NT5C2 Mutations Research Articles

Abstract 2058: Identifications of novel variants using system biology-based approaches in NT5C2, its association to relapse acute lymphoblastic leukaemia

Abstract Acute Lymphoblastic Leukaemia (ALL) patients experience relapse despite having a good prognosis; approximately 90% of children and 75% to 85% of adolescents and young adults survive for five years. Chemotherapy resistance and a poor prognosis are linked to relapsed acute lymphoblastic Leukaemia (R-ALL). Evidence suggests that the cytosolic 5 nucleotidase II (NT5C2) gene mutations play a crucial role in the emergence of recurrent ALL; The early R-ALL is usually accompanied by 6-MP resistance, which is typically brought on by gain-of-function mutations impacting NT5C2-driven mutation in relapse mutations by different mechanisms is still unknown. The study aims to identify novel top missense variants of NT5C2 that play a crucial role in the resistance of chemotherapy drugs, altered biological pathways and their impact on the treatment of relapse leukaemia. NT5C2 (5'-Nucleotidase, Cytosolic II) is a Protein Coding gene. This gene induces resistance to chemotherapeutic drug 6 mercaptopurine Which causes leukaemia cell growth and leukaemia-initiating cell activity. The NT5C2 gene variants are extracted from Genome Aggregation Database (gnomAD) and ExAC. The extracted data contained 2280 variants with chromosome number, position reference allele, and altered allele and these were functionally annotated using the ANNOVAR tool. The variants are screened through various computational tools to narrow down based on non-synonymous and stopgain mutations in the exonic region. The predicted 519 variants narrow down by scoring GERP (>2.0) and CADD PHRED (cut-off score >10), ClinVar, SIFT score, Polyphen, PhyloP, PhastCons, LRT score predictions and which indicates the top 10% deleterious variants including reported and unknown variants. The SNPs, insertions, deletions, CNVs or structural variants of top missense variants on genes, transcripts, and protein sequence determined on Variants Effect Predictor on the ensemble. These variants were verified on dbSNP and Clinvar through their variant IDs. The functional prediction of these variants was made to detect their significant role in R-ALL. These findings examine the future role of NT5C2 mutations in the chemoresistance of relapse ALL. This may help to find a new therapeutic combination of drugs to treat relapse acute lymphoblastic leukaemia to improve overall survival. Citation Format: Sugunakar V, Obul Reddy Bandapalli, Ramita Sharma. Identifications of novel variants using system biology-based approaches in NT5C2, its association to relapse acute lymphoblastic leukaemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2058.

CRISPR/Cas9-Mediated Induction of Relapse-Specific NT5C2 and PRPS1 Mutations Confers Thiopurine Resistance as a Relapsed Lymphoid Leukemia Model

6-Mercaptopurine (6-MP) is a key component in maintenance therapy for childhood acute lymphoblastic leukemia (ALL). Recent next-generation sequencing analysis of childhood ALL clarified the emergence of the relapse-specific mutations of the NT5C2 and PRPS1 genes, which are involved in thiopurine metabolism. In this scenario, minor clones of leukemia cells could acquire the 6-MP-resistant phenotype as a result of the NT5C2 or PRPS1 mutation during chemotherapy (including 6-MP treatment) and confer disease relapse after selective expansion. Thus, to establish new therapeutic modalities overcoming 6-MP resistance in relapsed ALL, human leukemia models with NT5C2 and PRPS1 mutations in the intrinsic genes are urgently required. Here, mimicking the initiation process of the above clinical course, we sought to induce two relapse-specific hotspot mutations (R39Q mutation of the NT5C2 gene and S103N mutation of the PRPS1 gene) into a human lymphoid leukemia cell line by homologous recombination (HR) using the CRISPR/Cas9 system. After 6-MP selection of the cells transfected with Cas9 combined with single-guide RNA and donor DNA templates specific for either of those two mutations, we obtained the sublines with the intended NT5C2-R39Q and PRPS1-S103N mutation as a result of HR. Moreover, diverse in-frame small insertion/deletions were also confirmed in the 6-MP-resistant sublines at the target sites of the NT5C2 and PRPS1 genes as a result of nonhomologous end joining. These sublines are useful for molecular pharmacological evaluation of the NT5C2 and PRPS1 gene mutations in the 6-MP sensitivity and development of therapy overcoming the thiopurine resistance of leukemia cells. SIGNIFICANCE STATEMENT: Mimicking the initiation process of relapse-specific mutations of the NT5C2 and PRPS1 genes in childhood acute lymphoblastic leukemia treated with 6-mercaptopurine (6-MP), this study sought to introduce NT5C2-R39Q and PRPS1-S103N mutations into a human lymphoid leukemia cell line by homologous recombination using the CRISPR/Cas9 system. In the resultant 6-MP-resistant sublines, the intended mutations and diverse in-frame small insertions/deletions were confirmed, indicating that the obtained sublines are useful for molecular pharmacological evaluation of the NT5C2 and PRPS1 gene mutations.

IMPDH inhibition activates TLR-VCAM1 pathway and suppresses the development of MLL-fusion leukemia.

Inosine monophosphate dehydrogenase (IMPDH) is a rate-limiting enzyme in de novo guanine nucleotide synthesis pathway. Although IMPDH inhibitors are widely used as effective immunosuppressants, their antitumor effects have not been proven in the clinical setting. Here, we found that acute myeloid leukemias (AMLs) with MLL-fusions are susceptible to IMPDH inhibitors invitro. We also showed that alternate-day administration of IMPDH inhibitors suppressed the development of MLL-AF9-driven AML invivo without having a devastating effect on immune function. Mechanistically, IMPDH inhibition induced overactivation of Toll-like receptor (TLR)-TRAF6-NF-κB signaling and upregulation of an adhesion molecule VCAM1, which contribute to the antileukemia effect of IMPDH inhibitors. Consequently, combined treatment with IMPDH inhibitors and the TLR1/2 agonist effectively inhibited the development of MLL-fusion AML. These findings provide a rational basis for clinical testing of IMPDH inhibitors against MLL-fusion AMLs and potentially other aggressive tumors with active TLR signaling.

The Rise and Fall of Leukemia Clones in Longitudinal Samples from Diagnosis to Relapse in KMT2A-rearranged Infant and Childhood Leukemia

The genomic landscape, evolutionary trajectories and the mechanisms driving relapse in KMT2A-rearranged (KMT2A-r) infant and childhood acute lymphoblastic (ALL) and acute myeloid leukemia (AML) are not completely understood. We therefore studied 30 KMT2A-r ALL (n=16) and AML (n=14) patients of which 19 relapsed. Eleven diagnose-relapse-germline trios were analyzed by whole genome (WGS) and whole exome sequencing (WES), and all patients by ultra-deep resequencing (average 3400X) of patient-specific mutations identified by WGS/WES on the diagnostic (n=30) and relapse (n=11) samples, at diagnosis (n=30), during treatment (n=203) and at relapse (n=30, 1-4 bone marrow (BM) relapses in 17 patients). The mutational burden increased from diagnosis to relapse in the diagnose-relapse-germline trios. The combined analysis of WGS/WES and ultra-deep data showed that the leukemias typically evolved through branching evolution, and that a selective sweep occurred at first relapse in 76% of patient. Further, additional subclones were often detected at relapse and in 69% the relapse clone was detected already at diagnosis as a subclone. Eight pathways were recurrently altered including signalling, cell cycle, epigenetic, B-cell development, transcription factor, glucocorticoid receptor signalling, purine metabolism and cohesin. Signalling mutations were the most common type of mutations at diagnosis (50%) and at relapse (41%) and the diagnostic frequency was similar in patients that remained in complete remission (CR) and in those that relapsed (55% versus 47%). Signalling mutations were often subclonal (60%) and 30% had more than one mutation and mutations in signalling genes were usually gained or maintained at relapse in ALL but mainly lost or reduced in size in AML. Alterations in cell cycle genes were enriched at relapse and either gained (60%) or maintained (27%), and included TP53 in ALL and AML, CDKN2A/B in ALL and CCND3 in AML. The TP53 alterations were typically biallelic at relapse. Only 2/30 patients had diagnostic TP53 mutations and both relapsed. Further, relapse-specific mutations in genes involved in glucocorticoid signalling and purine metabolism (CREBBP, NT5C2,PRPS2, NR3C1) were detected in all ALL patients with early relapse (n=4, during maintenance therapy). These relapse samples also had co-occurring IKZF1 deletions with 3 acquired at relapse and 1 maintained, as well as acquired TP53 mutations (3/4 patients). By contrast, infant ALL with a very early relapse (n=4, before maintenance therapy) lacked cell cycle and chemoresistance-associated mutations at relapse. Ultra-deep sequencing did not detect the CREBBP, NT5C2, PRPS2 or TP53 mutations at diagnosis and manual inspection of the WGS reads failed to detect the NR3C1 deletion. In AML, gain of WT1 mutations was seen in patients with late relapse (after >1 year in CR1). Longitudinal sequencing on the 30 patients showed that at day 15, ALL patients that remained in CR (n=5) had higher levels of molecularly detectable leukemia cells as compared to those that relapsed (n=8), however at day 29, the reverse was seen with relapse patients having higher levels (n.s). Further, infants with very early relapse (n=3) had a higher leukemic burden at both time points as compared to those with early relapse (n=5). Patients with very early relapse typically reached CR later and the relapse clone could be detected at diagnosis in all 4 patients compared to 2/4 with early relapse. In 7 patients, 4 that relapsed and 3 that remained in CR, low-frequency mutations and KMT2A-fusion positive leukemic clones (DNA-level) were found at remission. Moreover, 4 patients had molecularly detectable clones across all investigated time points until relapse (6-13 time points), 2 had persistent disease but 2 entered CR. Finally, the relapse clone could be detected 46-126 days before relapse in 6 patients. Combined, early relapse in infant and childhood KMT2A-r ALL was characterized by relapse-specific TP53, IKZF1, CREBBP, NR3C1, NTC52 or PRPS2 alterations. By contrast, very early relapse KMT2A-r infant ALL likely arises from pre-existing chemo resistant cells with a paucity of genetic alterations in relapse and chemoresistance-associated genes at relapse. Further, longitudinal molecular tracking provided biological insight into clonal response to treatment and captured the complexity of the temporal evolution in very early and early relapse patients.

In This Issue

In This Issue

Pharmacologic Inhibition of NT5C2 Reverses Genetic and Nongenetic Drivers of 6-MP Resistance in Acute Lymphoblastic Leukemia.

Relapse-associated NT5C2 mutations directly contribute to relapse in ALL by driving resistance to chemotherapy with 6-MP. Pharmacologic inhibition of NT5C2 with CRCD2, a first-in-class nucleotidase inhibitor, enhances the cytotoxic effects of 6-MP and effectively reverses thiopurine resistance mediated by genetic and nongenetic mechanisms of NT5C2 activation in ALL. This article is highlighted in the In This Issue feature, p. 2483.

NUDT15 polymorphism and NT5C2 and PRPS1 mutations influence thiopurine sensitivity in acute lymphoblastic leukaemia cells.

In chemotherapy for childhood acute lymphoblastic leukaemia (ALL), maintenance therapy consisting of oral daily mercaptopurine and weekly methotrexate is important. NUDT15 variant genotype is reportedly highly associated with severe myelosuppression during maintenance therapy, particularly in Asian and Hispanic populations. It has also been demonstrated that acquired somatic mutations of the NT5C2 and PRPS1 genes, which are involved in thiopurine metabolism, are detectable in a portion of relapsed childhood ALL. To directly confirm the significance of the NUDT15 variant genotype and NT5C2 and PRPS1 mutations in thiopurine sensitivity of leukaemia cells in the intrinsic genes, we investigated 84 B‐cell precursor‐ALL (BCP‐ALL) cell lines. Three and 14 cell lines had homozygous and heterozygous variant diplotypes of the NUDT15 gene, respectively, while 4 and 2 cell lines that were exclusively established from the samples at relapse had the NT5C2 and PRPS1 mutations, respectively. Both NUDT15 variant genotype and NT5C2 and PRPS1 mutations were significantly associated with DNA‐incorporated thioguanine levels after exposure to thioguanine at therapeutic concentration. Considering the continuous exposure during the maintenance therapy, we evaluated in vitro mercaptopurine sensitivity after 7‐day exposure. Mercaptopurine concentrations lethal to 50% of the leukaemia cells were comparable to therapeutic serum concentration of mercaptopurine. Both NUDT15 variant genotype and NT5C2 and PRPS1 mutations were significantly associated with mercaptopurine sensitivity in 83 BCP‐ALL and 23 T‐ALL cell lines. The present study provides direct evidence to support the general principle showing that both inherited genotype and somatically acquired mutation are crucially implicated in the drug sensitivity of leukaemia cells.

Clonal Evolution Mechanisms and Collateral Sensitivity to Impdh Inhibitor Therapy in Relapsed Lymphoblastic Leukemia

Improved support and intensified chemotherapy regimens have increased the overall survival rates of newly diagnosed pediatric ALL to over 80%. However the outcomes of patients with relapsed or refractory ALL remain poor, with cure rates of about only 40%. Thus, leukemia relapse and chemotherapy resistance are now the most prominent challenges in the treatment of ALL. Leukemia-initiating cells capable of self-renewal, protective microenvironment safe-haven niches and clonal evolution with acquisition of secondary genetic alterations driving chemotherapy resistance have all been implicated as drivers of ALL disease progression and relapse. In this context, heterozygous activating mutations in the NT5C2 nucleotidase gene are present in about 20% of relapsed pediatric T-cell ALL (T-ALL) cases and 3-10% of relapsed B-precursor ALLs. Yet, the mechanisms involved in NT5C2 mutation-driven clonal evolution during leukemia initiation, disease progression and relapse remain unknown. Using a conditional inducible leukemia model, we demonstrate that expression of Nt5c2 p.R367Q, a highly prevalent relapsed-ALL NT5C2 mutation, induces resistance to chemotherapy with 6-MP at the cost of impaired leukemia cell growth and leukemia-initiating cell activity. Consistently ultra-deep sequencing with molecular barcodes, allele specific PCR and droplet PCR analyses showed that NT5C2 mutations are typically absent at the time of diagnosis or represent very small clones below the threshold of detection (1:1000). Metabolomic profiling of isogenic Nt5c2 wild type and Nt5c2 p.R367Q mutant lymphoblasts showed that the loss of fitness phenotype of Nt5c2 mutant cells is associated with excess export of purines to the extracellular space and depletion of the intracellular purine nucleotide pool. Consequently, blocking guanosine synthesis via inosine-5'-monophosphate dehydrogenase (IMPDH) inhibition induced increased cytotoxicity against NT5C2-mutant leukemia lymphoblasts. Similar results -increased resistance to 6-MP, depleted intracellular nucleoside pool and excess export of purines to the culture media and increased sensitivity to mizoribine- were documented in human ALL cell lines with expression of relapse associated NT5C2 mutations (p.R238W, p.K359Q, p.R367Q and p.D407A). The specificity of these interactions was supported by metabolic rescue of mizoribine-induced cytotoxicity in cultures supplemented with guanosine. Similarly shRNA knockdown of IMPDH2 induced increased cytotoxicity in human cell lines expressing mutant NT5C2. Finally, we verified increased response to mizoribine in relapsed-leukemia derived xenograft cells harboring NT5C2 mutations compared with their corresponding NT5C2 wild type diagnostic-sample derived counterparts. In all, these results identify NT5C2 mutation-associated fitness cost and resistance to chemotherapy as key evolutionary drivers shaping clonal evolution in relapsed ALL and support a role for IMPDH inhibition in the treatment of ALL. DisclosuresNo relevant conflicts of interest to declare.

The genomic landscape of teenage and young adult T-cell acute lymphoblastic leukemia.

BackgroundTreatment on risk adapted intensive pediatric protocols has improved outcome for teenagers and young adults (TYA) with T‐cell acute lymphoblastic leukemia (T‐ALL). Understanding the biology of disease in this age group and the genetic basis of relapse is a key goal as patients with relapsed/refractory disease have poor outcomes with conventional chemotherapy and novel molecular targets are required. This study examines the question of whether TYA T‐ALL has a specific biological‐molecular profile distinct from pediatric or adult T‐ALL.MethodsGenomic characterization was undertaken of a retrospective discovery cohort of 80 patients aged 15–26 years with primary or relapsed T‐ALL, using a combination of Genome‐Wide Human SNP Array 6.0, targeted gene mutation and promoter methylation analyses. Findings were confirmed by MLPA, real‐time quantitative PCR, and FISH. Whole Exome Sequencing was performed in 4 patients with matched presentation and relapse to model clonal evolution. A prevalence analysis was performed on a final data set of 1,792 individual cases to identify genetic lesions with age specific frequency patterns, including 972 pediatric (1–14 years), 439 TYA (15–24 years) and 381 adult (≥25 years) cases. These cases were extracted from 19 publications with comparable genomic data identified through a PubMed search.ResultsGenomic characterization of this large cohort of TYA T‐ALL patients identified recurrent isochromosome 7q i(7q) in our discovery cohort (n = 3). Prevalence analysis did not identify any age specific genetic abnormalities. Genomic analysis of 6 pairs of matched presentation – relapsed T‐ALL established that all relapses were clonally related to the initial leukemia. Whole exome sequencing analysis revealed recurrent, targetable, mutations disrupting NOTCH, PI3K/AKT/mTOR, FLT3, NRAS as well as drug metabolism pathways.ConclusionsAll genetic aberrations in TYA T‐ALL occurred with an incidence similar or intermediate to that reported in the pediatric and adult literature, demonstrating that overall TYA T‐ALL exhibits a transitional genomic profile. Analysis of matched presentation – relapse supported the hypothesis that relapse is driven by the Darwinian evolution of sub‐clones associated with drug resistance (NT5C2 and TP53 mutations) and re‐iterative mutation of known key T‐ALL drivers, including NOTCH1.

Recognition of the organ-specific mutations in metastatic breast cancer by circulating tumor cells isolated in vivo.

The failure to treat and control the growth of metastases is the main cause of death in breast cancer (BC) patients. Compared to the traditional method of analyzing circulating tumor DNA (ctDNA), capturing intact circulating tumor cells (CTCs) allows us to more accurately characterize mutations and identify suitable targeted therapies. We used CellCollector to collect peripheral CTCs. Thirty metastatic breast cancer (MBC) patients were enrolled, and 17 were analyzed with next-generation sequencing (NGS) methods. Clinical characteristics were analyzed along with the CTCs enumeration and detection rates. Whole-genome amplification (WGA) was used to amplify the CTC genomic DNA of 127 genes. Patients younger than 45 years old, with brain metastasis, with three or more metastatic sites, or with HER2-positive had the highest number of CTCs collected. The CTCs detection rate was also correlated to the number of metastasis sites. Different metastasis sites such as the brain, viscus, bone, and soft tissue contained specific high-frequency gene mutations. AKT3, MYC, and NT5C2 mutations were only found in brain metastases. APC, BCL2L11, ESRP1, FLT3 mutations were only in the visceral metastases. KEAP1, KIT, MET were the specific mutation genes in patients with bone and soft tissue metastases. These findings provide evidence that we can detect gene mutation information for obtaining the biological characteristics by CTCs using CellCollector. Different metastasis sites contain specific high-frequency mutation genes, which provide guidance to the accurate gene therapy.

FPGS relapse-specific mutations in relapsed childhood acute lymphoblastic leukemia

Although the cure rate for childhood acute lymphoblastic leukemia (ALL) has exceeded 80% with contemporary therapy, relapsed ALL remains a leading cause of cancer-related death in children. Relapse-specific mutations can be identified by comprehensive genome sequencing and might have clinical significance. Applying whole-exome sequencing to eight triplicate samples, we identified in one patient relapse-specific mutations in the folylpolyglutamate synthetase (FPGS) gene, whose product catalyzes the addition of multiple glutamate residues (polyglutamation) to methotrexate upon their entry into the cells. To determine the prevalence of mutations of the FPGS mutations, and those of two important genes in the thiopurine pathway, NT5C2 and PRPS1, we studied 299 diagnostic and 73 relapsed samples in 372 patients. Three more FPGS mutants were identified in two patients, NT5C2 mutations in six patients, and PRPS1 mutants in two patients. One patient had both NT5C2 and PRPS1 mutants. None of these alterations were detected at diagnosis with a sequencing depth of 1000X, suggesting that treatment pressure led to increased prevalence of mutations during therapy. Functional characterization of the FPGS mutants showed that they directly resulted in decreased enzymatic activity, leading to significant reduction in methotrexate polyglutamation, and therefore likely contributed to drug resistance and relapse in these cases. Thus, besides genomic alterations in thiopurine metabolizing enzymes, the relapse-specific mutations of FPGS represent another critical mechanism of acquired antimetabolite drug resistance in relapsed childhood ALL.

Subclonal NT5C2 mutations are associated with poor outcomes after relapse of pediatric acute lymphoblastic leukemia

AbstractActivating mutations in cytosolic 5′-nucleotidase II (NT5C2) are considered to drive relapse formation in acute lymphoblastic leukemia (ALL) by conferring purine analog resistance. To examine the clinical effects of NT5C2 mutations in relapsed ALL, we analyzed NT5C2 in 455 relapsed B-cell precursor ALL patients treated within the ALL-REZ BFM 2002 relapse trial using sequencing and sensitive allele-specific real-time polymerase chain reaction. We detected 110 NT5C2 mutations in 75 (16.5%) of 455 B-cell precursor ALL relapses. Two-thirds of relapses harbored subclonal mutations and only one-third harbored clonal mutations. Event-free survival after relapse was inferior in patients with relapses with clonal and subclonal NT5C2 mutations compared with those without (19% and 25% vs 53%, P < .001). However, subclonal, but not clonal, NT5C2 mutations were associated with reduced event-free survival in multivariable analysis (hazard ratio, 1.89; 95% confidence interval, 1.28-2.69; P = .001) and with an increased rate of nonresponse to relapse treatment (subclonal 32%, clonal 12%, wild type 9%, P < .001). Nevertheless, 27 (82%) of 33 subclonal NT5C2 mutations became undetectable at the time of nonresponse or second relapse, and in 10 (71%) of 14 patients subclonal NT5C2 mutations were undetectable already after relapse induction treatment. These results show that subclonal NT5C2 mutations define relapses associated with high risk of treatment failure in patients and at the same time emphasize that their role in outcome is complex and goes beyond mutant NT5C2 acting as a targetable driver during relapse progression. Sensitive, prospective identification of NT5C2 mutations is warranted to improve the understanding and treatment of this aggressive ALL relapse subtype.

Post-Translational Mechanisms of NT5C2 Activation As Non-Genetic Drivers of Chemotherapy Resistance in Relapsed Acute Lymphoblastic Leukemia

Despite intensive chemotherapy, 20% of pediatric acute lymphoblastic leukemia (ALL) patients fail to achieve a complete remission or relapse after intensified chemotherapy, making relapse and resistance to therapy the most significant challenge in the treatment of this disease. We have shown that NT5C2 mutations resulting in deregulated enzymatic activity are present in 10% of relapsed B-precursor ALL and 20% of relapsed T-ALL cases. These genetic alterations abrogate the activity of an intramolecular switch-off mechanism resulting in increased nucleotidase activity. NT5C2 metabolizes and clears the activated forms of 6-mercaptopurine (6-MP), a critical drug in the treatment of ALL. As a result, activating mutations in the NT5C2 cytosolic nucleotidase gene are characteristically associated with early relapsed leukemia and progression under therapy and confer resistance to 6-mercaptopurine chemotherapy. A saturated mutagenesis positive selection screen for all possible NT5C2 variants (10640 alleles) conferring resistance to 6-MP recovers mutational hotspots involving recurrent relapse-associated mutations and identifies new residues and protein domains involved in NT5C2 regulation whose inactivation drives resistance to 6-MP. Moreover, a genome wide CRISPR screen analysis of 6-MP-gene interactions in NT5C2 wild type REH ALL cells identifies NT5C2 as the most prominent hit whose inactivation increases sensitivity to 6-MP. Taken together, these results point to heretofore uncharacterized mechanisms of NT5C2 regulation and support a role for wild type NT5C2 in 6-MP metabolism and inactivation. Thus post-translational modifications enhancing NT5C2 activity could attenuate the therapeutic activity of 6-MP in NT5C2 wild type cells as non-mutational mechanism of 6-MP resistance. Mass spectrometry analysis of NT5C2 protein revealed the presence of two NT5C2 acetylations and two NT5C2 phosphorylation sites. Functional analyses of these modifications revealed increased nucleotidase activity for the NT5C2 S502D phospho-mimic mutation. Consistently, expression of NT5C2 S502D in leukemia lymphoblasts induced resistance to 6-MP. Importantly, western blot analysis revealed increased NT5C2 S502 phosphorylation in relapsed leukemia xenograft samples compared with matched diagnosis derived ALL xenografts. Crystal structure analysis of NT5C2 recombinant protein supports that S502 engages D229 in the partner protomer of the NT5C2 dimer. Structure-function analysis of S502D, S502A and D229A mutants targeting this interaction supports the disruption of S502-D229 interaction via S502 phosphorylation as mechanism of NT5C2 activation. In all, these results highlight a prominent role for wild type NT5C2 activity in the detoxification of 6-MP in ALL lymphoblasts, identifies NT5C2 S502 phosphorylation as a prevalent non-genetic mechanism of NT5C2 activation at relapse and provides novel insight on the mechanisms of NT5C2 regulation of relevance for the therapeutic targeting of NT5C2 in relapsed ALL. Disclosures No relevant conflicts of interest to declare.

Mechanisms of NT5C2-Mediated Thiopurine Resistance in Acute Lymphoblastic Leukemia.

Relapse remains a formidable challenge for acute lymphoblastic leukemia (ALL). Recently, recurrent mutations in NT5C2 were identified as a common genomic lesion unique in relapsed ALL and were linked to acquired thiopurine resistance. However, molecular mechanisms by which NT5C2 regulates thiopurine cytotoxicity were incompletely understood. To this end, we sought to comprehensively characterize the biochemical and cellular effects of NT5C2 mutations. Compared with wild-type NT5C2, mutant proteins showed elevated 5'-nucleotidase activity with a stark preference of thiopurine metabolites over endogenous purine nucleotides, suggesting neomorphic effects specific to thiopurine metabolism. Expression of mutant NT5C2 mutations also significantly reduced thiopurine uptake in vitro with concomitant increase in efflux of 6-mercaptopurine (MP) metabolites, plausibly via indirect effects on drug transporter pathways. Finally, intracellular metabolomic profiling revealed significant shifts in nucleotide homeostasis induced by mutant NT5C2 at baseline; MP treatment also resulted in global changes in metabolomic profiles with completely divergent effects in cells with mutant versus wild-type NT5C2. Collectively, our data indicated that NT5C2 mutations alter thiopurine metabolism and cellular disposition, but also influence endogenous nucleotide homeostasis and thiopurine-induced metabolomic response. These complex mechanisms contributed to NT5C2-mediated drug resistance in ALL and pointed to potential opportunities for therapeutic targeting in relapsed ALL.

S130 TRANSIENT SUBCLONES CARRYING NT5C2 MUTATIONS DEFINE A HIGH‐RISK PATIENT GROUP WITH POOR OUTCOME IN PEDIATRIC RELAPSED B‐CELL PRECURSOR ACUTE LYMPHOBLASTIC LEUKEMIA

Background:Acute lymphoblastic leukemia (ALL) is the most common cancer in children. Despite an overall favorable prognosis, 15–20% of patients suffer a relapse. In the treatment of relapsed ALL, resistance to chemotherapy is a major challenge. The purine nucleotide metabolizing cytosolic 5́‐nucleotidase II (NT5C2) harbors activating mutations in 20% of pediatric relapsed T‐ALL and in 3–10% of relapsed B‐cell precursor ALL cases, which are considered to drive relapse formation by causing resistance to purine analogue‐based maintenance treatment of ALL. However, the impact of NT5C2 mutations for second‐line treatment and long‐term outcome of relapsed patients is unknown.Aims:To elucidate the clinical significance of NT5C2 mutations in relapsed ALL, we studied the NT5C2 gene in a large cohort of 455 patients with relapsed B‐cell precursor ALL and assessed correlations with clinical presentation, genetics, response to treatment and outcome.Methods:We detected NT5C2 mutations by Sanger sequencing and amplicon‐based next generation sequencing. To detect subclonal NT5C2 mutations, we established allele‐specific quantitative real‐time PCR assays following minimal residual disease measurement guidelines. All relapsed patients were treated according to the German ALL‐REZ BFM 2002 protocol.Results:By sequencing, we found n = 36 NT5C2 mutations in n = 34 samples. About 30% of NT5C2 mutations appeared subclonal with an estimated allele frequency of less than 20%. The variants p.R39Q (8/36, 22%) and p.R367Q (14/36, 39%) were the most prevalent mutations in our cohort. Using allele‐specific quantitative real‐time PCR targeted to p.R39Q and p.R367Q, we identified additional 69 subclonal NT5C2 mutations. In total, NT5C2 mutations were present in 16% of patients with relapsed B‐cell precursor ALL (74/455), but the majority of cases (66%) showed subclonal mutations only. NT5C2 mutations most frequently occurred in relapses of so‐called B‐other‐ALL that lacks established cytogenetic changes (P &lt; 0.001) and were correlated with CDKN2A/B loss. In addition, predominant, but not subclonal NT5C2 mutations were associated with NRAS mutations indicating that RAS signaling may be involved in NT5C2‐driven relapse formation. Both, subclonal and predominant NT5C2 mutations, were associated with inferior event‐free survival rates of relapsed patients compared to wild‐type NT5C2 (0.189±0.058 and 0.333 ± 0.096, respectively, versus 0.575 ± 0.026; P &lt; 0.001). Response to relapse treatment was particularly poor in relapsed patients with subclonal NT5C2 mutations only. This group showed an increased rate of nonresponse of more than 30% (P &lt; 0.001). Moreover, patients of this group who responded to relapse treatment, showed high minimal residual disease levels at the end of relapse induction treatment in 80% of cases. To investigate whether outgrowth of NT5C2 mutant subclones during relapse treatment contributes to the poor response and outcome, we analyzed follow‐up samples and found that subclonal NT5C2 mutations never grew out to predominant mutations at the time of nonresponse or second relapse. In fact, analysis of samples taken after relapse induction treatment showed that NT5C2 mutant clones were frequently eradicated early during relapse treatment (14/20, 70%), whereas NT5C2 wild‐type leukemic cells persisted at minimal residual disease levels higher than 10E‐03 (16/20, 80%).Summary/Conclusion:Subclonal NT5C2 mutations define a patient group with poor response to treatment and outcome in relapsed B‐cell precursor ALL, but due to their transient character they may not play a driving role in this clinical phenotype.

NT5C2 Mutations Drive Thiopurine Resistance via Distinct Mechanisms

Abstract In patients with ALL the most common NT5C2 mutation class disrupted its switch-off mechanism.

Structure and Mechanisms of NT5C2 Mutations Driving Thiopurine Resistance in Relapsed Lymphoblastic Leukemia

Activating mutations in the cytosolic 5'-nucleotidase II gene NT5C2 drive resistance to 6-mercaptopurine in acute lymphoblastic leukemia. Here we demonstrate that constitutively active NT5C2 mutations K359Q and L375F reconfigure the catalytic center for substrate access and catalysis in the absence of allosteric activator. In contrast, most relapse-associated mutations, which involve the arm segment and residues along the surface of the inter-monomeric cavity, disrupt a built-in switch-off mechanism responsible for turning off NT5C2. In addition, we show that the C-terminal acidic tail lost in the Q523X mutation functions to restrain NT5C2 activation. These results uncover dynamic mechanisms of enzyme regulation targeted by chemotherapy resistance-driving NT5C2 mutations, with important implications for the development of NT5C2 inhibitor therapies.

Relapsed acute lymphoblastic leukemia-specific mutations in NT5C2 cluster into hotspots driving intersubunit stimulation

Activating mutations in NT5C2, a gene encoding cytosolic purine 5'-nucleotidase (cN-II), confer chemoresistance in relapsed acute lymphoblastic leukemia. Here we show that all mutants became independent of allosteric effects of ATP and thus constitutively active. Structural mapping of mutations described in patients demonstrates that 90% of leukemia-specific allelles directly affect two regulatory hotspots within the cN-II molecule-the helix A region: residues 355-365, and the intersubunit interface: helix B (232-242) and flexible interhelical loop L (400-418). Furthermore, analysis of hetero-oligomeric complexes combining wild-type (WT) and mutant subunits showed that the activation is transmitted from the mutated to the WT subunit. This intersubunit interaction forms structural basis of hyperactive NT5C2 in drug-resistant leukemia in which heterozygous NT5C2 mutation gave rise to hetero-tetramer mutant and WT proteins. This enabled us to define criteria to aid the prediction of NT5C2 drug resistance mutations in leukemia.

Clonal evolution mechanisms in NT5C2 mutant-relapsed acute lymphoblastic leukaemia.

Relapsed acute lymphoblastic leukemia (ALL) is associated with chemotherapy resistance and poor prognosis1. Gain-of-function mutations in the 5′-nucleotidase, cytosolic II (NT5C2) gene induce resistance to 6-mercaptopurine (6-MP) and are selectively present in relapsed ALL2,3. Yet, the mechanisms involved in NT5C2 mutation-driven clonal evolution during leukemia initiation, disease progression and relapse remain unknown. Using a conditional inducible leukemia model, we demonstrate that expression of Nt5c2 p.R367Q, a highly prevalent relapsed-ALL NT5C2 mutation, induces resistance to chemotherapy with 6-MP at the cost of impaired leukemia cell growth and leukemia-initiating cell activity. The loss of fitness phenotype of Nt5c2+/R367Q mutant cells is associated with excess export of purines to the extracellular space and depletion of the intracellular purine nucleotide pool. Consequently, blocking guanosine synthesis via inosine-5′-monophosphate dehydrogenase (IMPDH) inhibition induced increased cytotoxicity against NT5C2-mutant leukemia lymphoblasts. These results identify NT5C2 mutation-associated fitness cost and resistance to chemotherapy as key evolutionary drivers shaping clonal evolution in relapsed ALL and support a role for IMPDH inhibition in the treatment of ALL.

Abstract PR02: Mechanisms of NT5C2 activating mutations driving thiopurine resistance in relapsed lymphoblastic leukemia

Abstract Activating mutations in cytosolic 5'-nucleotidase II (NT5C2) drive resistance to 6-mercaptopurine (6-MP) in relapsed acute lymphoblastic leukemia (ALL). These gain-of function alleles encode proteins with increased nucleotidase activity, yet their specific molecular mechanisms are poorly understood. Allosteric activation of NT5C2 is primarily mediated by a marked conformational change in the helix A region, which reconfigures the catalytic center for substrate access and catalysis. Here we demonstrate that constitutively active NT5C2 mutant proteins (K359Q and L375F) adopt active helix A region structures in the absence of allosteric activator. Moreover, crystallographic, structural modeling, genetic, and functional antibody analyses identify a switch-off mechanism mediated by the dynamic mobilization of Asp407 in the tip region of the arm segment which, guided by positively charged residues located in the surface of a basic inter-monomeric cavity exposed upon allosteric activation, turns off NT5C2 by interacting with and disrupting the helical conformation of helix A. Loss of this regulatory mechanism in NT5C2 mutants involving the tip region of the arm segment and the inter-monomeric cavity drives increased nucleotidase activity and allosteric response. Finally, increased allosteric activation by the Q523X mutation results from loss of the NT5C2 C-terminal acidic tail segment, which promotes a closed inactive state in basal conditions. These results uncover dynamic mechanisms responsible for NT5C2 regulation targeted by chemotherapy resistance-driving NT5C2 mutations, with important implications for the development of NT5C2 inhibitor therapies. This abstract is also being presented as Poster 05. Citation Format: Chelsea L. Dieck, Gannie Tzoneva, Farhad Forouhar, Zachary Carpenter, Marta Sanchez-Martin, Alberto Ambesi-Impiombato, Renate Kirschner-Schwabe, Scott Lew, Jayaraman Seetharaman, Liang Tong, Adolfo Ferrando. Mechanisms of NT5C2 activating mutations driving thiopurine resistance in relapsed lymphoblastic leukemia [abstract]. In: Proceedings of the Second AACR Conference on Hematologic Malignancies: Translating Discoveries to Novel Therapies; May 6-9, 2017; Boston, MA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(24_Suppl):Abstract nr PR02.