Mutational landscape, clonal evolution patterns, and role of RAS mutations in relapsed acute lymphoblastic leukemia

Abstract

Although multiagent combination chemotherapy is curative in a significant fraction of childhood acute lymphoblastic leukemia (ALL) patients, 20% of cases relapse and most die because of chemorefractory disease. Here we used whole-exome and whole-genome sequencing to analyze the mutational landscape at relapse in pediatric ALL cases. These analyses identified numerous relapse-associated mutated genes intertwined in chemotherapy resistance-related protein complexes. In this context, RAS-MAPK pathway-activating mutations in the neuroblastoma RAS viral oncogene homolog (NRAS), kirsten rat sarcoma viral oncogene homolog (KRAS), and protein tyrosine phosphatase, nonreceptor type 11 (PTPN11) genes were present in 24 of 55 (44%) cases in our series. Interestingly, some leukemias showed retention or emergence of RAS mutant clones at relapse, whereas in others RAS mutant clones present at diagnosis were replaced by RAS wildtype populations, supporting a role for both positive and negative selection evolutionary pressures in clonal evolution of RAS-mutant leukemia. Consistently, functional dissection of mouse and human wild-type and mutant RAS isogenic leukemia cells demonstrated induction of methotrexate resistance but also improved the response to vincristine in mutant RAS-expressing lymphoblasts. These results highlight the central role of chemotherapy-driven selection as a central mechanism of leukemia clonal evolution in relapsed ALL, and demonstrate a previously unrecognized dual role of RAS mutations as drivers of both sensitivity and resistance to chemotherapy.acute lymphoblastic leukemia | relapsed leukemia | chemotherapy resistance | genome sequencing A cute lymphoblastic leukemia (ALL) is the most common malignancy in children (1-4). Current therapy of pediatric newly diagnosed ALL includes initial clearance of leukemic lymphoblasts with cytotoxic drugs and glucocorticoids followed by delivery of chemotherapy to the central nervous system and a prolonged lower intensity maintenance treatment phase aimed at securing long-term remission by reducing the rates of leukemia relapse (3). Altogether 95% of pediatric ALL patients achieve a complete hematologic remission during induction and 80% of them remain leukemia free (5). However, the prognosis of patients showing refractory disease or those whose leukemia relapses after an initial transient response remains disappointingly poor, with cure rates of less than 40% (6, 7). Several mechanisms have been implicated as drivers of leukemia relapse, including the presence of rare quiescent and intrinsically chemoresistant leukemia stem cells with increased self-renewal capacity (8), protection from chemotherapy by safe-haven microenvironment niches (9, 10), and selection of secondary genetic alterations promoting chemotherapy resistance in leukemic lymphoblasts (11)(12)(13). In this regard, early studies described the presence of tumor protein p53 (TP53) mutations in relapsed ALL, supporting a role for escape from genotoxic stress in leukemia progression (14). Similarly, lo...

Suppressors and activators of JAK-STAT signaling at diagnosis and relapse of acute lymphoblastic leukemia in Down syndrome

“…Many of these mutations are frameshift or missense mutations within the UCH domain, suggesting loss-of-function. Similar to our findings, the USP9X-mutated BCP-ALLs described by Oshima et al (25) carried JAK2 and JAK3 activating mutations (Fig. S5E) (and hence, are likely to be CRLF2 pos ).…”

“…The very early occurrence of USP9X loss-of-function mutations and their presence in other subtypes of ALL [including T-ALL (25)] are consistent with additional tumor-suppressive mechanisms. In fact, it is also possible that the selection of activating JAK-STAT mutations may have occurred to compensate for the loss of USP9X.…”

“…In four CRLF2 pos patients and one CRLF2 neg patient, either the primary (R1) or the second relapse (R2) emerged from RAS-mutated clones that were undetectable in the preceding time point. This relative durability of clones with RAS mutation could be explained by increased resistance to chemotherapy, as has been suggested by Oshima et al (25).…”

“…To further validate these findings, we explored publicly available data. Additional mutations identified in USP9X in several studies (25,(41)(42)(43)(44) are depicted in Fig. 4B.…”

Genetic drivers of vulnerability and resistance in relapsed acute lymphoblastic leukemia

“…In PNAS, Oshima et al elucidate both the mutational landscape as well as patterns of clonal evolution of pediatric relapsed ALL and identify potential therapeutic targets in this challenging illness (4). Although prior studies have performed SNP array analysis (SNPa), wholeexome sequencing (WES), whole-genome sequencing (WGS), and/or mRNA sequencing (RNA-seq) at diagnosis and relapse (Table 1), the majority of prior analyses have focused on relapsed pediatric B-ALL specifically.…”