Genomic Profiling of Pediatric Acute Myeloid Leukemia Reveals a Changing Mutational Landscape from Disease Diagnosis to Relapse

The genomic and clinical information used to develop and implement therapeutic approaches for acute myelogenous leukemia (AML) originated primarily from adult patients and has been generalized to patients with pediatric AML. However, age-specific molecular alterations are becoming more evident and may signify the need to age-stratify treatment regimens. The NCI/COG TARGET-AML initiative used whole exome capture sequencing (WXS) to interrogate the genomic landscape of matched trios representing specimens collected upon diagnosis, remission, and relapse from 20 cases of de novo childhood AML. One hundred forty-five somatic variants at diagnosis (median 6 mutations/patient) and 149 variants at relapse (median 6.5 mutations) were identified and verified by orthogonal methodologies. Recurrent somatic variants [in (greater than or equal to) 2 patients] were identified for 10 genes (FLT3, NRAS, PTPN11, WT1, TET2, DHX15, DHX30, KIT, ETV6, KRAS), with variable persistence at relapse. The variant allele fraction (VAF), used to measure the prevalence of somatic mutations, varied widely at diagnosis. Mutations that persisted from diagnosis to relapse had a significantly higher diagnostic VAF compared with those that resolved at relapse (median VAF 0.43 vs. 0.24, P < 0.001). Further analysis revealed that 90% of the diagnostic variants with VAF >0.4 persisted to relapse compared with 28% with VAF <0.2 (P < 0.001). This study demonstrates significant variability in the mutational profile and clonal evolution of pediatric AML from diagnosis to relapse. Furthermore, mutations with high VAF at diagnosis, representing variants shared across a leukemic clonal structure, may constrain the genomic landscape at relapse and help to define key pathways for therapeutic targeting. Cancer Res; 76(8); 2197-205. ©2016 AACR.

Abstract 4592: Exome sequencing of hepatoblastoma reveals recurrent mutations in NFE2L2

Hepatoblastoma (HB), the most common malignant liver tumor in children, is a biologically and clinically heterogeneous embryonal malignancy. Activation of the Wnt pathway is known to occur in the vast majority of HBs, most frequently through somatic mutation of CTNNB1 and less often from germline mutation of APC, but knowledge of other gene alterations is scant. To identify critical genes and pathways in the pathogenesis of HB and provide insight into potential clinically-relevant targets, we performed whole exome sequencing on 35 clinically-annotated tumor-normal pairs. Putative mutations identified through exome sequencing on Illumina-based instruments were confirmed on a second sequencing platform. A total of 130 somatic mutations were identified in 24 patients (3.7 mutations per tumor; range of 0 to 22 mutations), resulting in a somatic mutation rate of &lt; 0.2 mutations per Mb. CTNNB1 mutations were identified in 13 HBs (37%), confirming the central role of the Wnt pathway in HB. Somatic mutations were also found in other cancer genes, including the chromatin-remodeling genes MLL2 and ARID1A. Frequent somatic mutations were identified in genes related to regulation of oxidative stress, including recurrent point mutations in NFE2L2 (NRF2) and inactivating mutations in the thioredoxin-domain containing genes TXNDC15 and TXNDC16. An additional 27 HBs were sequenced for NFE2L2 mutations, revealing a mutation frequency of 6.5% (4 of 62 tumors). Mutations of NFE2L2 are known to occur in 5-10% of adult hepatocellular carcinomas (HCC) as well as in other tumor types: as in those tumors, the NFE2L2 mutations identified in HB (p.D29N in one patient and p.R34G in three patients) are clustered within the Neh2 domain and are expected to inhibit KEAP1-mediated degradation of NRF2, resulting in stabilization and nuclear accumulation of NRF2 and activation of downstream oxidative stress response genes. Most NFE2L2-mutated adult HCCs also contain mutations in CTNNB1 or other Wnt pathway genes, suggesting a biological link between NFE2L2-mutated HB and HCC. In addition, whole exome and SNP array data (Affymetrix 6.0 SNPChip) have revealed copy number alterations in previously-described regions of the HB genome, including 1q, 4q and 11p15, as well as novel focal alterations. Finally, germline variants in APC and other Wnt pathway genes have also been identified in this HB patient cohort. In summary, next-generation sequencing of HB has provided an unprecedented view of the genetic landscape of HB, confirmed the primary importance of dysregulation of Wnt signaling in this tumor type, and revealed recurrent hotspot mutations in NFE2L2, a potential therapeutic target. Supported by the Cancer Prevention & Research Institute of Texas (RP101195) and the National Institutes of Health (CA098543).

Citation Format: Lisa R. Trevino, David A. Wheeler, Milton J. Finegold, Murali Chintagumpala, Kayuri U. Patel, Stephen F. Sarabia, Sarah A. Comerford, Robert E. Hammer, Dinesh Rakheja, Rebecka L. Meyers, Yidong Chen, Bradley H. Pollock, Gail E. Tomlinson, Dolores H. López-Terrada, D. Williams Parsons. Exome sequencing of hepatoblastoma reveals recurrent mutations in NFE2L2. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4592. doi:10.1158/1538-7445.AM2013-4592

Abstract 5113: Functional analysis of genomic variants identified through whole exome sequencing for susceptibility to lymphocytic leukemia

The underlying genetic basis of many childhood cancers remains largely unknown, which places a significant focus on the discovery and understanding of cancer susceptibility genes. Our research is focused on the identification of novel high risk childhood cancer susceptibility genes through next generation sequencing methods and functional assays. One kindred contained four individuals diagnosed during childhood with lymphocytic leukemia or lymphoma transmitted in an autosomal dominant pattern of inheritance. Whole exome sequencing was performed on the constitutional DNA of three of the patients diagnosed with childhood cancer and one non-transmitting parent as an internal control. This analysis resulted in over 1000 unique single nucleotide variant (SNV) sites shared among the three affected family members. Of these SNVs, greater than 95% were found in control databases and excluded. Also, any variant found in the non-transmitting parent was eliminated. Systematic bioinformatics analysis resulted in a short list of seven missense SNVs predicted to be functionally important. Within this list is the missense mutation of a conserved residue (L254P) of Human Cytosolic 5′ Nucleotidase (NT5C1A). NT5C1A has a role in nucleoside metabolism as this protein primarily catalyzes the production of adenosine through the dephosphorylation of AMP. Adenosine metabolism is essential for lymphocyte maturation and viability, making NT5C1A an attractive leukemia susceptibility candidate to pursue further through functional genomic assays. Prior studies have shown that overexpression of wild type NT5C1A in HEK293 cells improves cell survival after treatment with purine and pyrimidine analogs also used in leukemia treatment. We created multiple HEK293 cell lines that stably overexpress either the NT5C1A wild type or L254P mutant protein. These cells were tested for quantitative changes in NT5C1A mediated cytotoxicity to the nucleoside analogs, Cladribine and Gemcitabine. We have replicated the prior findings in cells overexpressing wild type NT5C1A and demonstrated that resistance is dependent on the amount of exogenous NT5C1A protein expressed. Importantly, overexpression of the L254P protein is deficient in mediating resistance to these analogs, which is consistent with this novel variant interfering with NT5C1A activity. This finding has led us to hypothesize that the L254P mutation leads to a reduction in protein function, most likely through reduced substrate binding, which may increase AMP levels in early lymphocytes and predispose to tumorigenesis. Future directions include experiments to determine the L254P protein's substrate binding affinity and activity and the introduction of the mutation into murine leukemia models as well as analysis of L254P as a pharmacogenetic variant.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5113. doi:1538-7445.AM2012-5113

Abstract LB-93: Demonstration of significant clonal evolution from diagnosis to relapse in childhood AML determined by exome capture sequencing: an NCI/COG TARGET AML study

Acute myeloid leukemia (AML) is a heterogeneous group of disorders with significant genomic complexity that contributes to variable clinical responses and poor outcomes despite intensive therapy. Although genomic alterations, including karyotypic alterations and somatic mutations have been identified in most patients with AML, their utility has been limited by an inability to accurately predict outcome in the majority of patients. There is also little information on the molecular evolution of AML from diagnosis to relapse. To define the genomic profile of relapse in AML and evaluate the extent of clonal evolution from diagnosis to relapse, we performed exome capture sequencing in matched trios of specimens (diagnostic, remission and relapse specimens) from 22 patients with AML (64 specimens) who were treated on COG clinical trials and lacked previously known high risk features. In the 22 matched diagnostic and 20 relapse cases, 729 somatic variants were identified with a variant allelic frequency ranging from 1% to 94% in diagnostic (N=384) or relapse (N=345) specimens (33.1 mutations/patient) of which 372 were verified with secondary deep sequencing of targeted regions. A verification rate of 86% in mutations with &gt;20% variant allelic frequency was achieved. 335 somatic mutations (median15.5 mutations/patient, range 8-42 mutations/patient) were observed in the 20 cases with diagnostic and relapse specimens. Of these 335 somatic mutations, 221 mutations (66%) in 193 genes were identified in the diagnostic specimens, of which 107 mutations (49%) in 101 genes were present at disease recurrence. In addition to the 107 mutations that persisted from diagnosis to relapse, there was emergence of an additional 114 mutations in 106 genes at the time of relapse, possibly due to clonal selection of a rare pre-existing clone. Somatic mutations in 17 genes were detected in more than one patient at either diagnosis or relapse or both. Of the mutations that were present at both diagnosis and relapse, only 2 genes (KIT and TET2) were mutated in more than one patient, highlighting the paucity of common, novel relapse-associated mutations in the studied cohort. In addition evaluation of copy number (CN) alterations by SNP genotyping in the diagnostic and relapse specimens revealed similar clonal evolution with apparent resolution of diagnostic CN variations and appearance of novel somatic CN alterations in relapse specimens. The study results highlight the genomic complexity of childhood AML, and suggest significant clonal evolution from diagnosis to relapse, with resolution of mutations associated with chemotherapy sensitive clones. Newly evolved mutations may represent rare, chemotherapy resistant clones present at diagnosis, which are selected by exposure to chemotherapy, and may cooperate with other mutations to lead to therapy resistance and poor outcome.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-93. doi:1538-7445.AM2012-LB-93