Mechanisms controlling gene expression offer avenues for leukemia treatment and diagnosis

Most pediatric leukemia cases are highly treatable — but certain subtypes are either persistent or resistant to current treatments. About 15 to 20% of patients experience either relapsed or refractory leukemia, and many do not reach remission. Scientists at St. Jude are working to understand the factors that contribute to these cases better, including epigenetic control of gene expression.

Epigenetic mechanisms include histone modification, which can control access to DNA and packaging in chromatin, and DNA methylation, which can regulate gene expression. By uncovering patterns in these processes, researchers can pinpoint which patients are at higher risk of treatment relapse or resistance. Increased understanding of how these epigenetic mechanisms go awry in cancer can also point researchers toward previously unknown or unconsidered therapies that are potentially more effective and less toxic than conventional treatments.

Discovering the genetic and epigenetic mechanisms that drive disease

As genetic and epigenetic underpinnings of diseases are systematically identified, researchers have been able to diagnose and treat patients with high-risk leukemias more specifically. These include pediatric acute myeloid leukemia (AML), myelodysplastic syndromes (MDS), rare types of acute lymphoblastic leukemia (ALL) and mixed phenotype acute leukemia (MPAL).

Nearly 15 years ago, researchers, as part of the St. Jude–Washington University Pediatric Cancer Genome Project (PCGP), provided preliminary clues into the cause of refractory cancers. They found that mutations in genes encoding epigenetic regulators were more common in patients with a type of ALL called early T-cell precursor ALL (ETP-ALL) and that this disease has more in common genetically with AML. This suggested AML therapies may be of benefit. Around the same time, a 2013 study published in the Journal of Clinical Investigation, positioned epigenetic programming as a hallmark of ALL, occurring in all patients regardless of the presence of genetic mutations. These studies showcase how St. Jude researchers were at the forefront of emphasizing the roles played by epigenetic mechanisms in childhood cancer.  

“Much like there are signatures of gene expression that classify leukemia, we showed that there are also signatures of DNA methylation between different subtypes of leukemia,” said Charles Mullighan, MBBS (Hons), MSc, MD, St. Jude Comprehensive Cancer Center senior deputy director, and Department of Pathology member. “The strength of that signature varied between subtypes. We also found that for a subset of genes, it appeared that their level of expression was being controlled by methylation. There is currently quite a lot of interest in using sequencing-based approaches to profile methylation as classifiers of disease subtype.”

Treatment targets emerge from epigenetic findings

Today, more sophisticated technologies, including whole genome sequencing, RNA sequencing, and genome editing strategies, have enabled researchers to develop a deeper understanding of epigenetics. “We have a better set of tools that allow us to not only look at epigenetic states, but also to perturb them and understand their role in biology,” said Jeffery Klco, MD, PhD, Department of Pathology.  

Recent results from a multi-institutional trial led by St. Jude researchers, including Klco, and presented at the 2025 American Society of Hematology Annual Meeting found that five days of epigenetic priming with azacitidine or decitabine before each course of chemotherapy improved outcomes in children with AML. Priming lowered total genome-wide methylation and improved three-year event-free survival outcomes compared to historical controls.

“The study showed us that epigenetic priming is tolerable and effective for pediatric AML,” said Klco. “We should evaluate it as a potential standard of care for future AML trials.”

Mullighan, whose earlier work helped establish methylation patterns as a hallmark of ALL, has also been part of a team that is investigating how fusion oncoproteins drive leukemia at the epigenetic level. In a 2020 study published in Blood, Klco, Mullighan, Taosheng Chen, PhD, Department of Chemical Biology & Therapeutics and Richard Kriwacki, PhD, Department of Structural Biology, teamed up with other research institutions to study NUP98 fusion oncoproteins, which are present in pediatric leukemias with poor outcomes. They found that changes in chromatin structure and gene expression influence whether certain cells transform into malignant leukemic cells.

They built on this research in a 2022 study, which described the association between biomolecular phase separation in NUP98 fusion oncoproteins and leukemogenesis. More recently, St. Jude and other research institutions continued to investigate NUP98, finding that KAT6/KAT7 (MOZ/MORF), which are part of the MYST family of histone acetyltransferase complex proteins, are important druggable targets for AML.

“The results we presented in 2020 were part of a journey,” said Mullighan. “There are several other compounds that show activity in NUP98-rearranged leukemias, and we’re testing those in additional models and in different combinations to identify the most potent drug combinations. Coming at the complex from multiple nodes simultaneously can be more effective and synergistic than trying one drug to kill a high-risk leukemia.”

While many potential epigenetic therapies are in development for pediatric patients with leukemias, those with high-risk relapsed or refractory disease with a KMT2A rearrangement or a nucleophosmin 1 (NPM1) mutation have the option of a Food and Drug Administration approved targeted therapy. Revumenib, a menin inhibitor, blocks the interaction between the menin protein and KMT2A fusion oncoproteins. St. Jude is currently recruiting for a clinical trial to test if revumenib is safe in pediatric patients with AML or acute leukemia of ambiguous lineage (ALAL) when used with azacitidine and venetoclax, a BCL-2 inhibitor.

Chunliang Li, PhD, Department of Tumor Cell Biology, is diving deeper into KMT2A-rearranged leukemia to find the next generation of targets. By leveraging the power of CRISPR/Cas9 screens, Li’s lab recently showed how combining BET and GSK3 inhibitors impedes the growth of KMT2A-rearranged leukemia.  

By focusing on the oncogene HOXA9, a protein overexpressed in high-risk leukemia, investigators in Li’s lab revealed functional targets bound and regulated by HOXA9, many of which are druggable. Inspired by these studies, Li’s lab conducted a genome-wide CRISPR screen to identify the most important drivers of disease in KMT2A-rearranged leukemia. The results led them to focus on poorly studied RNA-binding proteins. They conducted an additional screen to filter out proteins that also affect normal blood cells. "By comparing these two lists, we focus on only the KMT2A-rearranged leukemia–dependent candidates,” Li said. “Many of the candidates were predicted to have drug potential. This is the list we think will be more promising as therapeutic targets.”

Li’s lab also studies the implications of gene transcription, chromatin architecture and chromatin accessibility maintenance in cancer. They published a study in Genome Biology last year that examined RNA and gene expression from a different angle; specifically, how it influences CTCF, a protein that helps organize DNA architecture in leukemia cells. DNA architecture determines which genes and their corresponding regulatory sequences crosstalk, which is an important aspect of understanding the epigenetic control of gene expression.

The future of epigenetic therapeutics in leukemia

As research unlocks more clues into the epigenetic underpinnings of high-risk types of leukemia, St. Jude physicians and researchers continue to work together to uncover methods for earlier diagnosis and more targeted treatment regimens. “We can clinically identify fusion oncogenes rapidly at St. Jude, which may allow us to change the way patients are treated,” said Klco. “That might include using epigenetic drugs, or it may allow us to quickly identify which patients are high-risk because we know their genetic alterations are associated with inferior outcomes.”

“Knowing more about the epigenetic factors and how they work will provide more targeted approaches against this mechanism,” said Li. “That’s one of the directions my research program mainly focuses on with RNA-binding proteins. They play a critical role in controlling tumorigenesis, maintenance and drug response. We are still at the early phase, but I think this is a gold mine.”