Mutational Landscape and Patterns of Clonal Evolution in Relapsed Pediatric Acute Lymphoblastic Leukemia

Abstract

Relapse of acute lymphoblastic leukemia (ALL) remains a leading cause of childhood cancer-related death. Prior studies have shown clonal mutations at relapse often arise from relapse-fated subclones that exist at diagnosis. However, the genomic landscape, evolutionary trajectories, and mutational mechanisms driving relapse are incompletely understood. In an analysis of 92 cases of relapsed childhood ALL incorporating multimodal DNA and RNA sequencing, deep digital mutational tracking, and xenografting to formally define clonal structure, we identied 50 significant targets of mutation with distinct patterns of mutational acquisition or enrichment. CREBBP, NOTCH1, and RAS signaling mutations arose from diagnosis subclones, whereas variants in NCOR2, USH2A, and NT5C2 were exclusively observed at relapse. Evolutionary modeling and xenografting demonstrated that relapse-fated clones were minor (50%), major (27%), or multiclonal (18%) at diagnosis. Putative second leukemias, including those with lineage shift, were shown to most commonly represent relapse from an ancestral clone rather than a truly independent second primary leukemia. A subset of leukemias prone to repeated relapse exhibited hypermutation driven by at least three distinct mutational processes, resulting in heightened neoepitope burden and potential vulnerability to immunotherapy. Finally, relapse-driving sequence mutations were detected prior to relapse using droplet digital PCR at levels comparable with orthogonal approaches to monitor levels of measurable residual disease. These results provide a genomic framework to anticipate and circumvent relapse by earlier detection and targeting of relapse-fated clones. SIGNIFICANCE:This study defines the landscape of mutations that preexist and arise after commencement of ALL therapy and shows that relapse may be propagated from ancestral, major, or minor clones at initial diagnosis. A subset of cases exhibit hypermutation that results in expression of neoepitopes that may be substrates for immunotherapeutic intervention.

The acquisition of molecular drivers in pediatric therapy-related myeloid neoplasms

“…Eight cases did not have a detectable drug signature but rather clock-like signatures 1, 5, and 40 ( Fig. 2d) 29,30 , while 2 additional patients had a signature similar to one of unknown etiology recently reported in relapsed mismatch repair (MMR)-deficient ALL 31 which we term the "relapse MMR" signature. Both had germline (SJ016519) or somatic (SJ016494) pathogenic PMS2 mutations.…”

T-cell Acute Lymphoblastic Leukemia: A Roadmap to Targeted Therapies

“…Potential limitations to the use of targeted drugs in pediatric T-ALL include clonal heterogeneity of the disease, resulting in only partial elimination of leukemia cells upon therapy. Therefore, resistant clones may be selected and survive under the selective pressure of treatment (8,9). Similar resistance mechanisms have already been demonstrated for conventional chemotherapeutics such as the glucocorticoid-selected NR3C1 mutations (10)(11)(12) and the 6-mercaptopurine-selected NT5C2 mutations in chemoresistant relapsed ALL (11,13).…”

Pediatric acute lymphoblastic leukemia

“…79 In B-ALL, mutations in genes such as the histone acetyl transferase gene CREBBP, the histone methyltransferase gene SETD2, and the steroid receptor genes NR3C1 and NR3C2 are enriched at relapse. [80][81][82][83] At diagnosis, minor relapse-initiating subclones can exhibit inherent resistance to chemotherapy, even before secondary mutation acquisition. 84 Other relapse-specific mutations in PRPS1, PRSP2, NT5C2, or MSH6, each influencing thiopurine metabolism, may emerge only during therapy, being driven by selective therapeutic pressure.…”

“…84 Other relapse-specific mutations in PRPS1, PRSP2, NT5C2, or MSH6, each influencing thiopurine metabolism, may emerge only during therapy, being driven by selective therapeutic pressure. 81,83,85,86 These mutations confer chemotherapy resistance and might have implications for disease monitoring and therapeutic decisions. 85,86 Inherited genomic variants in specific ethnic/racial groups also contribute to relapse risk as a result of differential drug metabolism or acquisition of distinct somatic mutations.…”