Literature DB >> 22739505

From cancer genomes to oncogenic drivers, tumour dependencies and therapeutic targets.

Cheryl Eifert1, R Scott Powers.   

Abstract

The analysis of human cancer by genome sequencing and various types of arrays has proved that many tumours harbour hundreds of genes that are mutated or substantially altered by copy number changes. But how many of these changes are meaningful? And how can we exploit these massive data sets to yield new targets for cancer treatment? In this Opinion article, we describe emerging approaches that aim to determine which altered genes are actually contributing to cancer, as well as their potential as therapeutic targets.

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Year:  2012        PMID: 22739505     DOI: 10.1038/nrc3299

Source DB:  PubMed          Journal:  Nat Rev Cancer        ISSN: 1474-175X            Impact factor:   60.716


  53 in total

1.  Systematic investigation of genetic vulnerabilities across cancer cell lines reveals lineage-specific dependencies in ovarian cancer.

Authors:  Hiu Wing Cheung; Glenn S Cowley; Barbara A Weir; Jesse S Boehm; Scott Rusin; Justine A Scott; Alexandra East; Levi D Ali; Patrick H Lizotte; Terence C Wong; Guozhi Jiang; Jessica Hsiao; Craig H Mermel; Gad Getz; Jordi Barretina; Shuba Gopal; Pablo Tamayo; Joshua Gould; Aviad Tsherniak; Nicolas Stransky; Biao Luo; Yin Ren; Ronny Drapkin; Sangeeta N Bhatia; Jill P Mesirov; Levi A Garraway; Matthew Meyerson; Eric S Lander; David E Root; William C Hahn
Journal:  Proc Natl Acad Sci U S A       Date:  2011-07-11       Impact factor: 11.205

2.  Identification of a therapeutic strategy targeting amplified FGF19 in liver cancer by Oncogenomic screening.

Authors:  Eric T Sawey; Maia Chanrion; Chunlin Cai; Guanming Wu; Jianping Zhang; Lars Zender; Alice Zhao; Ronald W Busuttil; Herman Yee; Lincoln Stein; Dorothy M French; Richard S Finn; Scott W Lowe; Scott Powers
Journal:  Cancer Cell       Date:  2011-03-08       Impact factor: 31.743

3.  Mutations in the DDR2 kinase gene identify a novel therapeutic target in squamous cell lung cancer.

Authors:  Peter S Hammerman; Martin L Sos; Alex H Ramos; Chunxiao Xu; Amit Dutt; Wenjun Zhou; Lear E Brace; Brittany A Woods; Wenchu Lin; Jianming Zhang; Xianming Deng; Sang Min Lim; Stefanie Heynck; Martin Peifer; Jeffrey R Simard; Michael S Lawrence; Robert C Onofrio; Helga B Salvesen; Danila Seidel; Thomas Zander; Johannes M Heuckmann; Alex Soltermann; Holger Moch; Mirjam Koker; Frauke Leenders; Franziska Gabler; Silvia Querings; Sascha Ansén; Elisabeth Brambilla; Christian Brambilla; Philippe Lorimier; Odd Terje Brustugun; Aslaug Helland; Iver Petersen; Joachim H Clement; Harry Groen; Wim Timens; Hannie Sietsma; Erich Stoelben; Jürgen Wolf; David G Beer; Ming Sound Tsao; Megan Hanna; Charles Hatton; Michael J Eck; Pasi A Janne; Bruce E Johnson; Wendy Winckler; Heidi Greulich; Adam J Bass; Jeonghee Cho; Daniel Rauh; Nathanael S Gray; Kwok-Kin Wong; Eric B Haura; Roman K Thomas; Matthew Meyerson
Journal:  Cancer Discov       Date:  2011-06       Impact factor: 39.397

4.  PIK3CA cooperates with other phosphatidylinositol 3'-kinase pathway mutations to effect oncogenic transformation.

Authors:  Katsutoshi Oda; Jennifer Okada; Luika Timmerman; Pablo Rodriguez-Viciana; David Stokoe; Keiko Shoji; Yuji Taketani; Hiroyuki Kuramoto; Zachary A Knight; Kevan M Shokat; Frank McCormick
Journal:  Cancer Res       Date:  2008-10-01       Impact factor: 12.701

5.  A human functional protein interaction network and its application to cancer data analysis.

Authors:  Guanming Wu; Xin Feng; Lincoln Stein
Journal:  Genome Biol       Date:  2010-05-19       Impact factor: 13.583

6.  Towards patient-based cancer therapeutics.

Authors:  Stuart L Schreiber; Alykhan F Shamji; Paul A Clemons; Cindy Hon; Angela N Koehler; Benito Munoz; Michelle Palmer; Andrew M Stern; Bridget K Wagner; Scott Powers; Scott W Lowe; Xuecui Guo; Alex Krasnitz; Eric T Sawey; Raffaella Sordella; Lincoln Stein; Lloyd C Trotman; Andrea Califano; Riccardo Dalla-Favera; Adolfo Ferrando; Antonio Iavarone; Laura Pasqualucci; José Silva; Brent R Stockwell; William C Hahn; Lynda Chin; Ronald A DePinho; Jesse S Boehm; Shuba Gopal; Alan Huang; David E Root; Barbara A Weir; Daniela S Gerhard; Jean Claude Zenklusen; Michael G Roth; Michael A White; John D Minna; John B MacMillan; Bruce A Posner
Journal:  Nat Biotechnol       Date:  2010-09       Impact factor: 54.908

7.  Distinct pathways of genomic progression to benign and malignant tumors of the liver.

Authors:  Aaron D Tward; Kirk D Jones; Stephen Yant; Siu Tim Cheung; Sheung Tat Fan; Xin Chen; Mark A Kay; Rong Wang; J Michael Bishop
Journal:  Proc Natl Acad Sci U S A       Date:  2007-09-04       Impact factor: 11.205

8.  An integrated genomic analysis of human glioblastoma multiforme.

Authors:  D Williams Parsons; Siân Jones; Xiaosong Zhang; Jimmy Cheng-Ho Lin; Rebecca J Leary; Philipp Angenendt; Parminder Mankoo; Hannah Carter; I-Mei Siu; Gary L Gallia; Alessandro Olivi; Roger McLendon; B Ahmed Rasheed; Stephen Keir; Tatiana Nikolskaya; Yuri Nikolsky; Dana A Busam; Hanna Tekleab; Luis A Diaz; James Hartigan; Doug R Smith; Robert L Strausberg; Suely Kazue Nagahashi Marie; Sueli Mieko Oba Shinjo; Hai Yan; Gregory J Riggins; Darell D Bigner; Rachel Karchin; Nick Papadopoulos; Giovanni Parmigiani; Bert Vogelstein; Victor E Velculescu; Kenneth W Kinzler
Journal:  Science       Date:  2008-09-04       Impact factor: 47.728

9.  A transposon-based genetic screen in mice identifies genes altered in colorectal cancer.

Authors:  Timothy K Starr; Raha Allaei; Kevin A T Silverstein; Rodney A Staggs; Aaron L Sarver; Tracy L Bergemann; Mihir Gupta; M Gerard O'Sullivan; Ilze Matise; Adam J Dupuy; Lara S Collier; Scott Powers; Ann L Oberg; Yan W Asmann; Stephen N Thibodeau; Lino Tessarollo; Neal G Copeland; Nancy A Jenkins; Robert T Cormier; David A Largaespada
Journal:  Science       Date:  2009-02-26       Impact factor: 47.728

10.  Functional viability profiles of breast cancer.

Authors:  Rachel Brough; Jessica R Frankum; David Sims; Alan Mackay; Ana M Mendes-Pereira; Ilirjana Bajrami; Sara Costa-Cabral; Rumana Rafiq; Amar S Ahmad; Maria Antonietta Cerone; Rachael Natrajan; Rachel Sharpe; Kai-Keen Shiu; Daniel Wetterskog; Konstantine J Dedes; Maryou B Lambros; Teeara Rawjee; Spiros Linardopoulos; Jorge S Reis-Filho; Nicholas C Turner; Christopher J Lord; Alan Ashworth
Journal:  Cancer Discov       Date:  2011-08-02       Impact factor: 39.397

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  37 in total

Review 1.  Extracellular assembly and activation principles of oncogenic class III receptor tyrosine kinases.

Authors:  Kenneth Verstraete; Savvas N Savvides
Journal:  Nat Rev Cancer       Date:  2012-10-18       Impact factor: 60.716

Review 2.  Mutant DNA methylation regulators endow hematopoietic stem cells with the preleukemic stem cell property, a requisite of leukemia initiation and relapse.

Authors:  Yuting Tan; Han Liu; Saijuan Chen
Journal:  Front Med       Date:  2015-12       Impact factor: 4.592

3.  Targeted genetic dependency screen facilitates identification of actionable mutations in FGFR4, MAP3K9, and PAK5 in lung cancer.

Authors:  Shameem Fawdar; Eleanor W Trotter; Yaoyong Li; Natalie L Stephenson; Franziska Hanke; Anna A Marusiak; Zoe C Edwards; Sara Ientile; Bohdan Waszkowycz; Crispin J Miller; John Brognard
Journal:  Proc Natl Acad Sci U S A       Date:  2013-07-08       Impact factor: 11.205

4.  ChromoHub V2: cancer genomics.

Authors:  Muhammad A Shah; Emily L Denton; Lihua Liu; Matthieu Schapira
Journal:  Bioinformatics       Date:  2013-12-06       Impact factor: 6.937

Review 5.  Mesenchymal stroma: primary determinant and therapeutic target for epithelial cancer.

Authors:  Sandro Goruppi; G Paolo Dotto
Journal:  Trends Cell Biol       Date:  2013-09-25       Impact factor: 20.808

6.  Cell-Line Selectivity Improves the Predictive Power of Pharmacogenomic Analyses and Helps Identify NADPH as Biomarker for Ferroptosis Sensitivity.

Authors:  Kenichi Shimada; Miki Hayano; Nen C Pagano; Brent R Stockwell
Journal:  Cell Chem Biol       Date:  2016-02-04       Impact factor: 8.116

7.  Copy-number and gene dependency analysis reveals partial copy loss of wild-type SF3B1 as a novel cancer vulnerability.

Authors:  Brenton R Paolella; William J Gibson; Laura M Urbanski; John A Alberta; Travis I Zack; Pratiti Bandopadhayay; Caitlin A Nichols; Pankaj K Agarwalla; Meredith S Brown; Rebecca Lamothe; Yong Yu; Peter S Choi; Esther A Obeng; Dirk Heckl; Guo Wei; Belinda Wang; Aviad Tsherniak; Francisca Vazquez; Barbara A Weir; David E Root; Glenn S Cowley; Sara J Buhrlage; Charles D Stiles; Benjamin L Ebert; William C Hahn; Robin Reed; Rameen Beroukhim
Journal:  Elife       Date:  2017-02-08       Impact factor: 8.140

8.  Novel cancer drivers: mining the kinome.

Authors:  Andrew V Biankin; Sean M Grimmond
Journal:  Genome Med       Date:  2013-02-28       Impact factor: 11.117

Review 9.  Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes.

Authors:  Feixiong Cheng; Junfei Zhao; Zhongming Zhao
Journal:  Brief Bioinform       Date:  2015-08-24       Impact factor: 11.622

Review 10.  Multifocal epithelial tumors and field cancerization: stroma as a primary determinant.

Authors:  G Paolo Dotto
Journal:  J Clin Invest       Date:  2014-04-01       Impact factor: 14.808

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