Literature DB >> 33217343

Molecular Features of Cancers Exhibiting Exceptional Responses to Treatment.

David A Wheeler1, Naoko Takebe2, Toshinori Hinoue3, Katherine A Hoadley4, Maria F Cardenas1, Alina M Hamilton4, Peter W Laird3, Linghua Wang5, Adrienne Johnson6, Ninad Dewal6, Vincent Miller6, David Piñeyro7, Manuel Castro de Moura8, Manel Esteller9, Hui Shen3, Jean Claude Zenklusen10, Roy Tarnuzzer10, Lisa M McShane2, James V Tricoli2, Paul M Williams11, Irina Lubensky2, Geraldine O'Sullivan-Coyne2, Elise C Kohn2, Richard F Little2, Jeffrey White2, Shakun Malik2, Lyndsay Harris2, Carol Weil2, Alice P Chen2, Chris Karlovich11, Brian Rodgers2, Lalitha Shankar2, Paula Jacobs2, Tracy Nolan12, Jianhong Hu13, Donna M Muzny13, Harshavardhan Doddapaneni13, Viktoriya Korchina13, Julie Gastier-Foster14, Jay Bowen14, Kristen Leraas14, Elijah F Edmondson15, James H Doroshow2, Barbara A Conley2, S Percy Ivy2, Louis M Staudt16.   

Abstract

A small fraction of cancer patients with advanced disease survive significantly longer than patients with clinically comparable tumors. Molecular mechanisms for exceptional responses to therapy have been identified by genomic analysis of tumor biopsies from individual patients. Here, we analyzed tumor biopsies from an unbiased cohort of 111 exceptional responder patients using multiple platforms to profile genetic and epigenetic aberrations as well as the tumor microenvironment. Integrative analysis uncovered plausible mechanisms for the therapeutic response in nearly a quarter of the patients. The mechanisms were assigned to four broad categories-DNA damage response, intracellular signaling, immune engagement, and genetic alterations characteristic of favorable prognosis-with many tumors falling into multiple categories. These analyses revealed synthetic lethal relationships that may be exploited therapeutically and rare genetic lesions that favor therapeutic success, while also providing a wealth of testable hypotheses regarding oncogenic mechanisms that may influence the response to cancer therapy. Published by Elsevier Inc.

Entities:  

Keywords:  DNA methylation analysis; DNA repair mechanisms; N of 1 experiment; RNA sequencing; combination cancer therapy; exceptional response to therapy; integrating molecular and clinical data; multi-platform genomic analyses; precision cancer medicine; rare mutations; synthetic lethality; whole-exome sequencing

Mesh:

Substances:

Year:  2020        PMID: 33217343      PMCID: PMC8478080          DOI: 10.1016/j.ccell.2020.10.015

Source DB:  PubMed          Journal:  Cancer Cell        ISSN: 1535-6108            Impact factor:   31.743


  74 in total

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Journal:  Genome Res       Date:  2012-02-02       Impact factor: 9.043

2.  Somatic POLE mutations cause an ultramutated giant cell high-grade glioma subtype with better prognosis.

Authors:  E Zeynep Erson-Omay; Ahmet Okay Çağlayan; Nikolaus Schultz; Nils Weinhold; S Bülent Omay; Koray Özduman; Yavuz Köksal; Jie Li; Akdes Serin Harmancı; Victoria Clark; Geneive Carrión-Grant; Jacob Baranoski; Caner Çağlar; Tanyeri Barak; Süleyman Coşkun; Burçin Baran; Doğan Köse; Jia Sun; Mehmet Bakırcıoğlu; Jennifer Moliterno Günel; M Necmettin Pamir; Ketu Mishra-Gorur; Kaya Bilguvar; Katsuhito Yasuno; Alexander Vortmeyer; Anita J Huttner; Chris Sander; Murat Günel
Journal:  Neuro Oncol       Date:  2015-03-03       Impact factor: 12.300

3.  SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions.

Authors:  Wanding Zhou; Timothy J Triche; Peter W Laird; Hui Shen
Journal:  Nucleic Acids Res       Date:  2018-11-16       Impact factor: 16.971

4.  APE1/REF-1 down-regulation enhances the cytotoxic effects of temozolomide in a resistant glioblastoma cell line.

Authors:  Ana P Montaldi; Paulo R D V Godoy; Elza T Sakamoto-Hojo
Journal:  Mutat Res Genet Toxicol Environ Mutagen       Date:  2015-06-05       Impact factor: 2.873

5.  Spatiotemporal dynamics of intratumoral immune cells reveal the immune landscape in human cancer.

Authors:  Gabriela Bindea; Bernhard Mlecnik; Marie Tosolini; Amos Kirilovsky; Maximilian Waldner; Anna C Obenauf; Helen Angell; Tessa Fredriksen; Lucie Lafontaine; Anne Berger; Patrick Bruneval; Wolf Herman Fridman; Christoph Becker; Franck Pagès; Michael R Speicher; Zlatko Trajanoski; Jérôme Galon
Journal:  Immunity       Date:  2013-10-17       Impact factor: 31.745

6.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.

Authors:  Michael I Love; Wolfgang Huber; Simon Anders
Journal:  Genome Biol       Date:  2014       Impact factor: 13.583

7.  HTSeq--a Python framework to work with high-throughput sequencing data.

Authors:  Simon Anders; Paul Theodor Pyl; Wolfgang Huber
Journal:  Bioinformatics       Date:  2014-09-25       Impact factor: 6.937

8.  QuPath: Open source software for digital pathology image analysis.

Authors:  Peter Bankhead; Maurice B Loughrey; José A Fernández; Yvonne Dombrowski; Darragh G McArt; Philip D Dunne; Stephen McQuaid; Ronan T Gray; Liam J Murray; Helen G Coleman; Jacqueline A James; Manuel Salto-Tellez; Peter W Hamilton
Journal:  Sci Rep       Date:  2017-12-04       Impact factor: 4.379

9.  Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design.

Authors:  Jo Lynne Rokita; Komal S Rathi; Maria F Cardenas; Kristen A Upton; Joy Jayaseelan; Katherine L Cross; Jacob Pfeil; Laura E Egolf; Gregory P Way; Alvin Farrel; Nathan M Kendsersky; Khushbu Patel; Krutika S Gaonkar; Apexa Modi; Esther R Berko; Gonzalo Lopez; Zalman Vaksman; Chelsea Mayoh; Jonas Nance; Kristyn McCoy; Michelle Haber; Kathryn Evans; Hannah McCalmont; Katerina Bendak; Julia W Böhm; Glenn M Marshall; Vanessa Tyrrell; Karthik Kalletla; Frank K Braun; Lin Qi; Yunchen Du; Huiyuan Zhang; Holly B Lindsay; Sibo Zhao; Jack Shu; Patricia Baxter; Christopher Morton; Dias Kurmashev; Siyuan Zheng; Yidong Chen; Jay Bowen; Anthony C Bryan; Kristen M Leraas; Sara E Coppens; HarshaVardhan Doddapaneni; Zeineen Momin; Wendong Zhang; Gregory I Sacks; Lori S Hart; Kateryna Krytska; Yael P Mosse; Gregory J Gatto; Yolanda Sanchez; Casey S Greene; Sharon J Diskin; Olena Morozova Vaske; David Haussler; Julie M Gastier-Foster; E Anders Kolb; Richard Gorlick; Xiao-Nan Li; C Patrick Reynolds; Raushan T Kurmasheva; Peter J Houghton; Malcolm A Smith; Richard B Lock; Pichai Raman; David A Wheeler; John M Maris
Journal:  Cell Rep       Date:  2019-11-05       Impact factor: 9.423

Review 10.  Immune checkpoint inhibitors for urothelial carcinoma.

Authors:  Hyung Suk Kim; Ho Kyung Seo
Journal:  Investig Clin Urol       Date:  2018-08-31
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  14 in total

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Authors:  Anson T Ku; Scott Wilkinson; Adam G Sowalsky
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Review 2.  Mesenchymal Stem Cell-Derived Antimicrobial Peptides as Potential Anti-Neoplastic Agents: New Insight into Anticancer Mechanisms of Stem Cells and Exosomes.

Authors:  Kasra Moeinabadi-Bidgoli; Malihe Rezaee; Hamidreza Rismanchi; Mohaddese Malek Mohammadi; Amirhesam Babajani
Journal:  Front Cell Dev Biol       Date:  2022-07-06

3.  Functional Precision Medicine: Putting Drugs on Patient Cancer Cells and Seeing What Happens.

Authors:  Anthony Letai
Journal:  Cancer Discov       Date:  2022-02       Impact factor: 38.272

4.  The Landscape of Immune Microenvironments in Racially Diverse Breast Cancer Patients.

Authors:  Melissa A Troester; Katherine A Hoadley; Alina M Hamilton; Amber N Hurson; Linnea T Olsson; Andrea Walens; Joseph Nsonwu-Farley; Erin L Kirk; Yara Abdou; Stephanie M Downs-Canner; Jonathan S Serody; Charles M Perou; Benjamin C Calhoun
Journal:  Cancer Epidemiol Biomarkers Prev       Date:  2022-07-01       Impact factor: 4.090

5.  Increased AOC1 Expression Promotes Cancer Progression in Colorectal Cancer.

Authors:  Fangyuan Liu; Weijun Ou; Wenbo Tang; Zhenyu Huang; Zhehui Zhu; Wenjun Ding; Jihong Fu; Yilian Zhu; Chenying Liu; Weimin Xu; Peng Du
Journal:  Front Oncol       Date:  2021-05-05       Impact factor: 6.244

Review 6.  Functional precision oncology: Testing tumors with drugs to identify vulnerabilities and novel combinations.

Authors:  Anthony Letai; Patrick Bhola; Alana L Welm
Journal:  Cancer Cell       Date:  2021-12-23       Impact factor: 31.743

7.  Selective Inhibition of DNA Polymerase β by a Covalent Inhibitor.

Authors:  Shelby C Yuhas; Daniel J Laverty; Huijin Lee; Ananya Majumdar; Marc M Greenberg
Journal:  J Am Chem Soc       Date:  2021-05-20       Impact factor: 16.383

Review 8.  Understanding and overcoming resistance to PARP inhibitors in cancer therapy.

Authors:  Mariana Paes Dias; Sarah C Moser; Shridar Ganesan; Jos Jonkers
Journal:  Nat Rev Clin Oncol       Date:  2021-07-20       Impact factor: 66.675

9.  TP73-AS1 is induced by YY1 during TMZ treatment and highly expressed in the aging brain.

Authors:  Gal Mazor; Dmitri Smirnov; Hila Ben David; Ekaterina Khrameeva; Debra Toiber; Barak Rotblat
Journal:  Aging (Albany NY)       Date:  2021-06-11       Impact factor: 5.682

10.  VRK1 Depletion Facilitates the Synthetic Lethality of Temozolomide and Olaparib in Glioblastoma Cells.

Authors:  Elena Navarro-Carrasco; Pedro A Lazo
Journal:  Front Cell Dev Biol       Date:  2021-06-14
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