Relapse-specific mutations in NT5C2 in childhood acute lymphoblastic leukemia

Children with Down syndrome (DS) are prone to development of high-risk B-cell precursor ALL (DS-ALL), which differs genetically from most sporadic pediatric ALLs. Increased expression of cytokine receptor-like factor 2 (CRLF2), the receptor to thymic stromal lymphopoietin (TSLP), characterizes about half of DS-ALLs and also a subgroup of sporadic "Philadelphia-like" ALLs. To understand the pathogenesis of relapsed DS-ALL, we performed integrative genomic analysis of 25 matched diagnosis-remission and -relapse DSALLs. We found that the CRLF2 rearrangements are early events during DS-ALL evolution and generally stable between diagnoses and relapse. Secondary activating signaling events in the JAK-STAT/ RAS pathway were ubiquitous but highly redundant between diagnosis and relapse, suggesting that signaling is essential but that no specific mutations are "relapse driving." We further found that activated JAK2 may be naturally suppressed in 25% of CRLF2 pos DSALLs by loss-of-function aberrations in USP9X, a deubiquitinase previously shown to stabilize the activated phosphorylated JAK2. Interrogation of large ALL genomic databases extended our findings up to 25% of CRLF2 pos , Philadelphia-like ALLs. Pharmacological or genetic inhibition of USP9X, as well as treatment with low-dose ruxolitinib, enhanced the survival of pre-B ALL cells overexpressing mutated JAK2. Thus, somehow counterintuitive, we found that suppression of JAK-STAT "hypersignaling" may be beneficial to leukemic B-cell precursors. This finding and the reduction of JAK mutated clones at relapse suggest that the therapeutic effect of JAK specific inhibitors may be limited. Rather, combined signaling inhibitors or direct targeting of the TSLP receptor may be a useful therapeutic strategy for DS-ALL.C hildren with Down syndrome (DS) are at a markedly increased risk for B-cell precursor acute lymphoblastic leukemia (BCP-ALL) (1). The poor survival of DS-ALL compared with ALL in children without DS ("sporadic" ALL) is related to increased treatment toxicity and to increased incidence of relapse (2). Thus, better therapy is needed for these patients.Previous studies by our group and others revealed differences between the genetics of DS-ALLs and of sporadic ALLs (3-6). The typical cytogenetic subgroups, ETV6-RUNX1 and hyperdiploid ALLs, are less common in DS-ALLs. Acquired somatic activation of the thymic stromal lymphopoietin (TSLP) pathway are present at diagnosis in about half of DS-ALLs. Aberrant expression of cytokine receptor-like factor 2 (CRLF2) in these leukemias is caused by chromosomal rearrangements consisting either of a microdeletion on chromosome X, juxtaposing the promoter of P2RY8 with the coding region of CRLF2, or by a translocation of CRLF2 into the Ig heavy chain (IgH) locus. CRLF2 heterodimerizes with IL7 receptor-α (IL7R) to form the receptor to TSLP (reviewed in ref. 7). TSLP receptors signal by activation of the JAK-STAT pathway. Interestingly, in the majority of DS-ALLs, SignificanceChildren with Down syndrome are at increased risk ...

Section: Discussioncontrasting

confidence: 39%

Section: Temporal Association Of Somatic Mutations Between Diagnosis Andcontrasting

confidence: 49%

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

Schwartzman

Savino

Gombert

et al. 2017

“…Given the need to develop novel targeted therapeutics for relapsed ALL, identification of therapeutically targetable genetic alterations enriched in relapse is critical. To this end, prior work from this group and others identified that mutations in the 5′-nucleotidase enzyme NT5C2 enhance inactivation of nucleoside-analog chemotherapeutic agents (6,7). The frequency of NT5C2 mutations at relapse and the fact that NT5C2 mutations confer enhanced enzymatic activity argue for efforts to develop small-molecule inhibitors of mutant NT5C2.…”

mentioning

confidence: 99%

Genetic drivers of vulnerability and resistance in relapsed acute lymphoblastic leukemia

Abdel‐Wahab

2016

Relapsed acute lymphoblastic leukemia (ALL) is associated with very poor outcomes despite modern therapies in both children and adults (1-3). 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. Here, the authors performed WES of 55 pediatric ALL patients (33 T-cell ALL and 22 B-cell precursor ALL) at diagnosis, remission, and relapse and complemented these data with RNA-seq of a validation cohort of 49 paired diagnosis/relapse B-ALL patient samples. This analysis has allowed for reevaluation of the pattern of clonal evolution in relapsed ALL and revealed that the majority of relapsed ALLs (∼85%) contain only some of the genetic lesions present in the major clone at diagnosis. In contrast, only in 4% of cases did the relapsed clones contain all mutations present at diagnosis plus additional secondary relapse-specific lesions. Together, these data identify that linear evolution is rarely involved in tumor progression in ALL and that relapsed ALL originates primarily as derivatives of ancestral subclones related to, but distinct from the main leukemic population present at diagnosis. This conclusion extends previous observations of the clonal basis of relapsed ALL by Mullighan et al. (5), which used SNPa to reveal that cells responsible for relapse were often minor subpopulations of the cells responsible for initial disease (Table 1).In addition to evaluating the clonal basis of relapsed ALL, the authors identified several new genes enriched at relapse including ZFHX3, USP9X, CACNA1H, EPHA3, SHROOM3, USP7, RPGR, HTR3A, MED12, ODZ3, and IL17RA. Mutations associated with relapsed ALL appear to fall into several categories. First, there are mutations functionally related to the mechanism of action of chemotherapy used in initial treatment and/or previously linked to chemotherapy resistance. These include mutations in NT5C2, TP53, NR3C1, CREBBP, and MLL2. Ultradeep sequencing of diagnostic samples failed to identify these mutations in most cases, which suggests they were acquired at relapse and/or present in very small subclones at diagnosis. Given the need to develop novel targeted therapeutics for relapsed ALL, identification of therapeutically targetable genetic alterations enriched in relapse is critical. To this end, prior work from this group and others identified that mutations in the 5′-nucleotidase enzyme NT5C2 enhance inactivation of nucleoside-analog chemotherapeutic agents (6, 7). The frequency of NT5C2 mutations at relapse and the fact that NT5C2 mutations confer enhanced enzymatic activity argue for efforts to develop small-molecule inhibitors of mutant NT5C2.Mutations in CREBBP ...

“…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).…”

mentioning

confidence: 99%

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

Oshima

Khiabanian

Silva-Almeida

et al. 2016

156

115

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...