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Epigenetic Therapies Could Modulate EGFR Amplification, Effecting Therapeutic Response

November 27, 2019

PHILADELPHIA (November 27, 2019) – One of the greatest challenges faced by cancer researchers today is understanding how tumor cells become resistant to therapies. Researchers from Fox Chase Cancer Center recently made a discovery that indicates that certain epigenetic modifiers and extracellular signals can directly control the amplification of an important oncogene, EGFR, a process previously thought to be random. 

EGFR DNA amplification–or copy gains–tends to occur in hard-to-treat cancers such as lung, colorectal, and brain tumors. Although amplification of EGFR results in increased sensitivity to drugs targeting that gene, prolonged treatment with these EGFR inhibitors can reduce the copies of EGFR, leading to therapy resistance, said Johnathan R. Whetstine, PhD. Whetstine, the study’s corresponding author, is the Jack Schultz Basic Science Endowed Chair and Program Leader of Cancer Epigenetics at Fox Chase.

The paper, “Histone Lysine Methylation Dynamics Control EGFR DNA Amplification,” was published in Cancer Discovery, a journal of the American Association for Cancer Research.

 “Our data suggests that if we target these epigenetic modifiers we can dial up or down EGFR amplification and, in turn, modulate the associated drug response. We believe that this could provide a more homogeneous cell population, which might result in more consistent response to drugs targeting the pathway,” Whetstine said.

Previous work by Whetstine and his lab demonstrated that an enzyme, called KDM4A, could control certain chromosomal region’s ability to re-replicate and be amplified. The current study, conducted in collaboration with his former lab at Massachusetts General Hospital, demonstrated that KDM4A overexpression promotes EGFR DNA amplification. “This control occurs with very specific combinations of enzymes,” Whetstine said.

Specifically, H3K4/9/27 lysine methyltransferases and demethylases were working in a concerted effort to maintain a balance, he said. As an example, KDM4A overexpression promotes copy gain in conjunction with three H3K4 methyltransferases: KMT2A/MLL1, SETD1A, and SETD1B, while the H3K27 methyltransferase EZH2 suppresses the amplification.

Additionally, Whetstine and his team showed that hypoxia and epidermal growth factor can directly promote EGFR amplification through modulation of the enzymes controlling EGFR copy gains.

After 24 hours of exposure to hypoxia, KDM4A in cultured cells was stabilized and promoted EGFR copy gains; a return to normoxia after 24 hours of hypoxia restored EGFR copy number to original levels.

Similarly, treating cells for 24 hours with epidermal growth factors resulted in significant copy number gains of the EGFR locus and these gains were entirely dependent on KDM4A, as any inhibition of the KDM4 family resulted in a loss of these gains. Of importance, they demonstrated that combined hypoxia and EGF exposure resulted in higher DNA amplification levels, which highlights the impact multiple input signals could have on DNA amplification.

“What this means is the generation of these amplifications is a natural cellular process and that these processes are allowing the cell to change copy number in a systematic way that could be used to promote cell viability and proliferation,” Whetstine said.

“We showed that copy number is druggable by targeting the epigenetic factors involved, which has significant clinical implications. Therefore, we can rheostat levels of copy gains up or down, and in return, change responses to growth factors and drugs.”

This work was supported by the American Lung Association, a R01GM097360 grant, and the National Institutes of Health/National Cancer Institute Cancer Center Support Grant P30 CA006927. The lead author, Thomas Clarke, PhD, was supported by a postdoctoral fellowship from the European Molecular Biology Organization.

Fox Chase Cancer Center (Fox Chase), which includes the Institute for Cancer Research and the American Oncologic Hospital and is a part of Temple Health, is one of the leading comprehensive cancer centers in the United States. Founded in 1904 in Philadelphia as one of the nation’s first cancer hospitals, Fox Chase was also among the first institutions to be designated a National Cancer Institute Comprehensive Cancer Center in 1974. Fox Chase is also one of just 10 members of the Alliance of Dedicated Cancer Centers. Fox Chase researchers have won the highest awards in their fields, including two Nobel Prizes. Fox Chase physicians are also routinely recognized in national rankings, and the Center’s nursing program has received the Magnet recognition for excellence five consecutive times. Today, Fox Chase conducts a broad array of nationally competitive basic, translational, and clinical research, with special programs in cancer prevention, detection, survivorship, and community outreach. It is the policy of Fox Chase Cancer Center that there shall be no exclusion from, or participation in, and no one denied the benefits of, the delivery of quality medical care on the basis of race, ethnicity, religion, sexual orientation, gender, gender identity/expression, disability, age, ancestry, color, national origin, physical ability, level of education, or source of payment.

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