Genomics Reveal New Layers of Pediatric Leukemia Biology

A strong sense of purpose permeated the AACR Special Conference in Cancer Research: Bridging Discovery and Clinical Impact in Pediatric Cancer, held in Philadelphia on September 22-25. While dedication is a hallmark of the scientific community, researchers and clinicians focused on pediatric cancer face a particularly compelling mission: improving outcomes for children diagnosed with cancer while reducing the lifelong burdens that treatment can impose.

For pediatric leukemia, meeting that challenge increasingly means looking beyond genetics, such as the mutations that revealed how these cancers develop, to genomics, which considers all of a patient’s genes alongside environmental influences and the complex interactions between them. Genomic approaches are now helping researchers understand how leukemia cells behave, respond to treatment, and why some survive therapy and return. These insights are revealing layers of leukemia biology that cannot be captured by a list of genetic alterations alone.

Redefining Pediatric Leukemia Classification with Genomics

During the keynote presentation of the opening session, Charles Mullighan, MBBS (Hons), MSc, MD, a member in the pathology department at St. Jude Children’s Research Hospital, discussed how genomic technologies have accelerated our understanding of pediatric acute leukemia. Acute leukemia is a blood cancer that begins in immature blood-forming cells and is primarily categorized based on the cell type implicated. Childhood acute lymphoblastic leukemia (ALL), which affects lymphocytes, is the most common type of cancer in children.

What began as an effort to catalog genetic alterations has evolved into a framework for defining disease subtypes, guiding treatment decisions, and identifying mechanisms of resistance. The clinical impact of this approach is already evident in precision medicine initiatives such as the INITIALL trial, which uses genomic information to help match pediatric patients to therapies based on their likelihood to respond.

However, not all leukemia subtypes have benefited equally from these advances. T-cell acute lymphoblastic leukemia (T-ALL) and B-cell acute lymphoblastic leukemia (B-ALL) are acute leukemias, but they originate from different cell types. T-ALL arises from early T cells, while B-ALL starts from developing B cells. “T-ALL has historically been less well characterized than its B-cell counterpart,” said Mullighan. Understanding relapsed and refractory T-ALL has been particularly limited, hampering efforts to identify the biological drivers underlying treatment failure.

To address this gap, Mullighan and collaborators conducted large-scale genomic analyses of childhood T-ALL and discovered that the disease is far more heterogenous than previously appreciated. “We defined 15 distinct molecular subtypes, each characterized by unique developmental states, gene expression programs, and genetic alterations,” said Mullighan.

The study also revealed that important driver events are not confined to protein-coding genes. Instead, some leukemias were powered by mutations in noncoding regions of the genome that alter gene regulation through a phenomenon known as enhancer hijacking, in which chromosomal rearrangements place powerful regulatory elements next to oncogenes, resulting in their inappropriate activation.

“We realized how important these results were for clinical implications. Risk stratification for T-ALL is currently based largely on immunophenotyping, which classifies leukemias according to the proteins expressed on cells. When patients were grouped according to the newly defined genomic subtypes, outcome prediction improved substantially,” explained Mullighan.

To Immunotherapy and Beyond: A Role for Genomics

Next, Mullighan highlighted research from his group showing how genomic analyses can help explain why some patients respond to immunotherapy while others relapse. “In the setting of CD19-directed therapies, we find resistance arising through mutations in or loss of the CD19 target itself—a very intuitive mechanism of escape,” described Mullighan. “But increasingly we’ve seen that CD19-directed therapy failed, but there is not an obvious answer for this result in the genetics. We now have some insights into why.”

Mullighan and his team, in collaboration with John Dick, PhD, FAACR, a professor of molecular genetics at the University of Toronto in Canada, took a look beyond DNA mutations and examined the developmental identity of B-ALL. By mapping individual leukemia cells onto a normal blood-developmental map, they found that some leukemias associated with treatment resistance contained cells resembling an earlier, less differentiated state known as a common lymphoid progenitor (CLP).

CLPs were traditionally thought to be committed to producing lymphoid cells. But Mullighan’s team found evidence that these CLP-like leukemia cells retain features associated with myeloid development. “Prior to this study, it was thought that CLPs were locked into a lymphoid state and did not have multilineage potential,” explained Mullighan. Instead, regions of DNA involved in monocyte development remained accessible in these cells, suggesting that they had not completely shut down the molecular programs needed to adopt to myeloid identity. Experiments confirmed that these cells could produce myeloid cells under appropriate conditions.

“This provides a developmental explanation for why a subset of leukemias—those enriched for CLP-like cells—can fail therapy without needing to have CD19 alteration,” Mullighan added. The findings suggest that a leukemia’s developmental identity, not just its genetic mutations, may influence how it responds to treatment.

Mullighan also spoke about emerging work from his lab showing how genomics can reveal ways tumors reprogram their microenvironments to suppress immune responses and uncover subtype-specific dependencies that could be targeted therapeutically.

NUP to No Good: NUP98 Fusion Oncogenes

The next speaker Nicole Michmerhuizen, PhD, an assistant professor in the pediatric department at the University of Rochester and the 2025 AACR-St. Baldrick’s Foundation Pediatric Cancer Research Grantee, took a deep dive into a subtype of childhood acute myeloid leukemia (AML) driven by NUP98 fusions. This subtype is observed in approximately 5% of children with AML and is associated with chemotherapy resistance and relapse.

Normally, NUP98, a key component of the nuclear pore complex, acts as a gatekeeper that regulates the transport of molecules in and out of the nucleus. The NUP98 gene is frequently involved in gene fusions, most often with partners that contain DNA binding or chromatin modifying domains. “These domains mediate the ability of the fusion protein to act as a transcription factor, interacting with chromatin, and influencing the expression of several leukemia-associated genes, including HOX genes which drive a stem cell-like expression program,” explained Michmerhuizen.

“During my postdoc with Dr. Mullighan, we published a study that showed that NUP98 fusion oncogenes formed transcriptional complexes, or condensates, in the nucleus through a process called phase separation,” said Michmerhuizen. “When we disrupted their ability to form these condensates, the fusion also lost its ability to promote leukemia-associated self-renewal and activate HOX genes. These data suggested that phase separation is important not only for localization of the fusion protein, but also for its role in cell transformation and gene deregulation.”

But understanding where the fusion protein goes was only the beginning. Michmerhuizen next asked what other proteins were present within these condensates, as they had a strong likelihood of interacting with—and maybe regulating—NUP98 fusions. “We wanted to comprehensively characterize the NUP98 fusion interactome and identify proteins that could potentially be therapeutically targeted,” explained Michmerhuizen.

Using protein interaction mapping, she uncovered a network of proteins, some already well known and others previously unrecognized, including KAT6A and KAT7 histone acetyltransferase complexes. Immunofluorescence experiments verified that these interactions occur within condensates. In parallel, Michmerhuizen used functional genomics to demonstrate that loss of KAT6A or KAT7 decreased the leukemia cells’ ability to persist, implying an important biological role.

Michmerhuizen then asked whether they could exploit the leukemia’s dependency on KAT6A and KAT7 therapeutically. The answer, she showed, was more complicated than simply finding a vulnerable target.

“When we pharmacologically inhibited KAT6 or KAT7A in a mouse model of a NUP98 fusion, we saw an initial reduction in leukemia burden, but when the drug was withdrawn, the leukemia reemerged. That led us to think that maybe targeting one interactor of NUP98 is not going to be sufficient,” said Michmerhuizen. “Combined inhibition may be more effective.”

That idea led the team to menin, another protein that has emerged as a promising new therapeutic approach for certain AML patients. When Michmerhuizen combined menin inhibition with KAT6A/KAT7A inhibition, the two treatments produced a much stronger response than either treatment alone.

The combination did more than simply kill more leukemia cells. “So we started to see that these two drugs were really doing something different,” said Michmerhuizen. “We were seeing more differentiation, and a much more profound transcriptional response with the combination, especially a greater reduction in stem-cell associated genes.”

But how does KAT6A/KAT7 therapy work, and why does it work even better when combined with a menin inhibitor? Michmerhuizen found a clue by looking at what happened to the NUP98 fusion itself. “We found that inhibiting KAT6A and KAT7 disrupted NUP8 fusion’s ability to drive transcription. Specifically, blocking KAT6A and KAT7 led to the displacement of the NUP98 fusion from the DNA,” she explained.

“The reason that the combination therapy synergized was because KAT6A/7 and menin robustly alter the expression of fusion target genes, as well as alter gene expression at other sites,” added Michmerhuizen.

Michmerhuizen also covered advances in targeting another group of proteins that interact with NUP98 fusions, highlighting the growing potential of targeting the molecular partners that help these fusions drive leukemia.