche raccolte sul tavolo ER del Focus Group IRIS coordinato dall’Università di Modena e Reggio Emilia e delle regole riportate nel DM 589/2018 e allegata Tabella A. Cineca, l’Università di Modena e Reggio Emilia e il Focus Group IRIS non si assumono alcuna responsabilità in merito all’uso che il diretto interessato o terzi faranno della simulazione. Si specifica inoltre che la simulazione contiene calcoli effettuati con dati e algoritmi di pubblico dominio e deve quindi essere considerata come un mero ausilio al calcolo svolgibile manualmente o con strumenti equivalenti.