Literature DB >> 28887051

Precision Oncology: The Road Ahead.

Daniela Senft1, Mark D M Leiserson2, Eytan Ruppin3, Ze'ev A Ronai4.   

Abstract

Current efforts in precision oncology largely focus on the benefit of genomics-guided therapy. Yet, advances in sequencing techniques provide an unprecedented view of the complex genetic and nongenetic heterogeneity within individual tumors. Herein, we outline the benefits of integrating genomic and transcriptomic analyses for advanced precision oncology. We summarize relevant computational approaches to detect novel drivers and genetic vulnerabilities, suitable for therapeutic exploration. Clinically relevant platforms to functionally test predicted drugs/drug combinations for individual patients are reviewed. Finally, we highlight the technological advances in single cell analysis of tumor specimens. These may ultimately lead to the development of next-generation cancer drugs, capable of tackling the hurdles imposed by genetic and phenotypic heterogeneity on current anticancer therapies.
Copyright © 2017 Elsevier Ltd. All rights reserved.

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Year:  2017        PMID: 28887051      PMCID: PMC5718207          DOI: 10.1016/j.molmed.2017.08.003

Source DB:  PubMed          Journal:  Trends Mol Med        ISSN: 1471-4914            Impact factor:   11.951


  226 in total

Review 1.  The journey from discoveries in fundamental immunology to cancer immunotherapy.

Authors:  Jacques F A P Miller; Michel Sadelain
Journal:  Cancer Cell       Date:  2015-04-06       Impact factor: 31.743

2.  Essential gene profiles in breast, pancreatic, and ovarian cancer cells.

Authors:  Richard Marcotte; Kevin R Brown; Fernando Suarez; Azin Sayad; Konstantina Karamboulas; Paul M Krzyzanowski; Fabrice Sircoulomb; Mauricio Medrano; Yaroslav Fedyshyn; Judice L Y Koh; Dewald van Dyk; Bodhana Fedyshyn; Marianna Luhova; Glauber C Brito; Franco J Vizeacoumar; Frederick S Vizeacoumar; Alessandro Datti; Dahlia Kasimer; Alla Buzina; Patricia Mero; Christine Misquitta; Josee Normand; Maliha Haider; Troy Ketela; Jeffrey L Wrana; Robert Rottapel; Benjamin G Neel; Jason Moffat
Journal:  Cancer Discov       Date:  2011-12-29       Impact factor: 39.397

3.  Rociletinib in EGFR-mutated non-small-cell lung cancer.

Authors:  Lecia V Sequist; Jean-Charles Soria; Jonathan W Goldman; Heather A Wakelee; Shirish M Gadgeel; Andrea Varga; Vassiliki Papadimitrakopoulou; Benjamin J Solomon; Geoffrey R Oxnard; Rafal Dziadziuszko; Dara L Aisner; Robert C Doebele; Cathy Galasso; Edward B Garon; Rebecca S Heist; Jennifer Logan; Joel W Neal; Melody A Mendenhall; Suzanne Nichols; Zofia Piotrowska; Antoinette J Wozniak; Mitch Raponi; Chris A Karlovich; Sarah Jaw-Tsai; Jeffrey Isaacson; Darrin Despain; Shannon L Matheny; Lindsey Rolfe; Andrew R Allen; D Ross Camidge
Journal:  N Engl J Med       Date:  2015-04-30       Impact factor: 91.245

4.  WeSME: uncovering mutual exclusivity of cancer drivers and beyond.

Authors:  Yoo-Ah Kim; Sanna Madan; Teresa M Przytycka
Journal:  Bioinformatics       Date:  2017-03-15       Impact factor: 6.937

5.  DNA-Targeted Precision Medicine; Have we Been Caught Sleeping?

Authors:  William C Reinhold; Anish Thomas; Yves Pommier
Journal:  Trends Cancer       Date:  2017-01

6.  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

7.  Novel mutant-selective EGFR kinase inhibitors against EGFR T790M.

Authors:  Wenjun Zhou; Dalia Ercan; Liang Chen; Cai-Hong Yun; Danan Li; Marzia Capelletti; Alexis B Cortot; Lucian Chirieac; Roxana E Iacob; Robert Padera; John R Engen; Kwok-Kin Wong; Michael J Eck; Nathanael S Gray; Pasi A Jänne
Journal:  Nature       Date:  2009-12-24       Impact factor: 49.962

8.  RNA-Seq of single prostate CTCs implicates noncanonical Wnt signaling in antiandrogen resistance.

Authors:  David T Miyamoto; Yu Zheng; Ben S Wittner; Richard J Lee; Huili Zhu; Katherine T Broderick; Rushil Desai; Douglas B Fox; Brian W Brannigan; Julie Trautwein; Kshitij S Arora; Niyati Desai; Douglas M Dahl; Lecia V Sequist; Matthew R Smith; Ravi Kapur; Chin-Lee Wu; Toshi Shioda; Sridhar Ramaswamy; David T Ting; Mehmet Toner; Shyamala Maheswaran; Daniel A Haber
Journal:  Science       Date:  2015-09-18       Impact factor: 47.728

9.  Methotrexate induces oxidative DNA damage and is selectively lethal to tumour cells with defects in the DNA mismatch repair gene MSH2.

Authors:  Sarah A Martin; Afshan McCarthy; Louise J Barber; Darren J Burgess; Suzanne Parry; Christopher J Lord; Alan Ashworth
Journal:  EMBO Mol Med       Date:  2009-09       Impact factor: 12.137

10.  Epithelial-to-mesenchymal transition is not required for lung metastasis but contributes to chemoresistance.

Authors:  Kari R Fischer; Anna Durrans; Sharrell Lee; Jianting Sheng; Fuhai Li; Stephen T C Wong; Hyejin Choi; Tina El Rayes; Seongho Ryu; Juliane Troeger; Robert F Schwabe; Linda T Vahdat; Nasser K Altorki; Vivek Mittal; Dingcheng Gao
Journal:  Nature       Date:  2015-11-11       Impact factor: 49.962

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  46 in total

1.  Single-Cell Analysis of BRAFV600E and NRASQ61R Mutation Status in Melanoma Cell Lines as Method Generation for Circulating Melanoma Cells.

Authors:  Joseph W Po; Yafeng Ma; Alison W S Luk; David Lynch; Bavanthi Balakrishnar; Daniel Brungs; Farhad Azimi; Adam Cooper; Erin Saricilar; Vinay Murthy; Paul de Souza; Therese M Becker
Journal:  Methods Mol Biol       Date:  2021

Review 2.  Addressing Patient Specificity in the Engineering of Tumor Models.

Authors:  Laura J Bray; Dietmar W Hutmacher; Nathalie Bock
Journal:  Front Bioeng Biotechnol       Date:  2019-09-12

Review 3.  Beyond the message: advantages of snapshot proteomics with single-cell mass cytometry in solid tumors.

Authors:  Akshitkumar M Mistry; Allison R Greenplate; Rebecca A Ihrie; Jonathan M Irish
Journal:  FEBS J       Date:  2019-01-07       Impact factor: 5.542

Review 4.  Application of non-negative matrix factorization in oncology: one approach for establishing precision medicine.

Authors:  Ryuji Hamamoto; Ken Takasawa; Hidenori Machino; Kazuma Kobayashi; Satoshi Takahashi; Amina Bolatkan; Norio Shinkai; Akira Sakai; Rina Aoyama; Masayoshi Yamada; Ken Asada; Masaaki Komatsu; Koji Okamoto; Hirokazu Kameoka; Syuzo Kaneko
Journal:  Brief Bioinform       Date:  2022-07-18       Impact factor: 13.994

5.  Biomechanical Modeling of Brachialis-to-Wrist Extensor Muscle Transfer Function for Daily Activities in Tetraplegia.

Authors:  Jongsang Son; Jan Fridén; Richard L Lieber
Journal:  JB JS Open Access       Date:  2022-07-21

Review 6.  Protein scaffolds: antibody alternatives for cancer diagnosis and therapy.

Authors:  Renli Luo; Hongguang Liu; Zhen Cheng
Journal:  RSC Chem Biol       Date:  2022-05-25

7.  Risk and benefit for umbrella trials in oncology: a systematic review and meta-analysis.

Authors:  Karolina Strzebonska; Mateusz Blukacz; Mateusz T Wasylewski; Maciej Polak; Bishal Gyawali; Marcin Waligora
Journal:  BMC Med       Date:  2022-07-08       Impact factor: 11.150

8.  A Middle-Out Modeling Strategy to Extend a Colon Cancer Logical Model Improves Drug Synergy Predictions in Epithelial-Derived Cancer Cell Lines.

Authors:  Eirini Tsirvouli; Vasundra Touré; Barbara Niederdorfer; Miguel Vázquez; Åsmund Flobak; Martin Kuiper
Journal:  Front Mol Biosci       Date:  2020-10-09

Review 9.  A census of pathway maps in cancer systems biology.

Authors:  Brent M Kuenzi; Trey Ideker
Journal:  Nat Rev Cancer       Date:  2020-02-17       Impact factor: 60.716

10.  Organotypic primary blood vessel models of clear cell renal cell carcinoma for single-patient clinical trials.

Authors:  María Virumbrales-Muñoz; Jiong Chen; Jose Ayuso; Moonhee Lee; E Jason Abel; David J Beebe
Journal:  Lab Chip       Date:  2020-11-24       Impact factor: 7.517

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