Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas
Summary: 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 alter...
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Format: | Article |
Language: | English |
Published: |
Elsevier
2018-04-01
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Series: | Cell Reports |
Online Access: | http://www.sciencedirect.com/science/article/pii/S2211124718304248 |
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Joshua D. Campbell Christina Yau Reanne Bowlby Yuexin Liu Kevin Brennan Huihui Fan Alison M. Taylor Chen Wang Vonn Walter Rehan Akbani Lauren Averett Byers Chad J. Creighton Cristian Coarfa Juliann Shih Andrew D. Cherniack Olivier Gevaert Marcos Prunello Hui Shen Pavana Anur Jianhong Chen Hui Cheng D. Neil Hayes Susan Bullman Chandra Sekhar Pedamallu Akinyemi I. Ojesina Sara Sadeghi Karen L. Mungall A. Gordon Robertson Christopher Benz Andre Schultz Rupa S. Kanchi Carl M. Gay Apurva Hegde Lixia Diao Jing Wang Wencai Ma Pavel Sumazin Hua-Sheng Chiu Ting-Wen Chen Preethi Gunaratne Larry Donehower Janet S. Rader Rosemary Zuna Hikmat Al-Ahmadie Alexander J. Lazar Elsa R. Flores Kenneth Y. Tsai Jane H. Zhou Anil K. Rustgi Esther Drill Ronglei Shen Christopher K. Wong Joshua M. Stuart Peter W. Laird Katherine A. Hoadley John N. Weinstein Myron Peto Curtis R. Pickering Zhong Chen Carter Van Waes Samantha J. Caesar-Johnson John A. Demchok Ina Felau Melpomeni Kasapi Martin L. Ferguson Carolyn M. Hutter Heidi J. Sofia Roy Tarnuzzer Zhining Wang Liming Yang Jean C. Zenklusen Jiashan (Julia) Zhang Sudha Chudamani Jia Liu Laxmi Lolla Rashi Naresh Todd Pihl Qiang Sun Yunhu Wan Ye Wu Juok Cho Timothy DeFreitas Scott Frazer Nils Gehlenborg Gad Getz David I. Heiman Jaegil Kim Michael S. Lawrence 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 Yuexin Liu Michael Miller Sheila Reynolds Ilya Shmulevich Vesteinn Thorsson Wei Zhang Rehan Akbani Bradley M. Broom Apurva M. Hegde Zhenlin Ju Rupa S. Kanchi Anil Korkut Jun Li Han Liang Shiyun Ling Wenbin Liu Yiling Lu Gordon B. Mills Kwok-Shing Ng Arvind Rao Michael Ryan Jing Wang John N. Weinstein Jiexin Zhang Adam Abeshouse Joshua Armenia Debyani Chakravarty Walid K. Chatila Ino de Bruijn Jianjiong Gao Benjamin E. Gross Zachary J. Heins Ritika Kundra Konnor La Marc Ladanyi Augustin Luna Moriah G. Nissan Angelica Ochoa Sarah M. Phillips Ed Reznik Francisco Sanchez-Vega Chris Sander Nikolaus Schultz Robert Sheridan S. Onur Sumer Yichao Sun Barry S. Taylor Jioajiao Wang Hongxin Zhang Pavana Anur Myron Peto Paul Spellman Christopher Benz Joshua M. Stuart Christopher K. Wong Christina Yau D. Neil Hayes Joel S. Parker Matthew D. Wilkerson Adrian Ally Miruna Balasundaram Reanne Bowlby Denise Brooks Rebecca Carlsen Eric Chuah Noreen Dhalla Robert Holt Steven J.M. Jones Katayoon Kasaian Darlene Lee Yussanne Ma Marco A. Marra Michael Mayo Richard A. Moore Andrew J. Mungall Karen Mungall A. Gordon Robertson Sara Sadeghi Jacqueline E. Schein Payal Sipahimalani Angela Tam Nina Thiessen Kane Tse Tina Wong Ashton C. Berger Rameen Beroukhim Andrew D. Cherniack Carrie Cibulskis Stacey B. Gabriel Galen F. Gao Gavin Ha Matthew Meyerson Steven E. Schumacher Juliann Shih Melanie H. Kucherlapati Raju S. Kucherlapati Stephen Baylin Leslie Cope Ludmila Danilova Moiz S. Bootwalla Phillip H. Lai Dennis T. Maglinte David J. Van Den Berg Daniel J. Weisenberger J. Todd Auman Saianand Balu Tom Bodenheimer Cheng Fan Katherine A. Hoadley Alan P. Hoyle Stuart R. Jefferys Corbin D. Jones Shaowu Meng Piotr A. Mieczkowski Lisle E. Mose Amy H. Perou Charles M. Perou Jeffrey Roach Yan Shi Janae V. Simons Tara Skelly Matthew G. Soloway Donghui Tan Umadevi Veluvolu Huihui Fan Toshinori Hinoue Peter W. Laird Hui Shen Wanding Zhou Michelle Bellair Kyle Chang Kyle Covington Chad J. Creighton Huyen Dinh HarshaVardhan Doddapaneni Lawrence A. Donehower Jennifer Drummond Richard A. Gibbs Robert Glenn Walker Hale Yi Han Jianhong Hu Viktoriya Korchina Sandra Lee Lora Lewis Wei Li Xiuping Liu Margaret Morgan Donna Morton Donna Muzny Jireh Santibanez Margi Sheth Eve Shinbrot Linghua Wang Min Wang David A. Wheeler Liu Xi Fengmei Zhao Julian Hess Elizabeth L. Appelbaum Matthew Bailey Matthew G. Cordes Li Ding Catrina C. Fronick Lucinda A. Fulton Robert S. Fulton Cyriac Kandoth Elaine R. Mardis Michael D. McLellan Christopher A. Miller Heather K. Schmidt Richard K. Wilson Daniel Crain Erin Curley Johanna Gardner Kevin Lau David Mallery Scott Morris Joseph Paulauskis Robert Penny Candace Shelton Troy Shelton Mark Sherman Eric Thompson Peggy Yena Jay Bowen Julie M. Gastier-Foster Mark Gerken Kristen M. Leraas Tara M. Lichtenberg Nilsa C. Ramirez Lisa Wise Erik Zmuda Niall Corcoran Tony Costello Christopher Hovens Andre L. Carvalho Ana C. de Carvalho José H. Fregnani Adhemar Longatto-Filho Rui M. Reis Cristovam Scapulatempo-Neto Henrique C.S. Silveira Daniel O. Vidal Andrew Burnette Jennifer Eschbacher Beth Hermes Ardene Noss Rosy Singh Matthew L. Anderson Patricia D. Castro Michael Ittmann David Huntsman Bernard Kohl Xuan Le Richard Thorp Chris Andry Elizabeth R. Duffy Vladimir Lyadov Oxana Paklina Galiya Setdikova Alexey Shabunin Mikhail Tavobilov Christopher McPherson Ronald Warnick Ross Berkowitz Daniel Cramer Colleen Feltmate Neil Horowitz Adam Kibel Michael Muto Chandrajit P. Raut Andrei Malykh Jill S. Barnholtz-Sloan Wendi Barrett Karen Devine Jordonna Fulop Quinn T. Ostrom Kristen Shimmel Yingli Wolinsky Andrew E. Sloan Agostino De Rose Felice Giuliante Marc Goodman Beth Y. Karlan Curt H. Hagedorn John Eckman Jodi Harr Jerome Myers Kelinda Tucker Leigh Anne Zach Brenda Deyarmin Hai Hu Leonid Kvecher Caroline Larson Richard J. Mural Stella Somiari Ales Vicha Tomas Zelinka Joseph Bennett Mary Iacocca Brenda Rabeno Patricia Swanson Mathieu Latour Louis Lacombe Bernard Têtu Alain Bergeron Mary McGraw Susan M. Staugaitis John Chabot Hanina Hibshoosh Antonia Sepulveda Tao Su Timothy Wang Olga Potapova Olga Voronina Laurence Desjardins Odette Mariani Sergio Roman-Roman Xavier Sastre Marc-Henri Stern Feixiong Cheng Sabina Signoretti Andrew Berchuck Darell Bigner Eric Lipp Jeffrey Marks Shannon McCall Roger McLendon Angeles Secord Alexis Sharp Madhusmita Behera Daniel J. Brat Amy Chen Keith Delman Seth Force Fadlo Khuri Kelly Magliocca Shishir Maithel Jeffrey J. Olson Taofeek Owonikoko Alan Pickens Suresh Ramalingam Dong M. Shin Gabriel Sica Erwin G. Van Meir Hongzheng Zhang Wil Eijckenboom Ad Gillis Esther Korpershoek Leendert Looijenga Wolter Oosterhuis Hans Stoop Kim E. van Kessel Ellen C. Zwarthoff Chiara Calatozzolo Lucia Cuppini Stefania Cuzzubbo Francesco DiMeco Gaetano Finocchiaro Luca Mattei Alessandro Perin Bianca Pollo Chu Chen John Houck Pawadee Lohavanichbutr Arndt Hartmann Christine Stoehr Robert Stoehr Helge Taubert Sven Wach Bernd Wullich Witold Kycler Dawid Murawa Maciej Wiznerowicz Ki Chung W. Jeffrey Edenfield Julie Martin Eric Baudin Glenn Bubley Raphael Bueno Assunta De Rienzo William G. Richards Steven Kalkanis Tom Mikkelsen Houtan Noushmehr Lisa Scarpace Nicolas Girard Marta Aymerich Elias Campo Eva Giné Armando López Guillermo Nguyen Van Bang Phan Thi Hanh Bui Duc Phu Yufang Tang Howard Colman Kimberley Evason Peter R. Dottino John A. Martignetti Hani Gabra Hartmut Juhl Teniola Akeredolu Serghei Stepa Dave Hoon Keunsoo Ahn Koo Jeong Kang Felix Beuschlein Anne Breggia Michael Birrer Debra Bell Mitesh Borad Alan H. Bryce Erik Castle Vishal Chandan John Cheville John A. Copland Michael Farnell Thomas Flotte Nasra Giama Thai Ho Michael Kendrick Jean-Pierre Kocher Karla Kopp Catherine Moser David Nagorney Daniel O’Brien Brian Patrick O’Neill Tushar Patel Gloria Petersen Florencia Que Michael Rivera Lewis Roberts Robert Smallridge Thomas Smyrk Melissa Stanton R. Houston Thompson Michael Torbenson Ju Dong Yang Lizhi Zhang Fadi Brimo Jaffer A. Ajani Ana Maria Angulo Gonzalez Carmen Behrens Jolanta Bondaruk Russell Broaddus Bogdan Czerniak Bita Esmaeli Junya Fujimoto Jeffrey Gershenwald Charles Guo Alexander J. Lazar Christopher Logothetis Funda Meric-Bernstam Cesar Moran Lois Ramondetta David Rice Anil Sood Pheroze Tamboli Timothy Thompson Patricia Troncoso Anne Tsao Ignacio Wistuba Candace Carter Lauren Haydu Peter Hersey Valerie Jakrot Hojabr Kakavand Richard Kefford Kenneth Lee Georgina Long Graham Mann Michael Quinn Robyn Saw Richard Scolyer Kerwin Shannon Andrew Spillane onathan Stretch Maria Synott John Thompson James Wilmott Hikmat Al-Ahmadie Timothy A. Chan Ronald Ghossein Anuradha Gopalan Douglas A. Levine Victor Reuter Samuel Singer Bhuvanesh Singh Nguyen Viet Tien Thomas Broudy Cyrus Mirsaidi Praveen Nair Paul Drwiega Judy Miller Jennifer Smith Howard Zaren Joong-Won Park Nguyen Phi Hung Electron Kebebew W. Marston Linehan Adam R. Metwalli Karel Pacak Peter A. Pinto Mark Schiffman Laura S. Schmidt Cathy D. Vocke Nicolas Wentzensen Robert Worrell Hannah Yang Marc Moncrieff Chandra Goparaju Jonathan Melamed Harvey Pass Natalia Botnariuc Irina Caraman Mircea Cernat Inga Chemencedji Adrian Clipca Serghei Doruc Ghenadie Gorincioi Sergiu Mura Maria Pirtac Irina Stancul Diana Tcaciuc Monique Albert Iakovina Alexopoulou Angel Arnaout John Bartlett Jay Engel Sebastien Gilbert Jeremy Parfitt Harman Sekhon George Thomas Doris M. Rassl Robert C. Rintoul Carlo Bifulco Raina Tamakawa Walter Urba Nicholas Hayward Henri Timmers Anna Antenucci Francesco Facciolo Gianluca Grazi Mirella Marino Roberta Merola Ronald de Krijger Anne-Paule Gimenez-Roqueplo Alain Piché Simone Chevalier Ginette McKercher Kivanc Birsoy Gene Barnett Cathy Brewer Carol Farver Theresa Naska Nathan A. Pennell Daniel Raymond Cathy Schilero Kathy Smolenski Felicia Williams Carl Morrison Jeffrey A. Borgia Michael J. Liptay Mark Pool Christopher W. Seder Kerstin Junker Larsson Omberg Mikhail Dinkin George Manikhas 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 Bahavna Kumar James Lang Norman L. Lehman Randy Mandt Phuong Nguyen Robert Pilarski Karan Rai Lynn Schoenfield Kelly Senecal Paul Wakely Paul Hansen Ronald Lechan James Powers Arthur Tischler William E. Grizzle Katherine C. Sexton Alison Kastl Joel Henderson Sima Porten Jens Waldmann Martin Fassnacht Sylvia L. Asa Dirk Schadendorf Marta Couce Markus Graefen Hartwig Huland Guido Sauter Thorsten Schlomm Ronald Simon Pierre Tennstedt Oluwole Olabode Mark Nelson Oliver Bathe Peter R. Carroll June M. Chan Philip Disaia Pat Glenn Robin K. Kelley Charles N. Landen Joanna Phillips Michael Prados Jeffry Simko Karen Smith-McCune Scott VandenBerg Kevin Roggin Ashley Fehrenbach Ady Kendler Suzanne Sifri Ruth Steele Antonio Jimeno Francis Carey Ian Forgie Massimo Mannelli Michael Carney Brenda Hernandez Benito Campos Christel Herold-Mende Christin Jungk Andreas Unterberg Andreas von Deimling Aaron Bossler Joseph Galbraith Laura Jacobus Michael Knudson Tina Knutson Deqin Ma Mohammed Milhem Rita Sigmund Andrew K. Godwin Rashna Madan Howard G. Rosenthal Clement Adebamowo Sally N. Adebamowo Alex Boussioutas David Beer Thomas Giordano Anne-Marie Mes-Masson Fred Saad Therese Bocklage Lisa Landrum Robert Mannel Kathleen Moore Katherine Moxley Russel Postier Joan Walker Rosemary Zuna Michael Feldman Federico Valdivieso Rajiv Dhir James Luketich Edna M. Mora Pinero Mario Quintero-Aguilo Carlos Gilberto Carlotti, Jr. Jose Sebastião Dos Santos Rafael Kemp Ajith Sankarankuty Daniela Tirapelli James Catto Kathy Agnew Elizabeth Swisher Jenette Creaney Bruce Robinson Carl Simon Shelley Eryn M. Godwin Sara Kendall Cassaundra Shipman Carol Bradford Thomas Carey Andrea Haddad Jeffey Moyer Lisa Peterson Mark Prince Laura Rozek Gregory Wolf Rayleen Bowman Kwun M. Fong Ian Yang Robert Korst W. Kimryn Rathmell J. Leigh Fantacone-Campbell Jeffrey A. Hooke Albert J. Kovatich Craig D. Shriver John DiPersio Bettina Drake Ramaswamy Govindan Sharon Heath Timothy Ley Brian Van Tine Peter Westervelt Mark A. Rubin Jung Il Lee Natália D. Aredes Armaz Mariamidze |
spellingShingle |
Joshua D. Campbell Christina Yau Reanne Bowlby Yuexin Liu Kevin Brennan Huihui Fan Alison M. Taylor Chen Wang Vonn Walter Rehan Akbani Lauren Averett Byers Chad J. Creighton Cristian Coarfa Juliann Shih Andrew D. Cherniack Olivier Gevaert Marcos Prunello Hui Shen Pavana Anur Jianhong Chen Hui Cheng D. Neil Hayes Susan Bullman Chandra Sekhar Pedamallu Akinyemi I. Ojesina Sara Sadeghi Karen L. Mungall A. Gordon Robertson Christopher Benz Andre Schultz Rupa S. Kanchi Carl M. Gay Apurva Hegde Lixia Diao Jing Wang Wencai Ma Pavel Sumazin Hua-Sheng Chiu Ting-Wen Chen Preethi Gunaratne Larry Donehower Janet S. Rader Rosemary Zuna Hikmat Al-Ahmadie Alexander J. Lazar Elsa R. Flores Kenneth Y. Tsai Jane H. Zhou Anil K. Rustgi Esther Drill Ronglei Shen Christopher K. Wong Joshua M. Stuart Peter W. Laird Katherine A. Hoadley John N. Weinstein Myron Peto Curtis R. Pickering Zhong Chen Carter Van Waes Samantha J. Caesar-Johnson John A. Demchok Ina Felau Melpomeni Kasapi Martin L. Ferguson Carolyn M. Hutter Heidi J. Sofia Roy Tarnuzzer Zhining Wang Liming Yang Jean C. Zenklusen Jiashan (Julia) Zhang Sudha Chudamani Jia Liu Laxmi Lolla Rashi Naresh Todd Pihl Qiang Sun Yunhu Wan Ye Wu Juok Cho Timothy DeFreitas Scott Frazer Nils Gehlenborg Gad Getz David I. Heiman Jaegil Kim Michael S. Lawrence 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 Yuexin Liu Michael Miller Sheila Reynolds Ilya Shmulevich Vesteinn Thorsson Wei Zhang Rehan Akbani Bradley M. Broom Apurva M. Hegde Zhenlin Ju Rupa S. Kanchi Anil Korkut Jun Li Han Liang Shiyun Ling Wenbin Liu Yiling Lu Gordon B. Mills Kwok-Shing Ng Arvind Rao Michael Ryan Jing Wang John N. Weinstein Jiexin Zhang Adam Abeshouse Joshua Armenia Debyani Chakravarty Walid K. Chatila Ino de Bruijn Jianjiong Gao Benjamin E. Gross Zachary J. Heins Ritika Kundra Konnor La Marc Ladanyi Augustin Luna Moriah G. Nissan Angelica Ochoa Sarah M. Phillips Ed Reznik Francisco Sanchez-Vega Chris Sander Nikolaus Schultz Robert Sheridan S. Onur Sumer Yichao Sun Barry S. Taylor Jioajiao Wang Hongxin Zhang Pavana Anur Myron Peto Paul Spellman Christopher Benz Joshua M. Stuart Christopher K. Wong Christina Yau D. Neil Hayes Joel S. Parker Matthew D. Wilkerson Adrian Ally Miruna Balasundaram Reanne Bowlby Denise Brooks Rebecca Carlsen Eric Chuah Noreen Dhalla Robert Holt Steven J.M. Jones Katayoon Kasaian Darlene Lee Yussanne Ma Marco A. Marra Michael Mayo Richard A. Moore Andrew J. Mungall Karen Mungall A. Gordon Robertson Sara Sadeghi Jacqueline E. Schein Payal Sipahimalani Angela Tam Nina Thiessen Kane Tse Tina Wong Ashton C. Berger Rameen Beroukhim Andrew D. Cherniack Carrie Cibulskis Stacey B. Gabriel Galen F. Gao Gavin Ha Matthew Meyerson Steven E. Schumacher Juliann Shih Melanie H. Kucherlapati Raju S. Kucherlapati Stephen Baylin Leslie Cope Ludmila Danilova Moiz S. Bootwalla Phillip H. Lai Dennis T. Maglinte David J. Van Den Berg Daniel J. Weisenberger J. Todd Auman Saianand Balu Tom Bodenheimer Cheng Fan Katherine A. Hoadley Alan P. Hoyle Stuart R. Jefferys Corbin D. Jones Shaowu Meng Piotr A. Mieczkowski Lisle E. Mose Amy H. Perou Charles M. Perou Jeffrey Roach Yan Shi Janae V. Simons Tara Skelly Matthew G. Soloway Donghui Tan Umadevi Veluvolu Huihui Fan Toshinori Hinoue Peter W. Laird Hui Shen Wanding Zhou Michelle Bellair Kyle Chang Kyle Covington Chad J. Creighton Huyen Dinh HarshaVardhan Doddapaneni Lawrence A. Donehower Jennifer Drummond Richard A. Gibbs Robert Glenn Walker Hale Yi Han Jianhong Hu Viktoriya Korchina Sandra Lee Lora Lewis Wei Li Xiuping Liu Margaret Morgan Donna Morton Donna Muzny Jireh Santibanez Margi Sheth Eve Shinbrot Linghua Wang Min Wang David A. Wheeler Liu Xi Fengmei Zhao Julian Hess Elizabeth L. Appelbaum Matthew Bailey Matthew G. Cordes Li Ding Catrina C. Fronick Lucinda A. Fulton Robert S. Fulton Cyriac Kandoth Elaine R. Mardis Michael D. McLellan Christopher A. Miller Heather K. Schmidt Richard K. Wilson Daniel Crain Erin Curley Johanna Gardner Kevin Lau David Mallery Scott Morris Joseph Paulauskis Robert Penny Candace Shelton Troy Shelton Mark Sherman Eric Thompson Peggy Yena Jay Bowen Julie M. Gastier-Foster Mark Gerken Kristen M. Leraas Tara M. Lichtenberg Nilsa C. Ramirez Lisa Wise Erik Zmuda Niall Corcoran Tony Costello Christopher Hovens Andre L. Carvalho Ana C. de Carvalho José H. Fregnani Adhemar Longatto-Filho Rui M. Reis Cristovam Scapulatempo-Neto Henrique C.S. Silveira Daniel O. Vidal Andrew Burnette Jennifer Eschbacher Beth Hermes Ardene Noss Rosy Singh Matthew L. Anderson Patricia D. Castro Michael Ittmann David Huntsman Bernard Kohl Xuan Le Richard Thorp Chris Andry Elizabeth R. Duffy Vladimir Lyadov Oxana Paklina Galiya Setdikova Alexey Shabunin Mikhail Tavobilov Christopher McPherson Ronald Warnick Ross Berkowitz Daniel Cramer Colleen Feltmate Neil Horowitz Adam Kibel Michael Muto Chandrajit P. Raut Andrei Malykh Jill S. Barnholtz-Sloan Wendi Barrett Karen Devine Jordonna Fulop Quinn T. Ostrom Kristen Shimmel Yingli Wolinsky Andrew E. Sloan Agostino De Rose Felice Giuliante Marc Goodman Beth Y. Karlan Curt H. Hagedorn John Eckman Jodi Harr Jerome Myers Kelinda Tucker Leigh Anne Zach Brenda Deyarmin Hai Hu Leonid Kvecher Caroline Larson Richard J. Mural Stella Somiari Ales Vicha Tomas Zelinka Joseph Bennett Mary Iacocca Brenda Rabeno Patricia Swanson Mathieu Latour Louis Lacombe Bernard Têtu Alain Bergeron Mary McGraw Susan M. Staugaitis John Chabot Hanina Hibshoosh Antonia Sepulveda Tao Su Timothy Wang Olga Potapova Olga Voronina Laurence Desjardins Odette Mariani Sergio Roman-Roman Xavier Sastre Marc-Henri Stern Feixiong Cheng Sabina Signoretti Andrew Berchuck Darell Bigner Eric Lipp Jeffrey Marks Shannon McCall Roger McLendon Angeles Secord Alexis Sharp Madhusmita Behera Daniel J. Brat Amy Chen Keith Delman Seth Force Fadlo Khuri Kelly Magliocca Shishir Maithel Jeffrey J. Olson Taofeek Owonikoko Alan Pickens Suresh Ramalingam Dong M. Shin Gabriel Sica Erwin G. Van Meir Hongzheng Zhang Wil Eijckenboom Ad Gillis Esther Korpershoek Leendert Looijenga Wolter Oosterhuis Hans Stoop Kim E. van Kessel Ellen C. Zwarthoff Chiara Calatozzolo Lucia Cuppini Stefania Cuzzubbo Francesco DiMeco Gaetano Finocchiaro Luca Mattei Alessandro Perin Bianca Pollo Chu Chen John Houck Pawadee Lohavanichbutr Arndt Hartmann Christine Stoehr Robert Stoehr Helge Taubert Sven Wach Bernd Wullich Witold Kycler Dawid Murawa Maciej Wiznerowicz Ki Chung W. Jeffrey Edenfield Julie Martin Eric Baudin Glenn Bubley Raphael Bueno Assunta De Rienzo William G. Richards Steven Kalkanis Tom Mikkelsen Houtan Noushmehr Lisa Scarpace Nicolas Girard Marta Aymerich Elias Campo Eva Giné Armando López Guillermo Nguyen Van Bang Phan Thi Hanh Bui Duc Phu Yufang Tang Howard Colman Kimberley Evason Peter R. Dottino John A. Martignetti Hani Gabra Hartmut Juhl Teniola Akeredolu Serghei Stepa Dave Hoon Keunsoo Ahn Koo Jeong Kang Felix Beuschlein Anne Breggia Michael Birrer Debra Bell Mitesh Borad Alan H. Bryce Erik Castle Vishal Chandan John Cheville John A. Copland Michael Farnell Thomas Flotte Nasra Giama Thai Ho Michael Kendrick Jean-Pierre Kocher Karla Kopp Catherine Moser David Nagorney Daniel O’Brien Brian Patrick O’Neill Tushar Patel Gloria Petersen Florencia Que Michael Rivera Lewis Roberts Robert Smallridge Thomas Smyrk Melissa Stanton R. Houston Thompson Michael Torbenson Ju Dong Yang Lizhi Zhang Fadi Brimo Jaffer A. Ajani Ana Maria Angulo Gonzalez Carmen Behrens Jolanta Bondaruk Russell Broaddus Bogdan Czerniak Bita Esmaeli Junya Fujimoto Jeffrey Gershenwald Charles Guo Alexander J. Lazar Christopher Logothetis Funda Meric-Bernstam Cesar Moran Lois Ramondetta David Rice Anil Sood Pheroze Tamboli Timothy Thompson Patricia Troncoso Anne Tsao Ignacio Wistuba Candace Carter Lauren Haydu Peter Hersey Valerie Jakrot Hojabr Kakavand Richard Kefford Kenneth Lee Georgina Long Graham Mann Michael Quinn Robyn Saw Richard Scolyer Kerwin Shannon Andrew Spillane onathan Stretch Maria Synott John Thompson James Wilmott Hikmat Al-Ahmadie Timothy A. Chan Ronald Ghossein Anuradha Gopalan Douglas A. Levine Victor Reuter Samuel Singer Bhuvanesh Singh Nguyen Viet Tien Thomas Broudy Cyrus Mirsaidi Praveen Nair Paul Drwiega Judy Miller Jennifer Smith Howard Zaren Joong-Won Park Nguyen Phi Hung Electron Kebebew W. Marston Linehan Adam R. Metwalli Karel Pacak Peter A. Pinto Mark Schiffman Laura S. Schmidt Cathy D. Vocke Nicolas Wentzensen Robert Worrell Hannah Yang Marc Moncrieff Chandra Goparaju Jonathan Melamed Harvey Pass Natalia Botnariuc Irina Caraman Mircea Cernat Inga Chemencedji Adrian Clipca Serghei Doruc Ghenadie Gorincioi Sergiu Mura Maria Pirtac Irina Stancul Diana Tcaciuc Monique Albert Iakovina Alexopoulou Angel Arnaout John Bartlett Jay Engel Sebastien Gilbert Jeremy Parfitt Harman Sekhon George Thomas Doris M. Rassl Robert C. Rintoul Carlo Bifulco Raina Tamakawa Walter Urba Nicholas Hayward Henri Timmers Anna Antenucci Francesco Facciolo Gianluca Grazi Mirella Marino Roberta Merola Ronald de Krijger Anne-Paule Gimenez-Roqueplo Alain Piché Simone Chevalier Ginette McKercher Kivanc Birsoy Gene Barnett Cathy Brewer Carol Farver Theresa Naska Nathan A. Pennell Daniel Raymond Cathy Schilero Kathy Smolenski Felicia Williams Carl Morrison Jeffrey A. Borgia Michael J. Liptay Mark Pool Christopher W. Seder Kerstin Junker Larsson Omberg Mikhail Dinkin George Manikhas 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 Bahavna Kumar James Lang Norman L. Lehman Randy Mandt Phuong Nguyen Robert Pilarski Karan Rai Lynn Schoenfield Kelly Senecal Paul Wakely Paul Hansen Ronald Lechan James Powers Arthur Tischler William E. Grizzle Katherine C. Sexton Alison Kastl Joel Henderson Sima Porten Jens Waldmann Martin Fassnacht Sylvia L. Asa Dirk Schadendorf Marta Couce Markus Graefen Hartwig Huland Guido Sauter Thorsten Schlomm Ronald Simon Pierre Tennstedt Oluwole Olabode Mark Nelson Oliver Bathe Peter R. Carroll June M. Chan Philip Disaia Pat Glenn Robin K. Kelley Charles N. Landen Joanna Phillips Michael Prados Jeffry Simko Karen Smith-McCune Scott VandenBerg Kevin Roggin Ashley Fehrenbach Ady Kendler Suzanne Sifri Ruth Steele Antonio Jimeno Francis Carey Ian Forgie Massimo Mannelli Michael Carney Brenda Hernandez Benito Campos Christel Herold-Mende Christin Jungk Andreas Unterberg Andreas von Deimling Aaron Bossler Joseph Galbraith Laura Jacobus Michael Knudson Tina Knutson Deqin Ma Mohammed Milhem Rita Sigmund Andrew K. Godwin Rashna Madan Howard G. Rosenthal Clement Adebamowo Sally N. Adebamowo Alex Boussioutas David Beer Thomas Giordano Anne-Marie Mes-Masson Fred Saad Therese Bocklage Lisa Landrum Robert Mannel Kathleen Moore Katherine Moxley Russel Postier Joan Walker Rosemary Zuna Michael Feldman Federico Valdivieso Rajiv Dhir James Luketich Edna M. Mora Pinero Mario Quintero-Aguilo Carlos Gilberto Carlotti, Jr. Jose Sebastião Dos Santos Rafael Kemp Ajith Sankarankuty Daniela Tirapelli James Catto Kathy Agnew Elizabeth Swisher Jenette Creaney Bruce Robinson Carl Simon Shelley Eryn M. Godwin Sara Kendall Cassaundra Shipman Carol Bradford Thomas Carey Andrea Haddad Jeffey Moyer Lisa Peterson Mark Prince Laura Rozek Gregory Wolf Rayleen Bowman Kwun M. Fong Ian Yang Robert Korst W. Kimryn Rathmell J. Leigh Fantacone-Campbell Jeffrey A. Hooke Albert J. Kovatich Craig D. Shriver John DiPersio Bettina Drake Ramaswamy Govindan Sharon Heath Timothy Ley Brian Van Tine Peter Westervelt Mark A. Rubin Jung Il Lee Natália D. Aredes Armaz Mariamidze Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas Cell Reports |
author_facet |
Joshua D. Campbell Christina Yau Reanne Bowlby Yuexin Liu Kevin Brennan Huihui Fan Alison M. Taylor Chen Wang Vonn Walter Rehan Akbani Lauren Averett Byers Chad J. Creighton Cristian Coarfa Juliann Shih Andrew D. Cherniack Olivier Gevaert Marcos Prunello Hui Shen Pavana Anur Jianhong Chen Hui Cheng D. Neil Hayes Susan Bullman Chandra Sekhar Pedamallu Akinyemi I. Ojesina Sara Sadeghi Karen L. Mungall A. Gordon Robertson Christopher Benz Andre Schultz Rupa S. Kanchi Carl M. Gay Apurva Hegde Lixia Diao Jing Wang Wencai Ma Pavel Sumazin Hua-Sheng Chiu Ting-Wen Chen Preethi Gunaratne Larry Donehower Janet S. Rader Rosemary Zuna Hikmat Al-Ahmadie Alexander J. Lazar Elsa R. Flores Kenneth Y. Tsai Jane H. Zhou Anil K. Rustgi Esther Drill Ronglei Shen Christopher K. Wong Joshua M. Stuart Peter W. Laird Katherine A. Hoadley John N. Weinstein Myron Peto Curtis R. Pickering Zhong Chen Carter Van Waes Samantha J. Caesar-Johnson John A. Demchok Ina Felau Melpomeni Kasapi Martin L. Ferguson Carolyn M. Hutter Heidi J. Sofia Roy Tarnuzzer Zhining Wang Liming Yang Jean C. Zenklusen Jiashan (Julia) Zhang Sudha Chudamani Jia Liu Laxmi Lolla Rashi Naresh Todd Pihl Qiang Sun Yunhu Wan Ye Wu Juok Cho Timothy DeFreitas Scott Frazer Nils Gehlenborg Gad Getz David I. Heiman Jaegil Kim Michael S. Lawrence 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 Yuexin Liu Michael Miller Sheila Reynolds Ilya Shmulevich Vesteinn Thorsson Wei Zhang Rehan Akbani Bradley M. Broom Apurva M. Hegde Zhenlin Ju Rupa S. Kanchi Anil Korkut Jun Li Han Liang Shiyun Ling Wenbin Liu Yiling Lu Gordon B. Mills Kwok-Shing Ng Arvind Rao Michael Ryan Jing Wang John N. Weinstein Jiexin Zhang Adam Abeshouse Joshua Armenia Debyani Chakravarty Walid K. Chatila Ino de Bruijn Jianjiong Gao Benjamin E. Gross Zachary J. Heins Ritika Kundra Konnor La Marc Ladanyi Augustin Luna Moriah G. Nissan Angelica Ochoa Sarah M. Phillips Ed Reznik Francisco Sanchez-Vega Chris Sander Nikolaus Schultz Robert Sheridan S. Onur Sumer Yichao Sun Barry S. Taylor Jioajiao Wang Hongxin Zhang Pavana Anur Myron Peto Paul Spellman Christopher Benz Joshua M. Stuart Christopher K. Wong Christina Yau D. Neil Hayes Joel S. Parker Matthew D. Wilkerson Adrian Ally Miruna Balasundaram Reanne Bowlby Denise Brooks Rebecca Carlsen Eric Chuah Noreen Dhalla Robert Holt Steven J.M. Jones Katayoon Kasaian Darlene Lee Yussanne Ma Marco A. Marra Michael Mayo Richard A. Moore Andrew J. Mungall Karen Mungall A. Gordon Robertson Sara Sadeghi Jacqueline E. Schein Payal Sipahimalani Angela Tam Nina Thiessen Kane Tse Tina Wong Ashton C. Berger Rameen Beroukhim Andrew D. Cherniack Carrie Cibulskis Stacey B. Gabriel Galen F. Gao Gavin Ha Matthew Meyerson Steven E. Schumacher Juliann Shih Melanie H. Kucherlapati Raju S. Kucherlapati Stephen Baylin Leslie Cope Ludmila Danilova Moiz S. Bootwalla Phillip H. Lai Dennis T. Maglinte David J. Van Den Berg Daniel J. Weisenberger J. Todd Auman Saianand Balu Tom Bodenheimer Cheng Fan Katherine A. Hoadley Alan P. Hoyle Stuart R. Jefferys Corbin D. Jones Shaowu Meng Piotr A. Mieczkowski Lisle E. Mose Amy H. Perou Charles M. Perou Jeffrey Roach Yan Shi Janae V. Simons Tara Skelly Matthew G. Soloway Donghui Tan Umadevi Veluvolu Huihui Fan Toshinori Hinoue Peter W. Laird Hui Shen Wanding Zhou Michelle Bellair Kyle Chang Kyle Covington Chad J. Creighton Huyen Dinh HarshaVardhan Doddapaneni Lawrence A. Donehower Jennifer Drummond Richard A. Gibbs Robert Glenn Walker Hale Yi Han Jianhong Hu Viktoriya Korchina Sandra Lee Lora Lewis Wei Li Xiuping Liu Margaret Morgan Donna Morton Donna Muzny Jireh Santibanez Margi Sheth Eve Shinbrot Linghua Wang Min Wang David A. Wheeler Liu Xi Fengmei Zhao Julian Hess Elizabeth L. Appelbaum Matthew Bailey Matthew G. Cordes Li Ding Catrina C. Fronick Lucinda A. Fulton Robert S. Fulton Cyriac Kandoth Elaine R. Mardis Michael D. McLellan Christopher A. Miller Heather K. Schmidt Richard K. Wilson Daniel Crain Erin Curley Johanna Gardner Kevin Lau David Mallery Scott Morris Joseph Paulauskis Robert Penny Candace Shelton Troy Shelton Mark Sherman Eric Thompson Peggy Yena Jay Bowen Julie M. Gastier-Foster Mark Gerken Kristen M. Leraas Tara M. Lichtenberg Nilsa C. Ramirez Lisa Wise Erik Zmuda Niall Corcoran Tony Costello Christopher Hovens Andre L. Carvalho Ana C. de Carvalho José H. Fregnani Adhemar Longatto-Filho Rui M. Reis Cristovam Scapulatempo-Neto Henrique C.S. Silveira Daniel O. Vidal Andrew Burnette Jennifer Eschbacher Beth Hermes Ardene Noss Rosy Singh Matthew L. Anderson Patricia D. Castro Michael Ittmann David Huntsman Bernard Kohl Xuan Le Richard Thorp Chris Andry Elizabeth R. Duffy Vladimir Lyadov Oxana Paklina Galiya Setdikova Alexey Shabunin Mikhail Tavobilov Christopher McPherson Ronald Warnick Ross Berkowitz Daniel Cramer Colleen Feltmate Neil Horowitz Adam Kibel Michael Muto Chandrajit P. Raut Andrei Malykh Jill S. Barnholtz-Sloan Wendi Barrett Karen Devine Jordonna Fulop Quinn T. Ostrom Kristen Shimmel Yingli Wolinsky Andrew E. Sloan Agostino De Rose Felice Giuliante Marc Goodman Beth Y. Karlan Curt H. Hagedorn John Eckman Jodi Harr Jerome Myers Kelinda Tucker Leigh Anne Zach Brenda Deyarmin Hai Hu Leonid Kvecher Caroline Larson Richard J. Mural Stella Somiari Ales Vicha Tomas Zelinka Joseph Bennett Mary Iacocca Brenda Rabeno Patricia Swanson Mathieu Latour Louis Lacombe Bernard Têtu Alain Bergeron Mary McGraw Susan M. Staugaitis John Chabot Hanina Hibshoosh Antonia Sepulveda Tao Su Timothy Wang Olga Potapova Olga Voronina Laurence Desjardins Odette Mariani Sergio Roman-Roman Xavier Sastre Marc-Henri Stern Feixiong Cheng Sabina Signoretti Andrew Berchuck Darell Bigner Eric Lipp Jeffrey Marks Shannon McCall Roger McLendon Angeles Secord Alexis Sharp Madhusmita Behera Daniel J. Brat Amy Chen Keith Delman Seth Force Fadlo Khuri Kelly Magliocca Shishir Maithel Jeffrey J. Olson Taofeek Owonikoko Alan Pickens Suresh Ramalingam Dong M. Shin Gabriel Sica Erwin G. Van Meir Hongzheng Zhang Wil Eijckenboom Ad Gillis Esther Korpershoek Leendert Looijenga Wolter Oosterhuis Hans Stoop Kim E. van Kessel Ellen C. Zwarthoff Chiara Calatozzolo Lucia Cuppini Stefania Cuzzubbo Francesco DiMeco Gaetano Finocchiaro Luca Mattei Alessandro Perin Bianca Pollo Chu Chen John Houck Pawadee Lohavanichbutr Arndt Hartmann Christine Stoehr Robert Stoehr Helge Taubert Sven Wach Bernd Wullich Witold Kycler Dawid Murawa Maciej Wiznerowicz Ki Chung W. Jeffrey Edenfield Julie Martin Eric Baudin Glenn Bubley Raphael Bueno Assunta De Rienzo William G. Richards Steven Kalkanis Tom Mikkelsen Houtan Noushmehr Lisa Scarpace Nicolas Girard Marta Aymerich Elias Campo Eva Giné Armando López Guillermo Nguyen Van Bang Phan Thi Hanh Bui Duc Phu Yufang Tang Howard Colman Kimberley Evason Peter R. Dottino John A. Martignetti Hani Gabra Hartmut Juhl Teniola Akeredolu Serghei Stepa Dave Hoon Keunsoo Ahn Koo Jeong Kang Felix Beuschlein Anne Breggia Michael Birrer Debra Bell Mitesh Borad Alan H. Bryce Erik Castle Vishal Chandan John Cheville John A. Copland Michael Farnell Thomas Flotte Nasra Giama Thai Ho Michael Kendrick Jean-Pierre Kocher Karla Kopp Catherine Moser David Nagorney Daniel O’Brien Brian Patrick O’Neill Tushar Patel Gloria Petersen Florencia Que Michael Rivera Lewis Roberts Robert Smallridge Thomas Smyrk Melissa Stanton R. Houston Thompson Michael Torbenson Ju Dong Yang Lizhi Zhang Fadi Brimo Jaffer A. Ajani Ana Maria Angulo Gonzalez Carmen Behrens Jolanta Bondaruk Russell Broaddus Bogdan Czerniak Bita Esmaeli Junya Fujimoto Jeffrey Gershenwald Charles Guo Alexander J. Lazar Christopher Logothetis Funda Meric-Bernstam Cesar Moran Lois Ramondetta David Rice Anil Sood Pheroze Tamboli Timothy Thompson Patricia Troncoso Anne Tsao Ignacio Wistuba Candace Carter Lauren Haydu Peter Hersey Valerie Jakrot Hojabr Kakavand Richard Kefford Kenneth Lee Georgina Long Graham Mann Michael Quinn Robyn Saw Richard Scolyer Kerwin Shannon Andrew Spillane onathan Stretch Maria Synott John Thompson James Wilmott Hikmat Al-Ahmadie Timothy A. Chan Ronald Ghossein Anuradha Gopalan Douglas A. Levine Victor Reuter Samuel Singer Bhuvanesh Singh Nguyen Viet Tien Thomas Broudy Cyrus Mirsaidi Praveen Nair Paul Drwiega Judy Miller Jennifer Smith Howard Zaren Joong-Won Park Nguyen Phi Hung Electron Kebebew W. Marston Linehan Adam R. Metwalli Karel Pacak Peter A. Pinto Mark Schiffman Laura S. Schmidt Cathy D. Vocke Nicolas Wentzensen Robert Worrell Hannah Yang Marc Moncrieff Chandra Goparaju Jonathan Melamed Harvey Pass Natalia Botnariuc Irina Caraman Mircea Cernat Inga Chemencedji Adrian Clipca Serghei Doruc Ghenadie Gorincioi Sergiu Mura Maria Pirtac Irina Stancul Diana Tcaciuc Monique Albert Iakovina Alexopoulou Angel Arnaout John Bartlett Jay Engel Sebastien Gilbert Jeremy Parfitt Harman Sekhon George Thomas Doris M. Rassl Robert C. Rintoul Carlo Bifulco Raina Tamakawa Walter Urba Nicholas Hayward Henri Timmers Anna Antenucci Francesco Facciolo Gianluca Grazi Mirella Marino Roberta Merola Ronald de Krijger Anne-Paule Gimenez-Roqueplo Alain Piché Simone Chevalier Ginette McKercher Kivanc Birsoy Gene Barnett Cathy Brewer Carol Farver Theresa Naska Nathan A. Pennell Daniel Raymond Cathy Schilero Kathy Smolenski Felicia Williams Carl Morrison Jeffrey A. Borgia Michael J. Liptay Mark Pool Christopher W. Seder Kerstin Junker Larsson Omberg Mikhail Dinkin George Manikhas 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 Bahavna Kumar James Lang Norman L. Lehman Randy Mandt Phuong Nguyen Robert Pilarski Karan Rai Lynn Schoenfield Kelly Senecal Paul Wakely Paul Hansen Ronald Lechan James Powers Arthur Tischler William E. Grizzle Katherine C. Sexton Alison Kastl Joel Henderson Sima Porten Jens Waldmann Martin Fassnacht Sylvia L. Asa Dirk Schadendorf Marta Couce Markus Graefen Hartwig Huland Guido Sauter Thorsten Schlomm Ronald Simon Pierre Tennstedt Oluwole Olabode Mark Nelson Oliver Bathe Peter R. Carroll June M. Chan Philip Disaia Pat Glenn Robin K. Kelley Charles N. Landen Joanna Phillips Michael Prados Jeffry Simko Karen Smith-McCune Scott VandenBerg Kevin Roggin Ashley Fehrenbach Ady Kendler Suzanne Sifri Ruth Steele Antonio Jimeno Francis Carey Ian Forgie Massimo Mannelli Michael Carney Brenda Hernandez Benito Campos Christel Herold-Mende Christin Jungk Andreas Unterberg Andreas von Deimling Aaron Bossler Joseph Galbraith Laura Jacobus Michael Knudson Tina Knutson Deqin Ma Mohammed Milhem Rita Sigmund Andrew K. Godwin Rashna Madan Howard G. Rosenthal Clement Adebamowo Sally N. Adebamowo Alex Boussioutas David Beer Thomas Giordano Anne-Marie Mes-Masson Fred Saad Therese Bocklage Lisa Landrum Robert Mannel Kathleen Moore Katherine Moxley Russel Postier Joan Walker Rosemary Zuna Michael Feldman Federico Valdivieso Rajiv Dhir James Luketich Edna M. Mora Pinero Mario Quintero-Aguilo Carlos Gilberto Carlotti, Jr. Jose Sebastião Dos Santos Rafael Kemp Ajith Sankarankuty Daniela Tirapelli James Catto Kathy Agnew Elizabeth Swisher Jenette Creaney Bruce Robinson Carl Simon Shelley Eryn M. Godwin Sara Kendall Cassaundra Shipman Carol Bradford Thomas Carey Andrea Haddad Jeffey Moyer Lisa Peterson Mark Prince Laura Rozek Gregory Wolf Rayleen Bowman Kwun M. Fong Ian Yang Robert Korst W. Kimryn Rathmell J. Leigh Fantacone-Campbell Jeffrey A. Hooke Albert J. Kovatich Craig D. Shriver John DiPersio Bettina Drake Ramaswamy Govindan Sharon Heath Timothy Ley Brian Van Tine Peter Westervelt Mark A. Rubin Jung Il Lee Natália D. Aredes Armaz Mariamidze |
author_sort |
Joshua D. Campbell |
title |
Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas |
title_short |
Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas |
title_full |
Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas |
title_fullStr |
Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas |
title_full_unstemmed |
Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas |
title_sort |
genomic, pathway network, and immunologic features distinguishing squamous carcinomas |
publisher |
Elsevier |
series |
Cell Reports |
issn |
2211-1247 |
publishDate |
2018-04-01 |
description |
Summary: 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. : Campbell et al. reveal that squamous cell cancers from different tissue sites may be distinguished from other cancers and subclassified molecularly by recurrent alterations in chromosomes, DNA methylation, messenger and microRNA expression, or by mutations. These affect squamous cell pathways and programs that provide candidates for therapy. Keywords: genomics, transcriptomics, proteomics, head and neck squamous cell carcinoma, lung squamous cell carcinoma, esophageal squamous cell carcinoma, cervical squamous cell carcinoma, bladder carcinoma with squamous differentiation, human papillomavirus |
url |
http://www.sciencedirect.com/science/article/pii/S2211124718304248 |
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doaj-62174f6d8a374a8e85f73a2b8d94c01a2020-11-25T01:32:30ZengElsevierCell Reports2211-12472018-04-01231194212.e6Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous CarcinomasJoshua D. Campbell0Christina Yau1Reanne Bowlby2Yuexin Liu3Kevin Brennan4Huihui Fan5Alison M. Taylor6Chen Wang7Vonn Walter8Rehan Akbani9Lauren Averett Byers10Chad J. Creighton11Cristian Coarfa12Juliann Shih13Andrew D. Cherniack14Olivier Gevaert15Marcos Prunello16Hui Shen17Pavana Anur18Jianhong Chen19Hui Cheng20D. Neil Hayes21Susan Bullman22Chandra Sekhar Pedamallu23Akinyemi I. Ojesina24Sara Sadeghi25Karen L. Mungall26A. Gordon Robertson27Christopher Benz28Andre Schultz29Rupa S. Kanchi30Carl M. Gay31Apurva Hegde32Lixia Diao33Jing Wang34Wencai Ma35Pavel Sumazin36Hua-Sheng Chiu37Ting-Wen Chen38Preethi Gunaratne39Larry Donehower40Janet S. Rader41Rosemary Zuna42Hikmat Al-Ahmadie43Alexander J. Lazar44Elsa R. Flores45Kenneth Y. Tsai46Jane H. Zhou47Anil K. Rustgi48Esther Drill49Ronglei Shen50Christopher K. Wong51Joshua M. Stuart52Peter W. Laird53Katherine A. Hoadley54John N. Weinstein55Myron Peto56Curtis R. Pickering57Zhong Chen58Carter Van Waes59Samantha J. Caesar-JohnsonJohn A. DemchokIna FelauMelpomeni KasapiMartin L. FergusonCarolyn M. HutterHeidi J. SofiaRoy TarnuzzerZhining WangLiming YangJean C. ZenklusenJiashan (Julia) ZhangSudha ChudamaniJia LiuLaxmi LollaRashi NareshTodd PihlQiang SunYunhu WanYe WuJuok ChoTimothy DeFreitasScott FrazerNils GehlenborgGad GetzDavid I. HeimanJaegil KimMichael S. LawrencePei LinSam MeierMichael S. NobleGordon SaksenaDoug VoetHailei ZhangBrady BernardNyasha ChambweVarsha DhankaniTheo KnijnenburgRoger KramerKalle LeinonenYuexin LiuMichael MillerSheila ReynoldsIlya ShmulevichVesteinn ThorssonWei ZhangRehan AkbaniBradley M. BroomApurva M. HegdeZhenlin JuRupa S. KanchiAnil KorkutJun LiHan LiangShiyun LingWenbin LiuYiling LuGordon B. MillsKwok-Shing NgArvind RaoMichael RyanJing WangJohn N. WeinsteinJiexin ZhangAdam AbeshouseJoshua ArmeniaDebyani ChakravartyWalid K. ChatilaIno de BruijnJianjiong GaoBenjamin E. GrossZachary J. HeinsRitika KundraKonnor LaMarc LadanyiAugustin LunaMoriah G. NissanAngelica OchoaSarah M. PhillipsEd ReznikFrancisco Sanchez-VegaChris SanderNikolaus SchultzRobert SheridanS. Onur SumerYichao SunBarry S. TaylorJioajiao WangHongxin ZhangPavana AnurMyron PetoPaul SpellmanChristopher BenzJoshua M. StuartChristopher K. WongChristina YauD. Neil HayesJoel S. ParkerMatthew D. WilkersonAdrian AllyMiruna BalasundaramReanne BowlbyDenise BrooksRebecca CarlsenEric ChuahNoreen DhallaRobert HoltSteven J.M. JonesKatayoon KasaianDarlene LeeYussanne MaMarco A. MarraMichael MayoRichard A. MooreAndrew J. MungallKaren MungallA. Gordon RobertsonSara SadeghiJacqueline E. ScheinPayal SipahimalaniAngela TamNina ThiessenKane TseTina WongAshton C. BergerRameen BeroukhimAndrew D. CherniackCarrie CibulskisStacey B. GabrielGalen F. GaoGavin HaMatthew MeyersonSteven E. SchumacherJuliann ShihMelanie H. KucherlapatiRaju S. KucherlapatiStephen BaylinLeslie CopeLudmila DanilovaMoiz S. BootwallaPhillip H. LaiDennis T. MaglinteDavid J. Van Den BergDaniel J. WeisenbergerJ. Todd AumanSaianand BaluTom BodenheimerCheng FanKatherine A. HoadleyAlan P. HoyleStuart R. JefferysCorbin D. JonesShaowu MengPiotr A. MieczkowskiLisle E. MoseAmy H. PerouCharles M. PerouJeffrey RoachYan ShiJanae V. SimonsTara SkellyMatthew G. SolowayDonghui TanUmadevi VeluvoluHuihui FanToshinori HinouePeter W. LairdHui ShenWanding ZhouMichelle BellairKyle ChangKyle CovingtonChad J. CreightonHuyen DinhHarshaVardhan DoddapaneniLawrence A. DonehowerJennifer DrummondRichard A. GibbsRobert GlennWalker HaleYi HanJianhong HuViktoriya KorchinaSandra LeeLora LewisWei LiXiuping LiuMargaret MorganDonna MortonDonna MuznyJireh SantibanezMargi ShethEve ShinbrotLinghua WangMin WangDavid A. WheelerLiu XiFengmei ZhaoJulian HessElizabeth L. AppelbaumMatthew BaileyMatthew G. CordesLi DingCatrina C. FronickLucinda A. FultonRobert S. FultonCyriac KandothElaine R. MardisMichael D. McLellanChristopher A. MillerHeather K. SchmidtRichard K. WilsonDaniel CrainErin CurleyJohanna GardnerKevin LauDavid MalleryScott MorrisJoseph PaulauskisRobert PennyCandace SheltonTroy SheltonMark ShermanEric ThompsonPeggy YenaJay BowenJulie M. Gastier-FosterMark GerkenKristen M. LeraasTara M. LichtenbergNilsa C. RamirezLisa WiseErik ZmudaNiall CorcoranTony CostelloChristopher HovensAndre L. CarvalhoAna C. de CarvalhoJosé H. FregnaniAdhemar Longatto-FilhoRui M. ReisCristovam Scapulatempo-NetoHenrique C.S. SilveiraDaniel O. VidalAndrew BurnetteJennifer EschbacherBeth HermesArdene NossRosy SinghMatthew L. AndersonPatricia D. CastroMichael IttmannDavid HuntsmanBernard KohlXuan LeRichard ThorpChris AndryElizabeth R. DuffyVladimir LyadovOxana PaklinaGaliya SetdikovaAlexey ShabuninMikhail TavobilovChristopher McPhersonRonald WarnickRoss BerkowitzDaniel CramerColleen FeltmateNeil HorowitzAdam KibelMichael MutoChandrajit P. RautAndrei MalykhJill S. Barnholtz-SloanWendi BarrettKaren DevineJordonna FulopQuinn T. OstromKristen ShimmelYingli WolinskyAndrew E. SloanAgostino De RoseFelice GiulianteMarc GoodmanBeth Y. KarlanCurt H. HagedornJohn EckmanJodi HarrJerome MyersKelinda TuckerLeigh Anne ZachBrenda DeyarminHai HuLeonid KvecherCaroline LarsonRichard J. MuralStella SomiariAles VichaTomas ZelinkaJoseph BennettMary IacoccaBrenda RabenoPatricia SwansonMathieu LatourLouis LacombeBernard TêtuAlain BergeronMary McGrawSusan M. StaugaitisJohn ChabotHanina HibshooshAntonia SepulvedaTao SuTimothy WangOlga PotapovaOlga VoroninaLaurence DesjardinsOdette MarianiSergio Roman-RomanXavier SastreMarc-Henri SternFeixiong ChengSabina SignorettiAndrew BerchuckDarell BignerEric LippJeffrey MarksShannon McCallRoger McLendonAngeles SecordAlexis SharpMadhusmita BeheraDaniel J. BratAmy ChenKeith DelmanSeth ForceFadlo KhuriKelly MaglioccaShishir MaithelJeffrey J. OlsonTaofeek OwonikokoAlan PickensSuresh RamalingamDong M. ShinGabriel SicaErwin G. Van MeirHongzheng ZhangWil EijckenboomAd GillisEsther KorpershoekLeendert LooijengaWolter OosterhuisHans StoopKim E. van KesselEllen C. ZwarthoffChiara CalatozzoloLucia CuppiniStefania CuzzubboFrancesco DiMecoGaetano FinocchiaroLuca MatteiAlessandro PerinBianca PolloChu ChenJohn HouckPawadee LohavanichbutrArndt HartmannChristine StoehrRobert StoehrHelge TaubertSven WachBernd WullichWitold KyclerDawid MurawaMaciej WiznerowiczKi ChungW. Jeffrey EdenfieldJulie MartinEric BaudinGlenn BubleyRaphael BuenoAssunta De RienzoWilliam G. RichardsSteven KalkanisTom MikkelsenHoutan NoushmehrLisa ScarpaceNicolas GirardMarta AymerichElias CampoEva GinéArmando López GuillermoNguyen Van BangPhan Thi HanhBui Duc PhuYufang TangHoward ColmanKimberley EvasonPeter R. DottinoJohn A. MartignettiHani GabraHartmut JuhlTeniola AkeredoluSerghei StepaDave HoonKeunsoo AhnKoo Jeong KangFelix BeuschleinAnne BreggiaMichael BirrerDebra BellMitesh BoradAlan H. BryceErik CastleVishal ChandanJohn ChevilleJohn A. CoplandMichael FarnellThomas FlotteNasra GiamaThai HoMichael KendrickJean-Pierre KocherKarla KoppCatherine MoserDavid NagorneyDaniel O’BrienBrian Patrick O’NeillTushar PatelGloria PetersenFlorencia QueMichael RiveraLewis RobertsRobert SmallridgeThomas SmyrkMelissa StantonR. Houston ThompsonMichael TorbensonJu Dong YangLizhi ZhangFadi BrimoJaffer A. AjaniAna Maria Angulo GonzalezCarmen BehrensJolanta BondarukRussell BroaddusBogdan CzerniakBita EsmaeliJunya FujimotoJeffrey GershenwaldCharles GuoAlexander J. LazarChristopher LogothetisFunda Meric-BernstamCesar MoranLois RamondettaDavid RiceAnil SoodPheroze TamboliTimothy ThompsonPatricia TroncosoAnne TsaoIgnacio WistubaCandace CarterLauren HayduPeter HerseyValerie JakrotHojabr KakavandRichard KeffordKenneth LeeGeorgina LongGraham MannMichael QuinnRobyn SawRichard ScolyerKerwin ShannonAndrew Spillaneonathan StretchMaria SynottJohn ThompsonJames WilmottHikmat Al-AhmadieTimothy A. ChanRonald GhosseinAnuradha GopalanDouglas A. LevineVictor ReuterSamuel SingerBhuvanesh SinghNguyen Viet TienThomas BroudyCyrus MirsaidiPraveen NairPaul DrwiegaJudy MillerJennifer SmithHoward ZarenJoong-Won ParkNguyen Phi HungElectron KebebewW. Marston LinehanAdam R. MetwalliKarel PacakPeter A. PintoMark SchiffmanLaura S. SchmidtCathy D. VockeNicolas WentzensenRobert WorrellHannah YangMarc MoncrieffChandra GoparajuJonathan MelamedHarvey PassNatalia BotnariucIrina CaramanMircea CernatInga ChemencedjiAdrian ClipcaSerghei DorucGhenadie GorincioiSergiu MuraMaria PirtacIrina StanculDiana TcaciucMonique AlbertIakovina AlexopoulouAngel ArnaoutJohn BartlettJay EngelSebastien GilbertJeremy ParfittHarman SekhonGeorge ThomasDoris M. RasslRobert C. RintoulCarlo BifulcoRaina TamakawaWalter UrbaNicholas HaywardHenri TimmersAnna AntenucciFrancesco FaccioloGianluca GraziMirella MarinoRoberta MerolaRonald de KrijgerAnne-Paule Gimenez-RoqueploAlain PichéSimone ChevalierGinette McKercherKivanc BirsoyGene BarnettCathy BrewerCarol FarverTheresa NaskaNathan A. PennellDaniel RaymondCathy SchileroKathy SmolenskiFelicia WilliamsCarl MorrisonJeffrey A. BorgiaMichael J. LiptayMark PoolChristopher W. SederKerstin JunkerLarsson OmbergMikhail DinkinGeorge ManikhasDomenico AlvaroMaria Consiglia BragazziVincenzo CardinaleGuido CarpinoEugenio GaudioDavid CheslaSandra CottinghamMichael DubinaFedor MoiseenkoRenumathy DhanasekaranKarl-Friedrich BeckerKlaus-Peter JanssenJulia Slotta-HuspeninaMohamed H. Abdel-RahmanDina AzizSue BellColleen M. CebullaAmy DavisRebecca DuellJ. Bradley ElderJoe HiltyBahavna KumarJames LangNorman L. LehmanRandy MandtPhuong NguyenRobert PilarskiKaran RaiLynn SchoenfieldKelly SenecalPaul WakelyPaul HansenRonald LechanJames PowersArthur TischlerWilliam E. GrizzleKatherine C. SextonAlison KastlJoel HendersonSima PortenJens WaldmannMartin FassnachtSylvia L. AsaDirk SchadendorfMarta CouceMarkus GraefenHartwig HulandGuido SauterThorsten SchlommRonald SimonPierre TennstedtOluwole OlabodeMark NelsonOliver BathePeter R. CarrollJune M. ChanPhilip DisaiaPat GlennRobin K. KelleyCharles N. LandenJoanna PhillipsMichael PradosJeffry SimkoKaren Smith-McCuneScott VandenBergKevin RogginAshley FehrenbachAdy KendlerSuzanne SifriRuth SteeleAntonio JimenoFrancis CareyIan ForgieMassimo MannelliMichael CarneyBrenda HernandezBenito CamposChristel Herold-MendeChristin JungkAndreas UnterbergAndreas von DeimlingAaron BosslerJoseph GalbraithLaura JacobusMichael KnudsonTina KnutsonDeqin MaMohammed MilhemRita SigmundAndrew K. GodwinRashna MadanHoward G. RosenthalClement AdebamowoSally N. AdebamowoAlex BoussioutasDavid BeerThomas GiordanoAnne-Marie Mes-MassonFred SaadTherese BocklageLisa LandrumRobert MannelKathleen MooreKatherine MoxleyRussel PostierJoan WalkerRosemary ZunaMichael FeldmanFederico ValdiviesoRajiv DhirJames LuketichEdna M. Mora PineroMario Quintero-AguiloCarlos Gilberto Carlotti, Jr.Jose Sebastião Dos SantosRafael KempAjith SankarankutyDaniela TirapelliJames CattoKathy AgnewElizabeth SwisherJenette CreaneyBruce RobinsonCarl Simon ShelleyEryn M. GodwinSara KendallCassaundra ShipmanCarol BradfordThomas CareyAndrea HaddadJeffey MoyerLisa PetersonMark PrinceLaura RozekGregory WolfRayleen BowmanKwun M. FongIan YangRobert KorstW. Kimryn RathmellJ. Leigh Fantacone-CampbellJeffrey A. HookeAlbert J. KovatichCraig D. ShriverJohn DiPersioBettina DrakeRamaswamy GovindanSharon HeathTimothy LeyBrian Van TinePeter WesterveltMark A. RubinJung Il LeeNatália D. AredesArmaz MariamidzeDepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Boston University School of Medicine, Boston, MA 02118, USADepartment of Surgery, University of California, San Francisco, San Francisco, CA 94115, USA; Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USACanada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, CanadaDepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USADepartment of Medicine-Biomedical Informatics Research, Stanford University, Stanford, CA 94305, USACenter for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USADepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USADivision of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USADepartment of Public Health Sciences, Penn State Milton Hershey Medical Center, Hershey, PA 17033, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USADepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USADepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USADepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Medicine and Dan L Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX 77030, USADepartment of Molecular & Cell Biology, Baylor College of Medicine, Houston, TX 77030, USADepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USADepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USADepartment of Medicine-Biomedical Informatics Research, Stanford University, Stanford, CA 94305, USADepartment of Medicine-Biomedical Informatics Research, Stanford University, Stanford, CA 94305, USACenter for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USADepartment of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97201, USAHead and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USAHead and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USALineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USADepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USADepartment of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USADepartment of Epidemiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA; Hudson Alpha Institute for Biotechnology, Huntsville, AL 35806, USACanada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, CanadaCanada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, CanadaCanada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, CanadaBuck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USADepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USADepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USADepartment of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USADepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USADepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USADepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USADepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USADepartment of Medicine-Pediatrics, Texas Children’s Cancer Center, Baylor College of Medicine, Houston, TX 77030, USADepartment of Medicine-Pediatrics, Texas Children’s Cancer Center, Baylor College of Medicine, Houston, TX 77030, USADepartment of Medicine-Pediatrics, Texas Children’s Cancer Center, Baylor College of Medicine, Houston, TX 77030, USADepartment of Biology & Biochemistry, UH-SeqNEdit Core, University of Houston, Houston, TX 77204, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USACenter for Comparative Medicine, Baylor College of Medicine, Houston, TX 77030, USADepartment of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI 53226, USAUniversity of Oklahoma Health Sciences Center, Department of Pathology, Oklahoma City, OK 73104, USADepartment of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USADepartments of Pathology, Genomic Medicine, Dermatology, and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77401, USAMolecular Oncology, Moffitt Cancer Center, Tampa, FL 33612, USADepartments of Anatomic Pathology and Tumor Biology, Moffitt Cancer Center, Tampa, FL 33612, USADepartment of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USADivision of Gastroenterology, Departments of Medicine and Genetics, Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USADepartment of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USADepartment of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USADepartment of Biomolecular Engineering, Center for Biomolecular Sciences and Engineering University of California, Santa Cruz, Santa Cruz, CA 95064, USADepartment of Biomolecular Engineering, Center for Biomolecular Sciences and Engineering University of California, Santa Cruz, Santa Cruz, CA 95064, USACenter for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USADepartment of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USADepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USADepartment of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97201, USADepartment of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USAHead and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA; Corresponding authorHead and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA; Corresponding authorSummary: 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. : Campbell et al. reveal that squamous cell cancers from different tissue sites may be distinguished from other cancers and subclassified molecularly by recurrent alterations in chromosomes, DNA methylation, messenger and microRNA expression, or by mutations. These affect squamous cell pathways and programs that provide candidates for therapy. Keywords: genomics, transcriptomics, proteomics, head and neck squamous cell carcinoma, lung squamous cell carcinoma, esophageal squamous cell carcinoma, cervical squamous cell carcinoma, bladder carcinoma with squamous differentiation, human papillomavirushttp://www.sciencedirect.com/science/article/pii/S2211124718304248 |