Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas
Joshua D. Campbell(Broad Institute), Christina Yau(Buck Institute for Research on Aging), Reanne Bowlby(BC Cancer Agency), Yuexin Liu(The University of Texas MD Anderson Cancer Center), Kevin Brennan(Stanford University), Huihui Fan(Van Andel Institute), Alison M. Taylor(Broad Institute), Chen Wang(Mayo Clinic in Florida), Vonn Walter(University of North Carolina at Chapel Hill), Rehan Akbani(The University of Texas MD Anderson Cancer Center), Lauren Averett Byers(The University of Texas MD Anderson Cancer Center), Chad J. Creighton(The University of Texas MD Anderson Cancer Center), Cristian Coarfa(Baylor College of Medicine), Juliann Shih(Broad Institute), Andrew D. Cherniack(Broad Institute), Olivier Gevaert(Stanford University), Marcos Prunello(Stanford University), Hui Shen(Van Andel Institute), Pavana Anur(Oregon Health & Science University), Jianhong Chen(National Institute on Deafness and Other Communication Disorders), Hui Cheng(National Institute on Deafness and Other Communication Disorders), D. Neil Hayes(University of North Carolina at Chapel Hill), Susan Bullman(Broad Institute), Chandra Sekhar Pedamallu(Broad Institute), Akinyemi I. Ojesina(University of Alabama at Birmingham), Sara Sadeghi(BC Cancer Agency), Karen Mungall(BC Cancer Agency), Lewis R. Roberts(BC Cancer Agency), Christopher C. Benz(Buck Institute for Research on Aging), André Schultz(The University of Texas MD Anderson Cancer Center), Rupa S. Kanchi(The University of Texas MD Anderson Cancer Center), Carl M. Gay(The University of Texas MD Anderson Cancer Center), Apurva M. Hegde(The University of Texas MD Anderson Cancer Center), Lixia Diao(The University of Texas MD Anderson Cancer Center), Jing Wang(The University of Texas MD Anderson Cancer Center), Wencai Ma(The University of Texas MD Anderson Cancer Center), Pavel Sumazin(Baylor College of Medicine), Hua‐Sheng Chiu(Baylor College of Medicine), Ting-Wen Chen(Baylor College of Medicine), Preethi H. Gunaratne(Baylor College of Medicine), L A Donehower(Baylor College of Medicine), Janet S. Rader(Medical College of Wisconsin), Rosemary E. Zuna(University of Oklahoma Health Sciences Center), Hikmat Al‐Ahmadie(Memorial Sloan Kettering Cancer Center), Alexander J. Lazar(The University of Texas MD Anderson Cancer Center), Elsa R. Flores(Moffitt Cancer Center), Kenneth Y. Tsai(Moffitt Cancer Center), Jane H. Zhou(Roswell Park Comprehensive Cancer Center), Anil K. Rustgi(University of Pennsylvania), Esther Drill(Memorial Sloan Kettering Cancer Center), Ronglei Shen(Memorial Sloan Kettering Cancer Center), Christopher K. Wong(University of California, Santa Cruz), Rory Johnson(University of California, Santa Cruz), John A. Demchok(Van Andel Institute), Ina Felau(University of North Carolina at Chapel Hill), Melpomeni Kasapi(The University of Texas MD Anderson Cancer Center), Martin L. Ferguson(Oregon Health & Science University), Carolyn M. Hutter(The University of Texas MD Anderson Cancer Center), Heidi J. Sofia(National Institute on Deafness and Other Communication Disorders), Roy Tarnuzzer(National Institute on Deafness and Other Communication Disorders), Zhining Wang, Liming Yang(The University of Texas MD Anderson Cancer Center), Jean C. Zenklusen(University of Alabama at Birmingham), Jiashan Zhang, Sudha Chudamani, Jia Liu, Laxmi Lolla, Rashi Naresh, Todd Pihl(The University of Texas MD Anderson Cancer Center), Qiang Sun, Yunhu Wan, Ye Wu, Juok Cho, Timothy Defreitas(The University of Texas MD Anderson Cancer Center), Scott Frazer, Nils Gehlenborg, Gad Getz, David I. Heiman, Jaegil Kim(The University of Texas MD Anderson Cancer Center), Michael S. Lawrence(University of Alabama at Birmingham), Pei Lin, Sam Meier, Michael S. Noble, Gordon Saksena, Doug Voet, Hailei Zhang, Brady Bernard, Nyasha Chambwe, Varsha Dhankani, Theo Knijnenburg, Roger Kramer, Kalle Leinonen(BC Cancer Agency), Yuexin Liu(The University of Texas MD Anderson Cancer Center), Michael Miller, Sheila M. Reynolds, Ilya Shmulevich, Vésteinn Thórsson, Wei Zhang, Rehan Akbani(The University of Texas MD Anderson Cancer Center), Bradley M. Broom, Apurva M. Hegde(The University of Texas MD Anderson Cancer Center), Zhenlin Ju, Rupa S. Kanchi(The University of Texas MD Anderson Cancer Center), Anil Korkut, Jun Li, Han Liang(The University of Texas MD Anderson Cancer Center), Shiyun Ling(The University of Texas MD Anderson Cancer Center), Wenbin Liu, Yiling Lu(The University of Texas MD Anderson Cancer Center), Gordon B. Mills(Broad Institute), Kwok-Shing Ng(The University of Texas MD Anderson Cancer Center), Arvind Rao(University of Pennsylvania), Michael Ryan(The University of Texas MD Anderson Cancer Center), Jing Wang(Broad Institute), John N. Weinstein(The University of Texas MD Anderson Cancer Center), Jiexin Zhang(The University of Texas MD Anderson Cancer Center), Adam Abeshouse(Broad Institute), Joshua Armenia, Debyani Chakravarty(National Institute on Deafness and Other Communication Disorders), Walid K. Chatila, Ino de Bruijn, Galen F. Gao(The University of Texas MD Anderson Cancer Center), Benjamin Groß(The University of Texas MD Anderson Cancer Center), Zachary Heins, Ritika Kundra, Konnor La(University of California, Santa Cruz), Marc Ladanyi, Augustin Luna, Moriah G. Nissan, Angelica Ochoa, Sarah Phillips, Ed Reznik, Francisco Sánchez-Vega, Chris Sander(Van Andel Institute), Nikolaus Schultz(Stanford University), Robert P. Sheridan, S. Onur Sumer, Yichao Sun, Barry S. Taylor, Jioajiao Wang(Broad Institute), Hongxin Zhang, Pavana Anur(Oregon Health & Science University), Myron Peto(The University of Texas MD Anderson Cancer Center), Paul T. Spellman(BC Cancer Agency), Christopher C. Benz(Buck Institute for Research on Aging), Joshua M. Stuart(University of California, Santa Cruz), Christopher K. Wong(Broad Institute), Christina Yau(Buck Institute for Research on Aging), D. Neil Hayes(University of North Carolina at Chapel Hill), Joel S. Parker(Oregon Health & Science University), Matthew D. Wilkerson(Oregon Health & Science University), Adrian Ally, Miruna Balasundaram(Buck Institute for Research on Aging), Reanne Bowlby(BC Cancer Agency), Denise Brooks(University of California, Santa Cruz), Rebecca Carlsen(Buck Institute for Research on Aging), Eric Chuah(University of North Carolina at Chapel Hill), Noreen Dhalla, Robert A. Holt, Steven J.M. Jones, Katayoon Kasaian, Darlene Lee(BC Cancer Agency), Yussanne Ma, Marco A. Marra, Michael Mayo, Richard A. Moore, Andrew J. Mungall(BC Cancer Agency), Karen Mungall(BC Cancer Agency), Lewis R. Roberts(BC Cancer Agency), Sara Sadeghi(BC Cancer Agency), Jacqueline E. Schein(Memorial Sloan Kettering Cancer Center), Payal Sipahimalani(Stanford University), Angela Tam, Nina Thiessen, Kane Tse(BC Cancer Agency), Tina Wong(BC Cancer Agency), Ashton C. Berger(BC Cancer Agency), Rameen Beroukhim(BC Cancer Agency), Andrew D. Cherniack(Dana-Farber Cancer Institute), Carrie Cibulskis, Stacey Gabriel, Galen F. Gao, Gavin Ha, Matthew Meyerson(University of California, Santa Cruz), Steven E. Schumacher, Juliann Shih(Dana-Farber Cancer Institute), Melanie H. Kucherlapati(Broad Institute), Raju Kucherlapati, Stephen B. Baylin, Leslie Cope, Ludmila Danilova(Broad Institute), Moiz Bootwalla, Phillip H. Lai, Dennis T. Maglinte(Broad Institute), David Van Den Berg, Daniel J. Weisenberger, J. Todd Auman, Saianand Balu, Tom Bodenheimer, Cheng Fan, Katherine A. Hoadley(University of North Carolina at Chapel Hill), Alan P. Hoyle, Stuart R. Jefferys, Corbin D. Jones, Shaowu Meng, Piotr A. Mieczkowski, Lisle E. Mose, Amy H. Perou(Van Andel Institute), Charles M. Perou(University of North Carolina at Chapel Hill), Jeffrey Roach, Yan Shi, Janae V. Simons, Tara Skelly, Matthew G. Soloway, Donghui Tan, Umadevi Veluvolu, Huihui Fan(Van Andel Institute), Toshinori Hinoue, Peter W. Laird(Broad Institute), Hui Shen(Van Andel Institute), Wanding Zhou, Michelle Bellair, Kyle Chang, Kyle R. Covington, Chad J. Creighton(Van Andel Institute), Huyen Dinh, HarshaVardhan Doddapaneni(Van Andel Institute), Lawrence A. Donehower(Van Andel Institute), Jennifer Drummond(Roswell Park Comprehensive Cancer Center), Richard A. Gibbs, Robert Glenn, Walker Hale, Yi Han(The University of Texas MD Anderson Cancer Center), Hai Hu, Viktoriya Korchina, Sandra Lee(Baylor College of Medicine), Lora Lewis, Wei Li, Xiuping Liu(BC Cancer Agency), Margaret Morgan, Donna Morton(Broad Institute), Donna M. Muzny(University of California, Santa Cruz), Jireh Santibanez, Margi Sheth, Eve Shinbrot, Linghua Wang(The University of Texas MD Anderson Cancer Center), Min Wang(The University of Texas MD Anderson Cancer Center), David A. Wheeler, Xi Liu, Fengmei Zhao, Julian M. Hess, Elizabeth L. Appelbaum, Matthew H. Bailey, Matthew G. Cordes(The University of Texas MD Anderson Cancer Center), Li Ding(The University of Texas MD Anderson Cancer Center), Catrina C. Fronick, Lucinda A. Fulton(The University of Texas MD Anderson Cancer Center), Robert S. Fulton, Cyriac Kandoth(Broad Institute), Elaine R. Mardis, Michael D. McLellan, Christopher A. Miller, Heather K. Schmidt(The University of Texas MD Anderson Cancer Center), Richard K. Wilson, Daniel Crain, Erin Curley(BC Cancer Agency), Johanna Gardner, Kevin Lau, David Mallery, Scott Morris(University of California, Santa Cruz), Joseph Paulauskis, Robert Penny, Candace Shelton, Troy Shelton(The University of Texas MD Anderson Cancer Center), Mark E. Sherman, Eric M. Thompson(The University of Texas MD Anderson Cancer Center), Peggy Yena, Jay Bowen, Julie M. Gastier-Foster, Mark Gerken(BC Cancer Agency), Kristen Leraas, Tara M. Lichtenberg, Nilsa C. Ramirez, Lisa Wise, Erik Zmuda, Niall M. Corcoran, Tony Costello, Christopher M. Hovens, André Lopes Carvalho, Ana Carolina de Carvalho, José Humberto Tavares Guerreiro Fregnani, Adhemar Longatto‐Filho, Rui Manuel Reis, Cristovam Scapulatempo‐Neto, Henrique C.S. Silveira, Daniel Onofre Vidal(University of California, Santa Cruz), Andrew Burnette, Jennifer Eschbacher, Beth Hermes, Ardene Noss, Rosy Singh, Matthew L. Anderson, Patricia D. Castro, Michael Ittmann, David G. Huntsman(Broad Institute), Bernard Kohl, Xuan Le, Richard Thorp, Chris Andry, Elizabeth R. Duffy, Vladimir Lyadov, Oxana Paklina, Galiya Setdikova, Shabunin Av, Mikhail Tavobilov(University of North Carolina at Chapel Hill), Christopher McPherson, Ronald E. Warnick(University of California, Santa Cruz), Ross S. Berkowitz, Daniel Cramer, Colleen M. Feltmate, Neil S. Horowitz, Adam S. Kibel, Michael G. Muto, Chandrajit P. Raut(University of California, Santa Cruz), Andrei Malykh, Jill S. Barnholtz‐Sloan, Wendi Barrett, Karen Devine, Jordonna Fulop(University of North Carolina at Chapel Hill), Quinn T. Ostrom, Kristen Shimmel, Yingli Wolinsky, Andrew E. Sloan, Agostino Maria De Rose, Felice Giuliante, Marc T. Goodman(BC Cancer Agency), Beth Y. Karlan, Curt H. Hagedorn, John Eckman, Jodi Harr, Jerome Myers, Kelinda Tucker, Leigh Anne Zach, Brenda Deyarmin(Stanford University), Hai Hu, Leonid Kvecher, Caroline Larson(The University of Texas MD Anderson Cancer Center), Richard Mural, Stella Somiari, Aleš Vícha, Tomáš Zelinka, Joseph Bennett, Mary Iacocca(University of California, Santa Cruz), Brenda Rabeno, Patricia Swanson, Mathieu Latour, Louis Lacombe, Bernard Têtu, Alain Bergeron, Mary McGraw, Susan M. Staugaitis(University of Oklahoma Health Sciences Center), John A. Chabot, Hanina Hibshoosh, Antonia R. Sepulveda, Tao Su, Timothy C. Wang, Olga Potapova, Olga Voronina(University of Oklahoma Health Sciences Center), Laurence Desjardins, Odette Mariani(The University of Texas MD Anderson Cancer Center), Sergio Roman‐Roman, Xavier Sastre, Marc‐Henri Stern(Baylor College of Medicine), Feixiong Cheng(The University of Texas MD Anderson Cancer Center), Sabina Signoretti, Andrew Berchuck, Darell D. Bigner, Eric Lipp, Jeffrey R. Marks, Shannon J. McCall, Roger E. McLendon, Angeles Alvarez Secord(National Institute on Deafness and Other Communication Disorders), Alexis Sharp, Madhusmita Behera(Broad Institute), Daniel J. Brat, Amy Chen, Keith A. Delman, Seth Force, Fadlo R. Khuri, Kelly R. Magliocca, Shishir K. Maithel, Jeffrey J. Olson, Taofeek K. Owonikoko, Alan Pickens(National Institute on Deafness and Other Communication Disorders), Suresh S. Ramalingam, Dong Min Shin, Gabriel Sica, Erwin G. Van Meir, Hongzheng Zhang, Wil Eijckenboom, Ad Gillis, Esther Korpershoek, Leendert H. J. Looijenga, Wolter Oosterhuis, Hans Stoop, Kim E. van Kessel, Ellen C. Zwarthoff, Chiara Calatozzolo, Lucia Cuppini(University of North Carolina at Chapel Hill), Stefania Cuzzubbo(Memorial Sloan Kettering Cancer Center), Francesco DiMeco, Gaetano Finocchiaro, Luca Mattei, Alessandro Perin, Bianca Pollo, Chen Chu, J. C. Houck, Pawadee Lohavanichbutr, Arndt Hartmann, Robert Stoehr, Robert Stoehr, Helge Täubert, Sven Wach, Bernd Wullich(National Institute on Deafness and Other Communication Disorders), Witold Kycler(The University of Texas MD Anderson Cancer Center), Dawid Murawa, Maciej Wiznerowicz, Ki Wung Chung, W. Jeffrey Edenfield(BC Cancer Agency), Julie Martin, Éric Baudin, Glenn J. Bubley, Raphael Bueno, Assunta De Rienzo, William G. Richards, Steven N. Kalkanis(University of Alabama at Birmingham), Tom Mikkelsen, Houtan Noushmehr, Lisa Scarpace, Nicolas Girard, Marta Aymerich, Elı́as Campo, Eva Giné, Armando López Guillermo, Nguyen Van Bang, Phan Thi Hanh, Bùi Đức Phú, Yufang Tang, Howard Colman, Kimberley Evason, Peter R. Dottino(Stanford University), John A. Martignetti, Hani Gabra, Hartmut Juhl, Teniola Akeredolu, Serghei Stepa, Dave S.�B. Hoon, Keunsoo Ahn, Koo Jeong Kang, Felix Beuschlein(The University of Texas MD Anderson Cancer Center), Anne Breggia, Michael J. Birrer, Debra Bell, Mitesh J. Borad, Alan H. Bryce, Erik P. Castle, Vishal S. Chandan, John C. Cheville, John A. Copland(BC Cancer Agency), Michael B. Farnell, Thomas J. Flotte(Broad Institute), Nasra H. Giama, Thai H. Ho, Michael L. Kendrick, Jean‐Pierre Kocher, Karla Kopp(The University of Texas MD Anderson Cancer Center), Catherine D. Moser(The University of Texas MD Anderson Cancer Center), David M. Nagorney, Daniel R. O’Brien, Brian Patrick O’Neill, Tushar Patel(National Institute on Deafness and Other Communication Disorders), Gloria Petersen, Florencia G. Que, Michael Rivera, Lewis R. Roberts, Robert C. Smallridge, Thomas C. Smyrk, Melissa Stanton, R. Houston Thompson, Michael Torbenson, Ju Dong Yang, Lizhi Zhang, Fadi Brimo(BC Cancer Agency), Jaffer A. Ajani(BC Cancer Agency), Ana Maria Angulo Gonzalez, Carmen Behrens, Jolanta Bondaruk, Russell Broaddus, Bogdan Czerniak, Bita Esmaeli, Junya Fujimoto, Jeffrey Gershenwald, Charles C. Guo, Alexander J. Lazar(The University of Texas MD Anderson Cancer Center), Christopher J. Logothetis, Funda Meric‐Bernstam, César A. Moran, Lois M. Ramondetta, David C. Rice, Anil K. Sood, Pheroze Tamboli, Timothy C. Thompson(The University of Texas MD Anderson Cancer Center), Patricia Troncoso(University of California, Santa Cruz), Anne S. Tsao, Ignacio Wistuba, Candace Carter, Lauren E. Haydu, Peter Hersey(University of Pennsylvania), Valerie Jakrot, Hojabr Kakavand, Richard Kefford, Kenneth Lee(BC Cancer Agency), Georgina V. Long, Graham J. Mann(National Institute on Deafness and Other Communication Disorders), Michael C. Quinn(The University of Texas MD Anderson Cancer Center), Robyn P.M. Saw(Van Andel Institute), Richard A. Scolyer, Kerwin F. Shannon, Andrew J. Spillane, onathan Stretch(Moffitt Cancer Center), Maria Synott, John Thompson, James S. Wilmott, Hikmat Al‐Ahmadie(Memorial Sloan Kettering Cancer Center), Timothy A. Chan, Ronald Ghossein, Anuradha Gopalan(Broad Institute), Douglas A. Levine, Victor Reuter, Samuel Singer(The University of Texas MD Anderson Cancer Center), Bhuvanesh Singh, Nguyen Viet Tien(Memorial Sloan Kettering Cancer Center), Thomas Broudy(Broad Institute), Cyrus Mirsaidi, Praveen Nair, Paul Drwiega, Judy Miller, Jennifer R. Smith, Howard A. Zaren, Joong‐Won Park, Nguyễn Phi Hùng, Electron Kebebew, W. Marston Linehan, Adam R. Metwalli, Karel Pacák, Peter A. Pinto, Mark Schiffman, Laura S. Schmidt, Cathy D. Vocke, Nicolas Wentzensen, Robert Worrell, Hannah Yang, Marc Moncrieff, Chandra Goparaju(Van Andel Institute), Jonathan Melamed, Harvey I. Pass, Natalia Botnariuc, Irina Caraman, Mircea Cernat(BC Cancer Agency), Inga Chemencedji, Adrian Clipca(Stanford University), Serghei Doruc(Broad Institute), Ghenadie Gorincioi, Sergiu Mura, Maria Pirtac, Irina Stancul, Diana Tcaciuc, Monique Albert, Iakovina Alexopoulou, Angel Arnaout, John G. Bartlett, Jay Engel, Sébastien Gilbert, Jeremy Parfitt, Harman Sekhon, George Thomas, Doris M. Rassl, Robert C. Rintoul, Carlo Bifulco(The University of Texas MD Anderson Cancer Center), Raina Tamakawa, Walter J. Urba, Nicholas K. Hayward, Henri Timmers, Anna Antenucci, Francesco Facciolo, Gian Luca Grazi, Mirella Marino, Roberta Merola, Ronald R. de Krijger(University of North Carolina at Chapel Hill), Anne‐Paule Gimenez‐Roqueplo, Alain Piché, Simone Chevalier, Ginette McKercher, Kıvanç Birsoy, Gene H. Barnett, Cathy Brewer, Carol Farver, Theresa Naska, Nathan A. Pennell, Daniel P. Raymond, Cathy Schilero, Kathy Smolenski, Felicia Williams, Quaid Morris, Jeffrey A. Borgia, Michael J. Liptay, Mark Pool, Christopher W. Seder, Kerstin Junker, Larsson Omberg, Mikhail Dinkin, George Manikhas(The University of Texas MD Anderson Cancer Center), Domenico Alvaro, Maria Consiglia Bragazzi, Vincenzo Cardinale, Guido Carpino, Eugenio Gaudio, David Chesla, Sandra Cottingham, Michael Dubina, Fedor Moiseenko, Renumathy Dhanasekaran, Karl‐Friedrich Becker, Klaus‐Peter Janssen, Julia Slotta‐Huspenina, Mohamed H. Abdel‐Rahman, Dina Aziz, Sue Bell, Colleen M. Cebulla, Amy Davis, Rebecca Duell, J. Bradley Elder, Joe Hilty(Broad Institute), Bahavna Kumar, James C. Lang, Norman L. Lehman(Broad Institute), Randy Mandt, Phuong Nguyen, Robert Pilarski, Karan Rai, Lynn Schoenfield, Kelly Senecal, Paul E. Wakely, Paul Hansen, Ronald M. Lechan, James F. Powers, Arthur S. Tischler(BC Cancer Agency), William E. Grizzle, Katherine C. Sexton, Alison Kastl, Joel Henderson, Sima P. Porten, Jens Waldmann, Martin Faßnacht, L. Sylvia, Dirk Schadendorf, Marta Couce, Markus Graefen(Broad Institute), Hartwig Huland, Guido Sauter, Thorsten Schlomm, Ronald Simon, Pierre Tennstedt(BC Cancer Agency), Oluwole Olabode, Mark A. Nelson, Oliver F. Bathe, Peter R. Carroll, June M. Chan, Philip J. DiSaia, Pat Glenn, Robin Kate Kelley, Charles N. Landen, Joanna Phillips, Michael Prados, Jeffry Simko, Karen Smith‐McCune(Broad Institute), Scott R. VandenBerg, Kevin K. Roggin, Ashley Fehrenbach, Ady Kendler, Suzanne Sifri, Ruth Steele, Antonio Jimeno, Francis A. Carey(BC Cancer Agency), Ian Forgie, Massimo Mannelli(Stanford University), Michael E. Carney, Brenda Hernandez, Benito Campos, Christel Herold‐Mende, Christin Jungk, Andreas Unterberg, Andreas von Deimling(National Institute on Deafness and Other Communication Disorders), Aaron Bossler, Joseph Galbraith, Laura Jacobus, Michael Knudson, Tina Knutson, Deqin Ma(Buck Institute for Research on Aging), Mohammed Milhem, Rita Sigmund, Andrew K. Godwin, Rashna Madan, Howard G. Rosenthal, Clement Adebamowo, Sally N. Adebamowo(Buck Institute for Research on Aging), Alex Boussioutas(Memorial Sloan Kettering Cancer Center), David G. Beer, Thomas J. Giordano, Anne‐Marie Mes‐Masson, Fred Saad, Thèrése Bocklage, Lisa M. Landrum, Robert S. Mannel, Kathleen Moore(The University of Texas MD Anderson Cancer Center), Katherine Moxley, Russel Postier, Joan Walker, Rosemary Zuna(University of Oklahoma Health Sciences Center), Michaël Feldman, Federico Valdivieso, Rajiv Dhir(BC Cancer Agency), James D. Luketich, Edna M. Mora Pinero(University of North Carolina at Chapel Hill), Mario Quintero-Aguilo, Carlos Gilberto Carlotti, José Sebastião dos Santos(University of Oklahoma Health Sciences Center), Rafael Kemp, Ajith Sankarankuty, Daniela Pretti da Cunha Tirapelli, James W.F. Catto, Kathy Agnew, Elizabeth M. Swisher, Jenette Creaney, Bruce Robinson, Carl Simon Shelley, Eryn M. Godwin, Sara Kendall, Cassaundra Shipman, Carol R. Bradford, Thomas E. Carey, Andrea Haddad, Jeffey Moyer, Lisa A. Peterson, Mark E. Prince, Laura S. Rozek(BC Cancer Agency), Gregory T. Wolf, Rayleen Bowman, Kwun M. Fong, Ian A. Yang, Robert J. Korst, W. Kimryn Rathmell, J. Leigh Fantacone-Campbell, Jeffrey A. Hooke, Albert J. Kovatich, Craig D. Shriver, John F. DiPersio, Bettina F. Drake(National Institute on Deafness and Other Communication Disorders), Ramaswamy Govindan(BC Cancer Agency), Sharon E. Heath, Timothy J. Ley, Brian A. Van Tine, Peter Westervelt, Mark A. Rubin, Jung Il Lee(The University of Texas MD Anderson Cancer Center), Natália D. Aredes, Armaz Mariamidze, Joshua M. Stuart(University of California, Santa Cruz), Peter W. Laird(University of North Carolina at Chapel Hill), Katherine A. Hoadley(University of North Carolina at Chapel Hill), John N. Weinstein(Van Andel Institute), Myron Peto(Oregon Health & Science University), Curtis R. Pickering(The University of Texas MD Anderson Cancer Center), Zhong Chen(National Institute on Deafness and Other Communication Disorders), Carter Van Waes(National Institute on Deafness and Other Communication Disorders)
Cited by 365Open Access
Abstract
This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smoking and/or human papillomavirus (HPV). SCCs harbor 3q, 5p, and other recurrent chromosomal copy-number alterations (CNAs), DNA mutations, and/or aberrant methylation of genes and microRNAs, which are correlated with the expression of multi-gene programs linked to squamous cell stemness, epithelial-to-mesenchymal differentiation, growth, genomic integrity, oxidative damage, death, and inflammation. Low-CNA SCCs tended to be HPV(+) and display hypermethylation with repression of TET1 demethylase and FANCF, previously linked to predisposition to SCC, or harbor mutations affecting CASP8, RAS-MAPK pathways, chromatin modifiers, and immunoregulatory molecules. We uncovered hypomethylation of the alternative promoter that drives expression of the ΔNp63 oncogene and embedded miR944. Co-expression of immune checkpoint, T-regulatory, and Myeloid suppressor cells signatures may explain reduced efficacy of immune therapy. These findings support possibilities for molecular classification and therapeutic approaches.
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