Histone lysine methylation dynamics control EGFR DNA copy-number amplification

Thomas L. Clarke, Ran Tang, Damayanti Chakraborty, Capucine Van Rechem, Fei Ji, Sweta Mishra, Anqi Ma, H. Ümit Kaniskan, Jian Jin, Michael S. Lawrence, Ruslan I. Sadreyev, Jonathan R. Whetstine

Research output: Contribution to journalArticlepeer-review

31 Scopus citations


Acquired chromosomal DNA copy gains are a feature of many tumors; however, the mechanisms that underpin oncogene amplification are poorly understood. Recent studies have begun to uncover the importance of epigenetic states and histone lysine methyltransferases (KMT) and demethylases (KDM) in regulating transient site-specific DNA copy-number gains (TSSG). In this study, we reveal a critical interplay between a myriad of lysine methyltransferases and demethylases in modulating H3K4/9/27 methylation balance to control extrachromosomal amplification of the EGFR oncogene. This study further establishes that cellular signals (hypoxia and EGF) are able to directly promote EGFR amplification through modulation of the enzymes controlling EGFR copy gains. Moreover, we demonstrate that chemical inhibitors targeting specific KMTs and KDMs are able to promote or block extrachromosomal EGFR amplification, which identifies potential therapeutic strategies for controlling EGFR copy-number heterogeneity in cancer, and, in turn, drug response. SIGNIFICANCE: This study identifies a network of epigenetic factors and cellular signals that directly control EGFR DNA amplification. We demonstrate that chemical inhibitors targeting enzymes controlling this amplification can be used to rheostat EGFR copy number, which uncovers therapeutic opportunities for controlling EGFR DNA amplification heterogeneity and the associated drug response.

Original languageEnglish
Pages (from-to)306-325
Number of pages20
JournalCancer Discovery
Issue number2
StatePublished - Feb 2020


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