Literature DB >> 26000852

The cancer cell map initiative: defining the hallmark networks of cancer.

Nevan J Krogan1, Scott Lippman2, David A Agard3, Alan Ashworth4, Trey Ideker5.   

Abstract

Progress in DNA sequencing has revealed the startling complexity of cancer genomes, which typically carry thousands of somatic mutations. However, it remains unclear which are the key driver mutations or dependencies in a given cancer and how these influence pathogenesis and response to therapy. Although tumors of similar types and clinical outcomes can have patterns of mutations that are strikingly different, it is becoming apparent that these mutations recurrently hijack the same hallmark molecular pathways and networks. For this reason, it is likely that successful interpretation of cancer genomes will require comprehensive knowledge of the molecular networks under selective pressure in oncogenesis. Here we announce the creation of a new effort, The Cancer Cell Map Initiative (CCMI), aimed at systematically detailing these complex interactions among cancer genes and how they differ between diseased and healthy states. We discuss recent progress that enables creation of these cancer cell maps across a range of tumor types and how they can be used to target networks disrupted in individual patients, significantly accelerating the development of precision medicine.
Copyright © 2015 Elsevier Inc. All rights reserved.

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Year:  2015        PMID: 26000852      PMCID: PMC5359018          DOI: 10.1016/j.molcel.2015.05.008

Source DB:  PubMed          Journal:  Mol Cell        ISSN: 1097-2765            Impact factor:   17.970


  118 in total

1.  Systematic pathway analysis using high-resolution fitness profiling of combinatorial gene deletions.

Authors:  Robert P St Onge; Ramamurthy Mani; Julia Oh; Michael Proctor; Eula Fung; Ronald W Davis; Corey Nislow; Frederick P Roth; Guri Giaever
Journal:  Nat Genet       Date:  2007-01-07       Impact factor: 38.330

2.  Personal genomes: The case of the missing heritability.

Authors:  Brendan Maher
Journal:  Nature       Date:  2008-11-06       Impact factor: 49.962

Review 3.  Boosting signal-to-noise in complex biology: prior knowledge is power.

Authors:  Trey Ideker; Janusz Dutkowski; Leroy Hood
Journal:  Cell       Date:  2011-03-18       Impact factor: 41.582

4.  Global mapping of herpesvirus-host protein complexes reveals a transcription strategy for late genes.

Authors:  Zoe H Davis; Erik Verschueren; Gwendolyn M Jang; Kevin Kleffman; Jeffrey R Johnson; Jimin Park; John Von Dollen; M Cyrus Maher; Tasha Johnson; William Newton; Stefanie Jäger; Michael Shales; Julie Horner; Ryan D Hernandez; Nevan J Krogan; Britt A Glaunsinger
Journal:  Mol Cell       Date:  2014-12-24       Impact factor: 17.970

5.  Complementary genomic approaches highlight the PI3K/mTOR pathway as a common vulnerability in osteosarcoma.

Authors:  Jennifer A Perry; Adam Kiezun; Peter Tonzi; Eliezer M Van Allen; Scott L Carter; Sylvan C Baca; Glenn S Cowley; Ami S Bhatt; Esther Rheinbay; Chandra Sekhar Pedamallu; Elena Helman; Amaro Taylor-Weiner; Aaron McKenna; David S DeLuca; Michael S Lawrence; Lauren Ambrogio; Carrie Sougnez; Andrey Sivachenko; Loren D Walensky; Nikhil Wagle; Jaume Mora; Carmen de Torres; Cinzia Lavarino; Simone Dos Santos Aguiar; Jose Andres Yunes; Silvia Regina Brandalise; Gabriela Elisa Mercado-Celis; Jorge Melendez-Zajgla; Rocío Cárdenas-Cardós; Liliana Velasco-Hidalgo; Charles W M Roberts; Levi A Garraway; Carlos Rodriguez-Galindo; Stacey B Gabriel; Eric S Lander; Todd R Golub; Stuart H Orkin; Gad Getz; Katherine A Janeway
Journal:  Proc Natl Acad Sci U S A       Date:  2014-12-15       Impact factor: 11.205

6.  Network modeling links breast cancer susceptibility and centrosome dysfunction.

Authors:  Miguel Angel Pujana; Jing-Dong J Han; Lea M Starita; Kristen N Stevens; Muneesh Tewari; Jin Sook Ahn; Gad Rennert; Víctor Moreno; Tomas Kirchhoff; Bert Gold; Volker Assmann; Wael M Elshamy; Jean-François Rual; Douglas Levine; Laura S Rozek; Rebecca S Gelman; Kristin C Gunsalus; Roger A Greenberg; Bijan Sobhian; Nicolas Bertin; Kavitha Venkatesan; Nono Ayivi-Guedehoussou; Xavier Solé; Pilar Hernández; Conxi Lázaro; Katherine L Nathanson; Barbara L Weber; Michael E Cusick; David E Hill; Kenneth Offit; David M Livingston; Stephen B Gruber; Jeffrey D Parvin; Marc Vidal
Journal:  Nat Genet       Date:  2007-10-07       Impact factor: 38.330

7.  Quantitative genetic-interaction mapping in mammalian cells.

Authors:  Assen Roguev; Dale Talbot; Gian Luca Negri; Michael Shales; Gerard Cagney; Sourav Bandyopadhyay; Barbara Panning; Nevan J Krogan
Journal:  Nat Methods       Date:  2013-02-13       Impact factor: 28.547

8.  Intratumor heterogeneity in localized lung adenocarcinomas delineated by multiregion sequencing.

Authors:  Jianjun Zhang; Junya Fujimoto; Jianhua Zhang; David C Wedge; Xingzhi Song; Jiexin Zhang; Sahil Seth; Chi-Wan Chow; Yu Cao; Curtis Gumbs; Kathryn A Gold; Neda Kalhor; Latasha Little; Harshad Mahadeshwar; Cesar Moran; Alexei Protopopov; Huandong Sun; Jiabin Tang; Xifeng Wu; Yuanqing Ye; William N William; J Jack Lee; John V Heymach; Waun Ki Hong; Stephen Swisher; Ignacio I Wistuba; P Andrew Futreal
Journal:  Science       Date:  2014-10-10       Impact factor: 47.728

9.  Protein networks as logic functions in development and cancer.

Authors:  Janusz Dutkowski; Trey Ideker
Journal:  PLoS Comput Biol       Date:  2011-09-29       Impact factor: 4.475

10.  COSMIC: exploring the world's knowledge of somatic mutations in human cancer.

Authors:  Simon A Forbes; David Beare; Prasad Gunasekaran; Kenric Leung; Nidhi Bindal; Harry Boutselakis; Minjie Ding; Sally Bamford; Charlotte Cole; Sari Ward; Chai Yin Kok; Mingming Jia; Tisham De; Jon W Teague; Michael R Stratton; Ultan McDermott; Peter J Campbell
Journal:  Nucleic Acids Res       Date:  2014-10-29       Impact factor: 16.971

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  52 in total

Review 1.  Comparative mapping of host-pathogen protein-protein interactions.

Authors:  Priya S Shah; Jason A Wojcechowskyj; Manon Eckhardt; Nevan J Krogan
Journal:  Curr Opin Microbiol       Date:  2015-08-10       Impact factor: 7.934

2.  Protein Interactomics by Two-Hybrid Methods.

Authors:  Soon Gang Choi; Aaron Richardson; Luke Lambourne; David E Hill; Marc Vidal
Journal:  Methods Mol Biol       Date:  2018

3.  The Evolutionary Pathway to Virulence of an RNA Virus.

Authors:  Adi Stern; Ming Te Yeh; Tal Zinger; Matt Smith; Caroline Wright; Guy Ling; Rasmus Nielsen; Andrew Macadam; Raul Andino
Journal:  Cell       Date:  2017-03-23       Impact factor: 41.582

4.  An Atlas of the Human Kinome Reveals the Mutational Landscape Underlying Dysregulated Phosphorylation Cascades in Cancer.

Authors:  Aleksandra Olow; Zhongzhong Chen; R Hannes Niedner; Denise M Wolf; Christina Yau; Aleksandr Pankov; Evelyn Pei Rong Lee; Lamorna Brown-Swigart; Laura J van 't Veer; Jean-Philippe Coppé
Journal:  Cancer Res       Date:  2016-02-26       Impact factor: 12.701

Review 5.  The extracellular matrix as a key regulator of intracellular signalling networks.

Authors:  Jordan F Hastings; Joanna N Skhinas; Dirk Fey; David R Croucher; Thomas R Cox
Journal:  Br J Pharmacol       Date:  2018-04-19       Impact factor: 8.739

Review 6.  Opportunities and Challenges in Building a Spatiotemporal Multi-scale Model of the Human Pancreatic β Cell.

Authors:  Jitin Singla; Kyle M McClary; Kate L White; Frank Alber; Andrej Sali; Raymond C Stevens
Journal:  Cell       Date:  2018-03-22       Impact factor: 41.582

Review 7.  Mapping the protein-protein and genetic interactions of cancer to guide precision medicine.

Authors:  Mehdi Bouhaddou; Manon Eckhardt; Zun Zar Chi Naing; Minkyu Kim; Trey Ideker; Nevan J Krogan
Journal:  Curr Opin Genet Dev       Date:  2019-07-06       Impact factor: 5.578

8.  Mapping phospho-catalytic dependencies of therapy-resistant tumours reveals actionable vulnerabilities.

Authors:  Jean-Philippe Coppé; Miki Mori; Bo Pan; Christina Yau; Denise M Wolf; Ana Ruiz-Saenz; Diede Brunen; Anirudh Prahallad; Paulien Cornelissen-Steijger; Kristel Kemper; Christian Posch; Changjun Wang; Courtney A Dreyer; Oscar Krijgsman; Pei Rong Evelyn Lee; Zhongzhong Chen; Daniel S Peeper; Mark M Moasser; René Bernards; Laura J van 't Veer
Journal:  Nat Cell Biol       Date:  2019-06-03       Impact factor: 28.824

Review 9.  The Psychiatric Cell Map Initiative: A Convergent Systems Biological Approach to Illuminating Key Molecular Pathways in Neuropsychiatric Disorders.

Authors:  A Jeremy Willsey; Montana T Morris; Sheng Wang; Helen R Willsey; Nawei Sun; Nia Teerikorpi; Tierney B Baum; Gerard Cagney; Kevin J Bender; Tejal A Desai; Deepak Srivastava; Graeme W Davis; Jennifer Doudna; Edward Chang; Vikaas Sohal; Daniel H Lowenstein; Hao Li; David Agard; Michael J Keiser; Brian Shoichet; Mark von Zastrow; Lennart Mucke; Steven Finkbeiner; Li Gan; Nenad Sestan; Michael E Ward; Ruth Huttenhain; Tomasz J Nowakowski; Hugo J Bellen; Loren M Frank; Mustafa K Khokha; Richard P Lifton; Martin Kampmann; Trey Ideker; Matthew W State; Nevan J Krogan
Journal:  Cell       Date:  2018-07-26       Impact factor: 41.582

10.  Single-Base Resolution Mapping of 5-Hydroxymethylcytosine Modifications in Hippocampus of Alzheimer's Disease Subjects.

Authors:  Elizabeth M Ellison; Melissa A Bradley-Whitman; Mark A Lovell
Journal:  J Mol Neurosci       Date:  2017-09-02       Impact factor: 3.444

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