Project Summary.
Acute leukemias are aggressive hematological tumors and the most common malignancy in children and
adolescents. Though cure rates have steadily improved over the last 50 years with the implementation of
intensive chemotherapy regimens, today 20% of pediatric acute lymphoblastic leukemia (ALL) patients will
relapse or develop refractory disease. Moreover, therapeutic outcomes in acute myeloid leukemia (AML) are
significantly worse with cure rates in the range of 65-70%. Despite much progress in the characterization of the
genetic and molecular basis of leukemia, the specific mechanisms mediating resistance, disease progression
and relapse remain largely unknown. Thus, genomic profiling analyses have shown marked genetic
heterogeneity at relapse which together with the complex combination chemotherapy protocols used in
treatment, make it difficult to directly assign precise roles in resistance for most of relapse-associated mutations.
My central hypothesis is that genetic mutations, signaling and epigenetic mechanisms controlling self-renewal,
response to stress and resistance converge on a restricted number of master regulators that drive the acquisition
of a drug-tolerant persistent phenotype at minimal residual disease and ultimately relapse. The objective of this
proposal is to establish the specific role of remission- and relapse-associated transcriptional and epigenetic
regulators as drivers of drug-tolerant persistent phenotypes and chemotherapy resistance across pediatric acute
leukemias. These studies will be impactful to our understanding of the mechanisms conducive to therapeutic
failure and will facilitate the rationale design of therapies directed to the eradication of high-risk minimal residual
disease and the prevention of leukemia relapse. Towards this goal I propose the following specific aims: Aim 1
(mentored phase): To interrogate by single cell mutational profiling the impact of minimal residual disease
composition and clonal dynamics in ALL relapse; Aim 2 (mentored/independent phase): To identify and target
master regulators of single cell transcriptional and epigenetic states driving ALL persistence, disease progression
and relapse; and Aim 3 (independent phase): To map and target genetic, transcriptional and epigenetic drivers
of minimal residual disease and leukemia relapse in pediatric AML. To address these questions, I will use
diagnostic-remission-relapse matched leukemia primary samples and leukemia xenografts, combined with
single-cell genomics, transcriptomics and epigenomics to functionally characterize convergent mechanisms
driving minimal residual disease, resistance and relapse. These analyses will inform functional testing of master
regulators and direct single-cell reverse genetic CRISPR screens to define the role of specific genes as drivers
of chemoresistance and relapse. These results will ultimately facilitate the rational design of therapies to improve
the treatment of this devastating childhood disease.