Researchers at the Cancer Epigenetics Institute (CEI) at Fox Chase Cancer Center have discovered how to control and stop the amplification of MYC - one of the most commonly altered cancer genes linked to aggressive tumor growth and treatment resistance.
The study, published in Molecular Cell, found that gene copy-number amplification is not a random mutation event, as long believed, but a biologically regulated process controlled by specific epigenetic machinery.
"For over 40 years, the MYC protein has been labeled 'undruggable' by the global scientific community due to its lack of a physical binding pocket for traditional small-molecule therapies, despite dysregulation into 70% of all human malignancies," said Johnathan R. Whetstine, PhD , senior author of the study and a professor and director of the CEI at Fox Chase. "Our Lab bypassed this hurdle by targeting the DNA structural assembly line rather than the finished protein, which impacts at least 30% of cancer."
The findings showed that epigenetic imbalance can directly trigger MYC amplification and drive its progression into aggressive forms like extrachromosomal DNA, according to Whetstine, who is also the co-leader of the Nuclear Dynamics and Cancer program at Fox Chase.
"Because MYC plays a central role in regulating normal cell growth, extra copies of the gene can fuel tumor development and understanding how these amplification events begin may help identify new approaches for targeting aggressive, treatment-resistant cancers," said Whetstine."
Halting the Engine of Tumor Evolution- A Direct Epigenetic Trigger
Tumors often adapt by aggressively multiplying copies of cancer-driving oncogenes, a process associated with rapid drug resistance and treatment failure. Researchers in the Whetstine lab identified the precise enzymatic "kill switches" within chromatin architecture that help regulate this targeted gene amplification.
Using human cell models, genomic analyses and mouse studies, the research team discovered that two chromatin-regulating proteins (KDM4C and SETD2) that normally help keep DNA stable and strictly regulated within cells are gatekeepers in controlling the powerful cancer gene MYC from amplifying. When SETD2 is blocked or lost, KDM4C can improperly access the MYC gene region and alter the surrounding DNA environment. Tumors also increase KDM4C, which also drives the deleterious amplifications.
The researchers found that KDM4C recruits the cell's DNA-copying machinery, causing the MYC gene to be copied repeatedly and produce extra MYC gene copies. The effect wasn't circumstantial: simply directing KDM4C with dCas9 technology to the MYC region was enough to trigger amplification - even in cells with a completely normal set of chromosomes.
"These findings demonstrate that MYC amplification is not simply a random byproduct of genomic instability," said Benjamin I. Ferman, a PhD student in Whetstine's lab and first author on the study. "There are specific epigenetic programs that actively control the process."
How Amplification Becomes Aggressive
However, copying MYC is only half the story - the real danger comes when MYC amplified cells do not die.
The findings also point to a paradox in MYC's impact on biology. MYC overactivation can normally trigger cell death, acting as a built-in safeguard against runaway growth. But the researchers found that disabling this fail-safe allowed hyper amplification and tumor formation.
The study found that when cells lose their normal ability to undergo programmed cell death, abnormal MYC amplifications can reach high levels and continue to grow. This observation was especially true when cells lost TP53, an important tumor suppressor gene that normally helps eliminate damaged cells.
Over time, the combination of disrupted epigenetic control and TP53 loss led to high levels of MYC amplification, including circular extrachromosomal DNA and ultimately promoted tumor formation in mouse models. In fact, the starting cells were non-transformed and did not cause tumors without MYC amplification.
The findings suggest that MYC amplification develops in stages. First, changes in chromatin regulation trigger the formation of extra MYC gene copies. Then, when normal cellular defense systems fail, those abnormal cells can survive, spread and become more aggressive over time. This type of relationship is related to the Two-Hit Theory that originated at Fox Chase.
A New Translational and Therapeutic Paradigm
The findings may have important implications for translational medicine. The newly identified regulatory mechanisms contain enzymatic targets that could be explored through small-molecule drug development, potentially opening new avenues for treating MYC-driven cancers, according to Whetstine.
Researchers in the Whetstine lab discovered that blocking KDM4C activity, either genetically or with targeted drugs, reduced MYC amplification in multiple experimental systems, including MYC-amplified cancer cells and animal models.
A clinically used KDM4 inhibitor, successfully suppressed MYC amplification in vivo. This study begins to tackle a major undruggable clinical challenge.
"MYC amplification appears to be much more dynamic and controlled than previously appreciated," Whetstine said. "That raises the possibility that these amplification states could potentially be therapeutically constrained."
The researchers said the findings could help identify biomarkers for cancers most likely to develop aggressive amplification states and inform new strategies to limit tumor evolution and treatment resistance. These studies are under development at the CEI and Fox Chase.
This research was supported by the National Institutes of Health and Fox Chase Cancer Center developmental funding.
In addition to Whetstine, Ferman and Fox Chase's Cancer Epigenetics Institute, collaborators from Massachusetts General Hospital, Harvard Medical School, Stanford University, the Broad Institute, and the Icahn School of Medicine at Mount Sinai, contributed to this research.
