Study Discovers a Mechanism for Genetic Changes in Therapy-Induced Leukemia, Builds on Fox Chase History of Exploring Links Between Epigenetics, Genetics, and Cancer

Johnathan Whetstine, PhD

In a recent study, researchers at Fox Chase Cancer Center demonstrated how amplification and rearrangement of a gene associated with leukemia known as MLL is directly controlled by epigenetic factors, providing needed insights into a new therapeutic opportunity.

The findings, which were published today in the prestigious journal Cell, indicate that these epigenetic regulators can be used as possible drug targets, paving the way for improved personalized, targeted medicines. The research by Johnathan Whetstine, PhD, director of the Cancer Epigenetics Institute (CEI) at Fox Chase, is part of the storied history of pioneering research at Fox Chase on the connections between epigenetics, genetics, and cancer. “

John’s study shows that chromosomal rearrangements driving cancer do not happen at random, but instead have very selective and specific pathways controlling them. His discovery establishes a new paradigm for understanding how chromosomal rearrangements occur,” said Alice Hungerford, a committed supporter of Fox Chase. She is also the widow of David Hungerford, PhD, a Fox Chase researcher and co-discoverer in 1959 of the Philadelphia chromosome, the first genetic defect linked to a specific type of cancer.

Image depicts the epigenetic balance to control MLL amplification and rearrangements published in Gray et al. Cell. Image source: Isabella G. Whetstine

Peter Jones, PhD, DSc (hon), a member of the CEI Advisory Board, agreed with Hungerford’s assessment of the study and added that it likely has implications beyond leukemia.

“While MLL is the focus of this particular study, the same is true for TCF3, a protein that plays a role in the development of lymphoid malignancies. This means that the probability is this is true for many other regions that undergo amplification and rearrangements,” said Jones, Chief Scientific Officer at the Van Andel Institute and past President of the American Association for Cancer Research.

Jones helped pioneer the field of epigenetics, particularly its role in cancer, and helped develop novel cancer therapies. Among his many accomplishments, he established the link between DNA methylation, gene expression, and differentiation.

For the Cell study, Whetstine and his colleagues focused on the factors surrounding the recurrence of leukemia following chemotherapy, specifically how the MLL gene breaks apart, repairs, and amplifies.

“The amplification and translocations of the MLL gene are prevalent factors in infant, adult, and therapy-induced leukemia,” said Whetstine. Translocation and amplification refer to processes that occur within chromosomes. Translocation occurs when a chromosome breaks and the fragment reattaches to another portion of the genome. Amplification refers to the increase in the number of copies of a gene, a process that characterizes many cancers.

“When patients receive chemotherapy using drugs like doxorubicin, they often develop secondary leukemia years down the road. So there’s been questions about how this process is facilitated and how or why MLL gene rearrangements arise so prevalently to drive these cases.”

Through multiple studies, Whetstine and colleagues showed for the first time that loss of a commonly deleted enzyme in leukemia, KDM3B, directly increases copies and rearrangement of MLL. KDM3B is an enzyme that erases methylation.

“To find out how this occurs, we did a screen and discovered that a very specific methyl transferase called G9a was important in driving methylation, and in turn, this process. When we inhibited G9a, we prevented the amplifications and rearrangements,” said Whetstine.

KDM3B and G9a add and remove methyl groups to the histones that DNA is wrapped around, which changes the properties around the DNA and in turn the stability. This process is called methylation.

“There is a specific region called the breakpoint cluster region, and that is where almost all genetic rearrangements happen for the MLL gene. This region had significant changes in methylation when KDM3B and G9a were genetically altered,” said Whetstine. “We showed that there is a mechanical reason that this region changes and it is not just random as initially thought. These enzymes directly control this location; therefore, there is actually a pathway that controls MLL translocation.”

Whetstine said this region contains a key transcription factor called CTCF, which sits in the middle of where these changes occur. When KDM3B is depleted, histone methylation increases and CTCF in this region is reduced, promoting amplification and rearrangements.

Additionally, and most importantly, the Whetstine team demonstrated that when cells are given a specific type of chemotherapy drug called topoisomerase inhibitors, such as doxorubicin, protein levels of CTCF and KDM3B are depleted by more than 50%. “Given that, you would predict that if we gave a G9a inhibitor, we should block the drug-induced change in MLL in our cells. We did,” said Whetstine.

He added that because their recent work showed positive results in both human cells and mice, a well-developed drug against the G9a target could set the stage for further research into whether it suppresses the changes in humans moving forward.

These findings stand on the shoulders of previous epigenetic discoveries at Fox Chase dating back to Beatrice Mintz, PhD, and most relevantly, the discovery of the Philadelphia chromosome rearrangement by David Hungerford and Peter Nowell, of the University of Pennsylvania. Hungerford was a research fellow pursuing his doctorate at the time of the discovery.

Hungerford and Nowell’s work, first published in 1960, laid the foundation for the field of targeted cancer therapies by discovering the rearrangement, ultimately helping to transform chronic myelogenous leukemia from a universally fatal form of cancer into one in which 95% of patients are successfully treated.

This new study sheds light on how epigenetics directly controls the emergence of amplifications and rearrangements, and could explain other events like the Philadelphia chromosome. In addition to this paradigm shift in understanding how rearrangements occur selectively, this study sheds light on how to therapeutically control the emergence of treatment-induced MLL amplifications and rearrangements driving therapy-induced leukemia.

The study titled, "Epigenetic balance ensures mechanistic control of MLL amplification and rearrangement" can be found here...