Abstract B023: An integrated approach to understanding the evolutionary dynamics of childhood acute lymphoblastic leukemia from diagnosis to relapse

Up to 20% of children with acute lymphoblastic leukemia (cALL) will relapse after initially responding to treatment. Dissecting the evolutionary population dynamics leading to relapse would help explain treatment failure from a mechanistic standpoint, aiding the design of more effective therapies. Comparisons of genetic heterogeneity at diagnosis and relapse have shown that relapse is often dominated by either a specific diagnostic subclone or its evolutionary progeny, leading to the idea that selection during treatment of cALL primarily operates at the genotype level. However, due to the technical difficulties associated with analyzing the rare cells that survive treatment in patients - definitive support for this idea is thus far missing. To overcome this challenge, we have previously developed a xenograft model of cALL induction chemotherapy treatment. Combining this with single-cell resolution analysis, we showed that, despite a massive reduction in leukemic burden, the first 28 days of chemotherapy have little impact on the genetic heterogeneity of cALL. This finding was inconsistent with the idea of selection acting at the level of genotypes. Instead, treatment induced a bottleneck at the level of cell state, determining the survival of a transcriptionally homogeneous population broadly characterized by reduced biosynthetic activity and cell dormancy. However, cALL treatment lasts several years and cannot be entirely modelled in vivo. Hence to assess whether genetic selection could act on a larger timescale or whether the clonal dominance frequently observed at relapse results from stochastic sweeps, we have implemented a data-driven mathematical model using the Hybrid Automata Library (HAL) to simulate longer treatment courses. The model allows for explicit spatial and temporal tracking of the evolutionary trajectories of individual cALL cells from diagnosis to relapse. Surprisingly we found that preserved genetic heterogeneity post-induction treatment and clonal dominance at relapse are features of virtually all relapsed leukemias; regardless of whether subclones with equal or varied fitness populate the diagnostic disease. This finding highlights the misinterpretation risks associated with limited disease snapshot analysis. Crucially, although genetically driven leukemias and leukemias in which all subclones have a similar probability of entering dormancy had similar endpoints, their temporal evolutionary dynamics largely differed. In the latter, reproducibly fewer cells survived induction chemotherapy, and relapse occurred on longer timelines, predominantly post-treatment. This observation provides the first empirical evidence of the notion that early and late relapse in cALLs may result from distinct selection mechanisms. Our preliminary data further suggest that even when high-fitness subclones are present, specifically targeting them is, in many cases, unlikely to improve overall outcome. Alternative dose fractionation protocols leveraging the epigenetically homogenous nature of residual cells may hold a better promise.

Citation Format: Virginia A. Turati, Javier Herrero Sanchez, Jeffrey West, Mark Robertson-Tessi, Tariq Enver, Andriy Marusyk, Alexander R. A. Anderson. An integrated approach to understanding the evolutionary dynamics of childhood acute lymphoblastic leukemia from diagnosis to relapse [abstract]. In: Proceedings of the AACR Special Conference on the Evolutionary Dynamics in Carcinogenesis and Response to Therapy; 2022 Mar 14-17. Philadelphia (PA): AACR; Cancer Res 2022;82(10 Suppl):Abstract nr B023.

An instructive role for Interleukin-7 receptor α in the development of human B-cell precursor leukemia

Kinase signaling fuels growth of B-cell precursor acute lymphoblastic leukemia (BCP-ALL). Yet its role in leukemia initiation is unclear and has not been shown in primary human hematopoietic cells. We previously described activating mutations in interleukin-7 receptor alpha (IL7RA) in poor-prognosis "ph-like" BCP-ALL. Here we show that expression of activated mutant IL7RA in human CD34+ hematopoietic stem and progenitor cells induces a preleukemic state in transplanted immunodeficient NOD/LtSz-scid IL2Rγnull mice, characterized by persistence of self-renewing Pro-B cells with non-productive V(D)J gene rearrangements. Preleukemic CD34+CD10highCD19+ cells evolve into BCP-ALL with spontaneously acquired Cyclin Dependent Kinase Inhibitor 2 A (CDKN2A) deletions, as commonly observed in primary human BCP-ALL. CRISPR mediated gene silencing of CDKN2A in primary human CD34+ cells transduced with activated IL7RA results in robust development of BCP-ALLs in-vivo. Thus, we demonstrate that constitutive activation of IL7RA can initiate preleukemia in primary human hematopoietic progenitors and cooperates with CDKN2A silencing in progression into BCP-ALL.

Chemotherapy induces canalization of cell state in childhood B-cell precursor acute lymphoblastic leukemia

Comparison of intratumor genetic heterogeneity in cancer at diagnosis and relapse suggests that chemotherapy induces bottleneck selection of subclonal genotypes. However, evolutionary events subsequent to chemotherapy could also explain changes in clonal dominance seen at relapse. We, therefore, investigated the mechanisms of selection in childhood B-cell precursor acute lymphoblastic leukemia (BCP-ALL) during induction chemotherapy where maximal cytoreduction occurs. To distinguish stochastic versus deterministic events, individual leukemias were transplanted into multiple xenografts and chemotherapy administered. Analyses of the immediate post-treatment leukemic residuum at single-cell resolution revealed that chemotherapy has little impact on genetic heterogeneity. Rather, it acts on extensive, previously unappreciated, transcriptional and epigenetic heterogeneity in BCP-ALL, dramatically reducing the spectrum of cell states represented, leaving a genetically polyclonal but phenotypically uniform population with hallmark signatures relating to developmental stage, cell cycle and metabolism. Hence, canalization of cell state accounts for a significant component of bottleneck selection during induction chemotherapy.

A Human IPS Model Implicates Embryonic B-Myeloid Fate Restriction as Developmental Susceptibility to B Acute Lymphoblastic Leukemia-Associated ETV6-RUNX1

ETV6-RUNX1 is associated with childhood acute B-lymphoblastic leukemia (cALL) functioning as a first-hit mutation that initiates a clinically silent pre-leukemia in utero. Because lineage commitment hierarchies differ between embryo and adult, and the impact of oncogenes is cell-context dependent, we hypothesized that the childhood affiliation of ETV6-RUNX1 cALL reflects its origins in a progenitor unique to embryonic life. We characterize the first emerging B cells in first-trimester human embryos, identifying a developmentally restricted CD19^-IL-7R⁺ progenitor compartment, which transitions from a myeloid to lymphoid program during ontogeny. This developmental series is recapitulated in differentiating human pluripotent stem cells (hPSCs), thereby providing a model for the initiation of cALL. Genome-engineered hPSCs expressing ETV6-RUNX1 from the endogenous ETV6 locus show expansion of the CD19^-IL-7R⁺ compartment, show a partial block in B lineage commitment, and produce proB cells with aberrant myeloid gene expression signatures and potential: features (collectively) consistent with a pre-leukemic state.

Characterization of Rare, Dormant, and Therapy-Resistant Cells in Acute Lymphoblastic Leukemia

Tumor relapse is associated with dismal prognosis, but responsible biological principles remain incompletely understood. To isolate and characterize relapse-inducing cells, we used genetic engineering and proliferation-sensitive dyes in patient-derived xenografts of acute lymphoblastic leukemia (ALL). We identified a rare subpopulation that resembled relapse-inducing cells with combined properties of long-term dormancy, treatment resistance, and stemness. Single-cell and bulk expression profiling revealed their similarity to primary ALL cells isolated from pediatric and adult patients at minimal residual disease (MRD). Therapeutically adverse characteristics were reversible, as resistant, dormant cells became sensitive to treatment and started proliferating when dissociated from the in vivo environment. Our data suggest that ALL patients might profit from therapeutic strategies that release MRD cells from the niche.