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

Abstract

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.

Complex genotype-phenotype relationships shape the response to treatment of Down Syndrome Childhood Acute Lymphoblastic Leukaemia

“…Of note, since SNP-arrays are limited in both genomic resolution (i.e., deletion size) and sensitivity to low abundance copy number variants (CNV) it is possible that our model might underestimate the number of clones (Figure 2B and supplementary methods). Nonetheless, this finding clearly illustrates the high clonal complexity of ALL and is in line with our earlier single-cell WGS based characterization of genetic heterogeneity in non-Down Syndrome ALL, which also identified branching clonal architectures with up to 19 descendant subclones 6 .…”

“…In studies of childhood acute lymphoblastic leukaemia (ALL), we and others previously used multicolour-FISH and whole genome sequencing to show that these tumours are clonally variegated, and to demonstrate through serial transplantation assays, that leukaemia tumour propagating cells (TPCs) are also genetically heterogeneous 4,5 . This finding was supported by our later genetic analysis of immunophenotypically distinct ALL diagnostic subpopulations which demonstrated similar distribution of subclones within a disease-specific primitive B-cell compartment (stemB, 34 + 38 - 19 + ) and the disease bulk in most but, crucially, not all leukaemias 6 . Such experiments relied on high-depth bulk whole-genome sequencing followed by single-cell qPCR and, together with our earlier work, suggested that genotype and phenotypes related to differentiation stage and cell-cycle state might not necessarily co-segregate within the disease.…”

“…Such experiments relied on high-depth bulk whole-genome sequencing followed by single-cell qPCR and, together with our earlier work, suggested that genotype and phenotypes related to differentiation stage and cell-cycle state might not necessarily co-segregate within the disease. Importantly, as chemotherapy-induced selection acts on these same phenotypic traits 6–8 , this lack of segregation also underpinned the survival of most genotypes following the early stages of childhood ALL treatment (namely, induction chemotherapy – where maximum cytotoxicity is achieved); as we demonstrated using a xenograft model of transplantation and treatment of primary leukaemias 6 .…”

Clonal Architecture and Evolutionary Dynamics in Acute Myeloid Leukemias

“…Such a phenomenon, where plasticity first allows the individuals (here, cancer cells) to explore the phenotypic space before adaptive traits (e.g., drug resistance) are enforced by heritable genetic or epigenetic alterations, is reminiscent of the 'Baldwin effect' in evolutionary biology [49]. A similar phenomenon has recently been described in childhood B-cell precursor acute lymphoblastic leukemia [50]. Indeed, transient changes involved in drug resistance have been reported to occur in vivo [51] and ex vivo [52], which may allow a subset of AML cells to survive long enough time to acquire heritable resistance (epi)mutation [43].…”

LiquidCNA: Tracking subclonal evolution from longitudinal liquid biopsies using somatic copy number alterations

“…For this potential application to be successful, we require that the emerging populations are uniquely marked by a number of SCNAs. In some cases, treatment response appears to be driven by ''phenotypic plasticity'' where cellular behavior changes without underlying genetic change (Turati et al, 2021;Shaffer et al, 2017). This scenario violates a key assumption of liquidCNA that the emerging population is dominated by a subclone of distinct karyotype, and so we would expect the application of liquidCNA to fail.…”