Literature DB >> 30262818

Pharmacogenomic landscape of patient-derived tumor cells informs precision oncology therapy.

Jin-Ku Lee1,2,3, Zhaoqi Liu4,5, Jason K Sa1,3, Sang Shin1,6, Jiguang Wang7,8,9, Mykola Bordyuh4,5, Hee Jin Cho1,3, Oliver Elliott4,5, Timothy Chu4,5, Seung Won Choi1,6, Daniel I S Rosenbloom4,5, In-Hee Lee1,3, Yong Jae Shin1,2,3, Hyun Ju Kang1,3, Donggeon Kim1,3, Sun Young Kim10, Moon-Hee Sim10, Jusun Kim10, Taehyang Lee10, Yun Jee Seo1,3, Hyemi Shin1,6, Mijeong Lee1,6, Sung Heon Kim1,2, Yong-Jun Kwon1, Jeong-Woo Oh1,6, Minsuk Song1, Misuk Kim1,3, Doo-Sik Kong2, Jung Won Choi2, Ho Jun Seol2, Jung-Il Lee2, Seung Tae Kim10, Joon Oh Park6,10, Kyoung-Mee Kim11, Sang-Yong Song11, Jeong-Won Lee12, Hee-Cheol Kim13, Jeong Eon Lee13, Min Gew Choi13, Sung Wook Seo14, Young Mog Shim15, Jae Ill Zo15, Byong Chang Jeong16, Yeup Yoon3,6, Gyu Ha Ryu3, Nayoung K D Kim3,17, Joon Seol Bae3,17, Woong-Yang Park3,6,17, Jeongwu Lee18, Roel G W Verhaak19, Antonio Iavarone20,21,22, Jeeyun Lee23,24, Raul Rabadan25,26, Do-Hyun Nam27,28,29.   

Abstract

Outcomes of anticancer therapy vary dramatically among patients due to diverse genetic and molecular backgrounds, highlighting extensive intertumoral heterogeneity. The fundamental tenet of precision oncology defines molecular characterization of tumors to guide optimal patient-tailored therapy. Towards this goal, we have established a compilation of pharmacological landscapes of 462 patient-derived tumor cells (PDCs) across 14 cancer types, together with genomic and transcriptomic profiling in 385 of these tumors. Compared with the traditional long-term cultured cancer cell line models, PDCs recapitulate the molecular properties and biology of the diseases more precisely. Here, we provide insights into dynamic pharmacogenomic associations, including molecular determinants that elicit therapeutic resistance to EGFR inhibitors, and the potential repurposing of ibrutinib (currently used in hematological malignancies) for EGFR-specific therapy in gliomas. Lastly, we present a potential implementation of PDC-derived drug sensitivities for the prediction of clinical response to targeted therapeutics using retrospective clinical studies.

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Year:  2018        PMID: 30262818     DOI: 10.1038/s41588-018-0209-6

Source DB:  PubMed          Journal:  Nat Genet        ISSN: 1061-4036            Impact factor:   38.330


  45 in total

Review 1.  Machine learning approaches to drug response prediction: challenges and recent progress.

Authors:  George Adam; Ladislav Rampášek; Zhaleh Safikhani; Petr Smirnov; Benjamin Haibe-Kains; Anna Goldenberg
Journal:  NPJ Precis Oncol       Date:  2020-06-15

2.  An avatar for precision cancer therapy.

Authors:  Shumei Kato; Razelle Kurzrock
Journal:  Nat Biotechnol       Date:  2018-11-09       Impact factor: 54.908

3.  High-throughput dynamic BH3 profiling may quickly and accurately predict effective therapies in solid tumors.

Authors:  Patrick D Bhola; Eman Ahmed; Jennifer L Guerriero; Ewa Sicinska; Emily Su; Elizaveta Lavrova; Jing Ni; Otari Chipashvili; Timothy Hagan; Marissa S Pioso; Kelley McQueeney; Kimmie Ng; Andrew J Aguirre; James M Cleary; David Cocozziello; Alaba Sotayo; Jeremy Ryan; Jean J Zhao; Anthony Letai
Journal:  Sci Signal       Date:  2020-06-16       Impact factor: 8.192

4.  Super.FELT: supervised feature extraction learning using triplet loss for drug response prediction with multi-omics data.

Authors:  Sejin Park; Jihee Soh; Hyunju Lee
Journal:  BMC Bioinformatics       Date:  2021-05-25       Impact factor: 3.169

5.  Pleural Fluid Has Pro-Growth Biological Properties Which Enable Cancer Cell Proliferation.

Authors:  Rachelle Asciak; Nikolaos I Kanellakis; Xuan Yao; Megat Abd Hamid; Rachel M Mercer; Maged Hassan; Eihab O Bedawi; Melissa Dobson; Peter Fsadni; Stephen Montefort; Tao Dong; Najib M Rahman; Ioannis Psallidas
Journal:  Front Oncol       Date:  2021-04-28       Impact factor: 6.244

6.  Patient-Derived Xenografts and Matched Cell Lines Identify Pharmacogenomic Vulnerabilities in Colorectal Cancer.

Authors:  Luca Lazzari; Giorgio Corti; Gabriele Picco; Claudio Isella; Monica Montone; Pamela Arcella; Erika Durinikova; Eugenia R Zanella; Luca Novara; Fabiane Barbosa; Andrea Cassingena; Carlotta Cancelliere; Enzo Medico; Andrea Sartore-Bianchi; Salvatore Siena; Mathew J Garnett; Andrea Bertotti; Livio Trusolino; Federica Di Nicolantonio; Michael Linnebacher; Alberto Bardelli; Sabrina Arena
Journal:  Clin Cancer Res       Date:  2019-08-02       Impact factor: 12.531

Review 7.  Current status and perspectives of patient-derived rare cancer models.

Authors:  Tadashi Kondo
Journal:  Hum Cell       Date:  2020-06-14       Impact factor: 4.174

8.  Network-based systems pharmacology reveals heterogeneity in LCK and BCL2 signaling and therapeutic sensitivity of T-cell acute lymphoblastic leukemia.

Authors:  Yoshihiro Gocho; Jingjing Liu; Jianzhong Hu; Wentao Yang; Neekesh V Dharia; Jingliao Zhang; Hao Shi; Guoqing Du; August John; Ting-Nien Lin; Jeremy Hunt; Xin Huang; Bensheng Ju; Lauren Rowland; Lei Shi; Dylan Maxwell; Brandon Smart; Kristine R Crews; Wenjian Yang; Kohei Hagiwara; Yingchi Zhang; Kathryn Roberts; Hong Wang; Elias Jabbour; Wendy Stock; Bartholomew Eisfelder; Elisabeth Paietta; Scott Newman; Giovanni Roti; Mark Litzow; John Easton; Jinghui Zhang; Junmin Peng; Hongbo Chi; Stanley Pounds; Mary V Relling; Hiroto Inaba; Xiaofan Zhu; Steven Kornblau; Ching-Hon Pui; Marina Konopleva; David Teachey; Charles G Mullighan; Kimberly Stegmaier; William E Evans; Jiyang Yu; Jun J Yang
Journal:  Nat Cancer       Date:  2021-01-21

9.  Quantitative In Vivo Analyses Reveal a Complex Pharmacogenomic Landscape in Lung Adenocarcinoma.

Authors:  Chuan Li; Wen-Yang Lin; Monte M Winslow; Hira Rizvi; Hongchen Cai; Christopher D McFarland; Zoe N Rogers; Maryam Yousefi; Ian P Winters; Charles M Rudin; Dmitri A Petrov
Journal:  Cancer Res       Date:  2021-07-02       Impact factor: 12.701

Review 10.  In Vitro Glioblastoma Models: A Journey into the Third Dimension.

Authors:  Mayra Paolillo; Sergio Comincini; Sergio Schinelli
Journal:  Cancers (Basel)       Date:  2021-05-18       Impact factor: 6.639

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