Epigenomic Biomarkers for Treatment Resistance & Lineage Switching Potential in Acute Leukemia

Acute lymphoblastic leukemia (ALL) is the most common childhood leukemia, and modern induction protocols secure remission in up to 98% of pediatric cases. But relapse rates are high, and late effects are common among survivors. Infant ALL, particularly KMT2A rearranged (KMT2Ar) disease, has poor long-term survival (about 50%) despite decades of treatment optimization.

KMT2A was originally named MLL, for Mixed Lineage Leukemia. Lineage switching via loss of transcriptional and antigenic programs defines an ultra-high-risk group of KMT2Ar ALL. Lineage specific immunotherapy in frontline ALL treatment has fueled increasing reports of lineage switching, spurring a search for markers predictive of switch potential. Relapses of ALL, such as acute myeloid leukemia (AML) or mixed-phenotype leukemia (MPAL), are almost uniformly refractory. Even among primary MPAL patients, KMT2Ar cases have notably unfavorable outcomes.

Menin inhibitors (MENi) target key vulnerabilities of KMT2Ar leukemia. Clinical reports of rapidly developing MENi resistance, often associated with lineage switching, have spawned a search for markers of resistance potential. However, a subset of KMT2Ar AML patients with monocytic features responds durably to CD33-targeted immunotherapy and chemotherapy. This suggests that myeloid transformation potential alone is insufficient to predict treatment outcome. We reasoned that epigenomic profiling of ALL, AML, and MPAL patient samples, before and after lineage switching and MENi resistance, could inform a search for treatment-relevant biomarkers.

In a cohort of 37 KMT2Ar cases profiled via AutoCUT&Tag, we identified an excess of the histone acetylation reader ENL at non-canonical AML-specific targets among lineage-switching ALL cases. ENL was significantly enriched at these sites in patient samples before lineage switching but absent in B-ALL cases that did not switch lineages. Previous work in a small cohort of adult MPAL cases showed significantly better outcomes in (mostly fusion-negative) cases whose AML-like or ALL-like DNA methylation signatures matched the target of therapy.

To investigate whether this observation could extend to KMT2Ar cases and inform MENi resistance, we analyzed DNA methylation across correlated blocks of CpG loci overlapping ENL binding sites in 1599 pediatric and adult ALL, AML, MPAL, and normal bone marrow samples. We found significant differences in DNA methylation between cases with favorable and unfavorable outcomes, particularly in KMT2Ar cases with lineage alterations at relapse, and these differences were more pronounced at noncanonical (lineage-switch-related) AML associated peaks. Our results illustrate the feasibility of rapid epigenomic profiling in high-risk acute leukemia for clinical trial optimization and improvement of outcomes in KMT2Ar cases.

Triche:NIH: Research Funding; Aqtual: Current equity holder in private company; QuantumSI: Current equity holder in private company.