CASC15-S Is a Tumor Suppressor lncRNA at the 6p22 Neuroblastoma Susceptibility Locus

Chromosome 6p22 was identified recently as a neuroblastoma susceptibility locus, but its mechanistic contributions to tumorigenesis are as yet undefined. Here we report that the most highly significant single-nucleotide polymorphism (SNP) associations reside within CASC15, a long noncoding RNA that we define as a tumor suppressor at 6p22. Low-level expression of a short CASC15 isoform (CASC15-S) associated highly with advanced neuroblastoma and poor patient survival. In human neuroblastoma cells, attenuating CASC15-S increased cellular growth and migratory capacity. Gene expression analysis revealed downregulation of neuroblastoma-specific markers in cells with attenuated CASC15-S, with concomitant increases in cell adhesion and extracellular matrix transcripts. Altogether, our results point to CASC15-S as a mediator of neural growth and differentiation, which impacts neuroblastoma initiation and progression.

Initial testing (stage 1) of BAL101553, a novel tubulin binding agent, by the pediatric preclinical testing program

BAL101553 is a highly water soluble prodrug of BAL27862 that arrests tumor cell proliferation and induces cell death in cancer cells through disruption of the microtubule network. In vitro BAL27862 demonstrated potent activity, with the median relative IC50 (rIC50 ) of 13.8 nM (range 5.4-25.2 nM). The in vitro activity of BAL27862 against the PPTP cell lines is distinctive from that previously described for vincristine. BAL101553 induced significant differences in EFS distribution compared to control in 16 of 30 (53%) solid tumor xenografts and in two of four (67%) of the evaluable ALL xenografts. No objective responses were observed.

Synergistic activity of PARP inhibition by talazoparib (BMN 673) with temozolomide in pediatric cancer models in the pediatric preclinical testing program

PURPOSE

Inhibitors of PARP, an enzyme involved in base excision repair, have demonstrated single-agent activity against tumors deficient in homologous repair processes. Ewing sarcoma cells are also sensitive to PARP inhibitors, although the mechanism is not understood. Here, we evaluated the stereo-selective PARP inhibitor, talazoparib (BMN 673), combined with temozolomide or topotecan.

EXPERIMENTAL DESIGN

Talazoparib was tested in vitro in combination with temozolomide (0.3-1,000 μmol/L) or topotecan (0.03-100 nmol/L) and in vivo at a dose of 0.1 mg/kg administered twice daily for 5 days combined with temozolomide (30 mg/kg/daily x 5; combination A) or 0.25 mg/kg administered twice daily for 5 days combined with temozolomide (12 mg/kg/daily x 5; combination B). Pharmacodynamic studies were undertaken after 1 or 5 days of treatment.

RESULTS

In vitro talazoparib potentiated the toxicity of temozolomide up to 85-fold, with marked potentiation in Ewing sarcoma and leukemia lines (30-50-fold). There was less potentiation for topotecan. In vivo, talazoparib potentiated the toxicity of temozolomide, and combination A and combination B represent the MTDs when combined with low-dose or high-dose talazoparib, respectively. Both combinations demonstrated significant synergism against 5 of 10 Ewing sarcoma xenografts. The combination demonstrated modest activity against most other xenograft models. Pharmacodynamic studies showed a treatment-induced complete loss of PARP only in tumor models sensitive to either talazoparib alone or talazoparib plus temozolomide.

CONCLUSIONS

The high level of activity observed for talazoparib plus temozolomide in Ewing sarcoma xenografts makes this an interesting combination to consider for pediatric evaluation.

Revisiting tissue specificity of germline cancer predisposing mutations

Heritable germline mutations in major cancer genes generally lead to a restricted pattern of tissue-specific malignancies, yet many of the same mutations frequently occur somatically in a broad range of spontaneous neoplasms affecting different organs. Might this reflect a difference in tumorigenesis in children and adults?

Initial testing (stage 1) of the PARP inhibitor BMN 673 by the pediatric preclinical testing program: PALB2 mutation predicts exceptional in vivo response to BMN 673

BACKGROUND

BMN 673 is a potent inhibitor of poly-ADP ribose polymerase (PARP) that is in clinical testing with a primary focus on BRCA-mutated cancers. BMN 673 is active both through inhibiting PARP catalytic activity and by tightly trapping PARP to DNA at sites of single strand breaks.

PROCEDURE

BMN 673 was tested in vitro at concentrations ranging from 0.1 nM to 1 μM and in vivo at a daily dose of 0.33 mg/kg administered orally twice daily (Mon-Fri) and once daily on weekends (solid tumors) for 28 days.

RESULTS

The median relative IC50 (rIC50 ) concentration against the PPTP cell lines was 25.8 nM. The median rIC50 for the Ewing cell lines was lower than for the remaining cell lines (6.4 vs. 31.1 nM, respectively). In vivo BMN 673 induced statistically significant differences in EFS distribution in 17/43 (39.5%) xenograft models. Three objective regressions were observed: a complete response (CR) in a medulloblastoma line (BT-45), a maintained CR in a Wilms tumor line (KT-10), and a maintained CR in an ependymoma line (BT-41). BMN 673 maintained its high level of activity against KT-10 with a threefold reduction in dose. KT-10 possesses a truncating mutation in PALB2 analogous to PALB2 mutations associated with hereditary breast and ovarian cancer that abrogate homologous recombination (HR) repair.

CONCLUSIONS

The PPTP results suggest that single agent BMN 673 may have limited clinical activity against pediatric cancers. Single agent activity is more likely for patients whose tumors have defects in HR repair.

Identifying rare events in rare diseases

Utilizing genomic signatures from diagnostic tumor samples to forecast clinical behavior and response to therapy has long been a goal, and we are now poised to further refine how we can identify the relatively rare patients with aggressive neuroblastoma masquerading as patients with a more benign form of the disease. Clin Cancer Res; 21(8); 1782-5. ©2014 AACR. See related article by Oberthuer et al., p. 1904.

Initial solid tumor testing (stage 1) of AZD1480, an inhibitor of Janus kinases 1 and 2 by the pediatric preclinical testing program

BACKGROUND

AZD1480 is an ATP competitive inhibitor of Janus kinases 1 and 2 (JAK1, 2) that has been shown to inhibit the growth of solid tumor models. This agent was selected for testing the putative role of JAK/STAT signaling in the standard PPTP solid tumor models.

PROCEDURES

AZD1480 was tested against the PPTP in vitro cell line panel at concentrations from 1.0 nM to 10 μM and against the PPTP in vivo solid tumor xenograft panels at (60 mg/kg once daily (SID) × 5) for three consecutive weeks. Additional studies evaluated 5 to 20 mg/kg BID × 5 with SID dosing at 7-30 mg/kg at weekends for three consecutive weeks.

RESULTS

In vitro the median relative IC50 (rIC50 ) for the PPTP cell lines was 1.5 µM, with a range from 0.3 µM to 5.9 µM. The two cell lines with rIC50 values of 0.3 µM both had ALK activating genomic alterations. AZD1480 demonstrated statistically significant differences (P < 0.05) in EFS distribution compared to control in 89% of the solid tumor xenografts. AZD1480 induced intermediate (EFS T/C > 2) or high-level growth inhibition in 15 of 30 (50%) solid tumor xenografts. Tumor regressions were observed in three of six Wilms tumor models at doses that induced inhibition of Stat3(Y705) phosphorylation.

CONCLUSIONS

AZD1480 demonstrated significant tumor growth inhibition against most PPTP solid tumor xenografts, similar to that observed for antiangiogenic agents tested by the PPTP. Tumor regressing activity was noted for Wilms tumor xenografts.

Abstract B36: Inhibition of Exportin 1 (XPO1) potently suppresses growth of human neuroblastoma cell lines

Background: Most children with high-risk neuroblastoma are not cured, and new therapies are needed. Exportin 1 (XPO1; Chromosome Region Maintenance 1 Protein Homolog, CRM1) is the sole nuclear exporter of TP53, FOXO1, RB1, CDKN1A, and other critical tumor suppressor proteins (TSPs). This suggests that inhibition of XPO1 is a rational anti-cancer strategy. KPT-330 is a Selective Inhibitor of Nuclear Export (SINE) that irreversibly binds XPO1 and is currently in Phase 1 clinical trials. SINE inhibits XPO1-mediated nuclear export across multiple tumor types leading to activation of TSPs and cancer cell death.

Methods: A panel of 14 genomically-characterized neuroblastoma cell lines was treated with KPT-330 across a 5-log range. Growth inhibition was measured using CellTiter-Glo (Promega) viability assays and a real time growth monitoring system (xCELLigence, Roche). Drug combinations were tested in vitro, and the combination index was calculated using CalcySyn (Biosoft). NOD/SCID mice with neuroblastoma xenografts (both flank and tail-vein injected) were treated orally with KPT-330 (15 mg/kg thrice weekly or 20-25 mg/kg twice weekly), and tumor size was monitored by direct measurement and luciferase luminescence.

Results: KPT-330 showed cytotoxicity against 14 neuroblastoma cell lines with a median IC50 of 236 nM (range 51-568). Sensitivity to KPT-330 was independent of MYCN amplification status. Combination of KPT-330 with commonly used cytotoxic agents (irinotecan, topotecan, cisplatin, and doxorubicin) showed additive effects. Flank xenografts using the neuroblastoma cell line SH-SY5Y showed significantly decreased tumor growth after oral administration of KPT-330. After allowing the tumors to grow following 28 days of drug withdrawal, re-exposure to the drug again showed growth suppression. In a model of metastatic neuroblastoma after tail-vein injection of luciferase-transfected neuroblastoma cell lines (SH-SY5Y, IMR-5, and Be2c), KPT-330 showed significant tumor growth inhibition (p&lt;0.001). KPT-330 treatment resulted in decreased Myc family protein levels as well as activation of apoptotic pathways. Major toxicity was weight loss which was overcome with nutritional supplementation.

Conclusions: Neuroblastomas show sensitivity to XPO1 inhibition both in vitro and in vivo. Ongoing work is focused on discovering the cellular and genomic factors responsible for increased sensitivity to nuclear export inhibition and potential synergistic combinations. With the expected completion of the first in human phase I trials this year, treatment with KPT-330 has the potential to be rapidly translated into a clinical trial for children with neuroblastoma.

Citation Format: Edward F. Attiyeh, Aaron McKeon-Fish, Rebecca Trillo, Yosef Landesman, William Senapedis, Dilara McCauley, Trinayan Kashyap, Sharon Shacham, Michael Kauffman, John M. Maris. Inhibition of Exportin 1 (XPO1) potently suppresses growth of human neuroblastoma cell lines. [abstract]. In: Proceedings of the AACR Special Conference on Pediatric Cancer at the Crossroads: Translating Discovery into Improved Outcomes; Nov 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2013;74(20 Suppl):Abstract nr B36.

Abstract B82: MEK 1/2 inhibition and biomarkers of response in preclinical models of neuroblastoma

Background: Despite an aggressive treatment regime, 40% of patients with high-risk neuroblastoma die of their disease. The mitogen-activated protein kinase (MAPK) signaling cascade is hyperactive in many cancers, including a subset of high-risk neuroblastomas. We, therefore, sought to determine the efficacy of MEK inhibition in neuroblastoma and develop a responder hypothesis of anti-tumor activity based on molecular genetic features.

Methods: MEK162 (Novartis Pharmaceuticals), an orally available MEK1/2 inhibitor, is currently in adult clinical trials for advanced malignancies harboring RAS/RAF mutations. In determining MEK162 IC50 values, we employed the RT-CES cell impedance assay as it measures both cytostatic and cytotoxic responses in a temporal manner. Additional in vitro analysis of MEK162 activity included immunoblotting, cell cycle analysis with flow cytometric methods, and phosphorylation arrays across a panel of 23 neuroblastoma cell lines. Four of these cell lines (2 sensitive and 2 resistant) were also tested in vivo in subcutaneous xenograft models with tumor volume endpoints. The cell line IC50 ranking was cross-referenced with HuGene1.0ST expression microarrays (Affymetrix), phosphorylation arrays (Full Moon Biosystems), and exome sequencing in order to identify the genetic and proteomic underpinnings predictive of response to MEK inhibition. Microarray analysis was performed using the Limma package (Bioconductor/R), unsupervised clustering, and gene set enrichment (GSEA).

Results: Neuroblastoma cell lines (N=23) showed a wide range of sensitivity to MEK162 across a 4-log dose range (median IC50 = 771 nM, range 5 nM-10 μM). Sensitive cell lines demonstrated G1 arrest within 24 hours of exposure to MEK162. In vivo subcutaneous xenograft experiments recapitulated the in vitro response of MEK162 sensitivity in each of the cell lines tested. In order to identify determinants of sensitivity, we profiled the genomic signature of 23 cell lines in the exponential growth phase prior to confluence. Of the ten most sensitive cell lines, six possessed mutations predicted to be damaging and indicative of RAS/MAPK pathway hyperactivation (NRAS-Q61K, NF1 copy number loss, KRAS-G12D). No resistant lines possessed genetic evidence of RAS hyperactivation. However, baseline phosphorylated-ERK status was not robustly predictive of drug activity. For the purpose of biomarker discovery, we considered a total of 4 cells lines as sensitive (IC50&lt; 200 nM) and 4 resistant (IC50&gt; 3,000 nM). Unsupervised clustering and GSEA of the most differentially expressed genes derived from comparing sensitive (N=4) and resistant (N=4) cell lines confirmed increased baseline MAPK pathway activity in the sensitive cell lines. In addition, resistance to MEK162 was found to be associated with MYCN expression (R=.70/p=0.00043), suggesting that MYCN may serve as a biomarker of MEK162 resistance. Independently, we have demonstrated a correlation between MYCN-amplification and sensitivity to CDK4/6 inhibition (p=0.0227), suggesting the combination of MEK and CDK4/6 inhibition may synergize in the inhibition of neuroblastoma growth.

Conclusions: MEK inhibition is effective in a definable subset of human-derived neuroblastoma preclinical models. Canonical activation of the RAS/MAPK pathway via RAS mutation and/or NF1 inactivation partially account for sensitivity to MEK inhibition, however, biomarkers predictive of sensitivity to MEK inhibition remain to be identified. We demonstrate that both MYCN expression and CDK4/6 activity are associated with MEK resistance, providing a basis for defining MEK162 combination strategies in the treatment of neuroblastoma.

Citation Format: Lori S. Hart, Vandana Batra, Pichai Raman, Maria Gagliardi, JulieAnn Rader, Lucy Chen, Christine Fritsch, Giordano Caponigro, Malte Peters, Markus Boehm, John M. Maris. MEK 1/2 inhibition and biomarkers of response in preclinical models of neuroblastoma. [abstract]. In: Proceedings of the AACR Special Conference on Pediatric Cancer at the Crossroads: Translating Discovery into Improved Outcomes; Nov 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2013;74(20 Suppl):Abstract nr B82.

Abstract A12: Systematic identification of germline mutations in rhabdomyosarcoma and neuroblastoma using massively paralleled sequencing

Despite improvement of survival rate with multimodal chemo- and immunotherapy, high mortality and morbidity is still substantial for patients with metastatic pediatric cancers. Recent studies of massively paralleled sequencing of pediatric tumors including rhabdomyosarcoma (RMS) and neuroblastoma (NB) have been focusing on somatic mutations, and revealed a low somatic mutation rate and surprisingly few recurrently somatic mutated genes in these childhood tumors. Therefore, only a small portion of pediatric cancer cases can be explained by somatic driver events; whereas the causal events for the majority of these diseases remain unknown. Here, we hypothesize that infrequent germline mutations may play a role in the initiation of sporadically occurring tumor.

To identify rare expressed germline protein-coding changing mutations, we utilized two cancer patient cohorts consisting of RMS (n=83) and NB (n=93) patients, of which latter is a part of the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) initiative for pediatric cancers. We first called high-quality protein-coding changing single nucleotide variants (SNVs) (≥100, Coverage ≥10, ≥3 variant reads, ≥30% variant allele frequency) in both paired germline and tumor genomic DNAs. Since both these two types of tumors are uncommon, we then excluded variants with frequencies of &gt;0.1% in the normal human population using the 1000 Genomes data, but retained all disease-causing SNVs annotated either by the Human Gene Mutation Database (HGMD) or ClinVar. Previous studies have highlighted the importance of expression of variant genes (including tumor suppressor genes) for identification of driver mutations in cancers. Therefore we utilized transcriptome sequencing experiments to identify expressed variants in tumor. In addition, we performed Fisher's exact tests comparing germline mutations in these two patient cohorts with the ESP dataset comprising 6503 non-cancer subjects to identify significant overrepresentation of germline mutations in these cancers. Finally we performed pathway analyses using the significant genes.

We initially identified a total of 783169 high-quality protein-coding changing SNVs detected in both paired germline and tumor genomic DNAs, corresponding to a median of 4818 (2093-7569) SNVs per patient. After exclusion of common variants of ≥0.1% frequency in the 1000 Genomes and inclusion of all disease-causing SNVs, there are total of 91924 SNVs, representing a median of 535 (155-877) SNVs per patient corresponding to a median of 468 (153-752) genes. Approximately 59% (total 54664, Median of 319 (94-549) SNVs) of these germline variants can be detected in the transcriptome in their corresponding tumors, suggesting potential functions in these tumors. Statistical analysis is currently underway to determine potential pathological or casual germline mutations associated with neuroblastoma and rhabdomyosarcoma.

Citation Format: Jun S. Wei, Rajesh Patidar, John Shern, Shile Zhang, Trevor Pugh, Sharon J. Diskin, Sivasish Sindiri, Young K. Song, Hongling Liao, Xinyu Wen, Jianjun Wang, Stephen X. Skapek, James R. Anderson, Frederic G. Barr, Robert C. Seeger, John M. Maris, Douglas Hawkins, Javed Khan. Systematic identification of germline mutations in rhabdomyosarcoma and neuroblastoma using massively paralleled sequencing. [abstract]. In: Proceedings of the AACR Special Conference on Pediatric Cancer at the Crossroads: Translating Discovery into Improved Outcomes; Nov 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2013;74(20 Suppl):Abstract nr A12.

Abstract B40: MYCN/MYC protein expression in high-MKI (Mitosis-Karyorrhexis Index) neuroblastomas: A report from the Children's Oncology Group

Background: In neuroblastoma (NB), Mitosis-Karyorrhexis Index (MKI; low-L, &lt;100/5,000 cells; intermediate-I, 100-200/5,000 cells; high-H, &gt;200/5,000 cells) is one of the histologic indicators for predicting a patient's clinical outcome. Event-Free Survival (EFS) and Overall Survival (OS) are significantly worse as MKI increases (p&lt;0.0001): 3-year EFS for L-MKI (81.2+1.0%), I-MKI (68.6+1.8%), H-MKI (51.0+2.2%); and 3-year OS for L-MKI (92.0+0.7%), I-MKI (81.0+1.6%), H-MKI (64.4+2.1%). MYCN amplification (MYCN-A) is significantly associated with H-MKI, which indicates markedly increased mitotic (cellular proliferation) and karyorrhectic (cellular death) cells. However, about one-third of H-MKI tumors do not have MYCN-A.

Study design: A total of 4,712 NB cases reviewed by the Children's Oncology Group (COG) Neuroblastoma Pathology Reference Laboratory (Children's Hospital Los Angeles) between 06/18/2001 and 06/06/2013 included 2,595 L-MKI (3% with MYCN-A), 1,197 I-MKI (16% with MYCN-A), and 920 H-MKI (70% with MYCN-A) tumors. In this study, immunohistochemical detection of MYCN and MYC (C-myc) protein was performed on 82 H-MKI tumors (53 with MYCN-A and 29 without MYCN-A).

Results: 50/53 (94%) of H-MKI tumors having MYCN-A were positive for MYCN protein (including one case positive for both MYCN and MYC proteins), and only 3 cases were negative for both proteins immunohistochemically. Among the H-MKI tumors without MYCN-A, 16 cases (55%) showed positive staining for MYC protein, 6 cases (21%) were positive for MYCN protein, 2 cases (7%) were positive for both proteins, and 5 cases (17%) were negative for both proteins.

Conclusions: MYCN-A and subsequent MYCN protein expression are considered as the starting point for leading NB tumors to H-MKI status. However, when MYCN is not amplified, high mitotic/karyorrhectic (M/K) activities in NB tumors are often associated with MYC protein expression. Even some MYCN non-amplified tumors can express MYCN protein, which is associated with H-MKI. There is still a small group of H-MKI tumors whose increased M/K activities are not related to MYCN/MYC protein expression.

Citation Format: Larry L. Wang, Risa Teshiba, Lejian He, Arlene Naranjo, Wendy B. London, Julie M. Gastier-Foster, Robert C. Seeger, Susan L. Cohn, John M. Maris, Julie R. Park, Michael D. Hogarty, Hiroyuki Shimada. MYCN/MYC protein expression in high-MKI (Mitosis-Karyorrhexis Index) neuroblastomas: A report from the Children's Oncology Group. [abstract]. In: Proceedings of the AACR Special Conference on Pediatric Cancer at the Crossroads: Translating Discovery into Improved Outcomes; Nov 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2013;74(20 Suppl):Abstract nr B40.

Abstract A28: Clinical next-generation sequencing (NGS) reveals genomic alterations (GAs) to guide targeted therapy in advanced neuroblastoma patients

Introduction: High-risk neuroblastoma patients have a survival rate below 50% despite dose-intensive chemoradiotherapy. Treatment using molecularly targeted therapy could more effectively manage patients with less toxicity, but would be best deployed through identification of GAs that suggest responsiveness to such therapies. Recent work from the TARGET initiative (Pugh et al., Nature Genetics 2013) demonstrates a near 10% frequency of ALK GAs in high-risk neuroblastoma patients; such patients could benefit from crizotinib or similar agents targeting the ALK kinase. However, the majority of high-risk neuroblastoma patients still lack identifiable options for targeted therapy. We reviewed the GAs in 17 advanced, high-risk neuroblastoma patients who underwent prospective genomic profiling by clinical NGS to identify actionable alterations that might allow successful trials of targeted therapy.

Methods: Diagnostic genomic profiling was performed to characterize all classes of GAs (base substitutions, small insertions/deletions, copy number alterations, and rearrangements) on primary tumors or metastatic specimens, either pre- or post-chemotherapy, of 17 advanced neuroblastoma patients. For each specimen, 3,320 exons of 182 cancer-related genes and selected introns of 14 frequently rearranged genes or 3769 exons of 236 cancer-related genes and selected introns of 19 frequently rearranged genes (earlier and current version of assay, respectively) were sequenced to a minimum coverage depth of 250x in a CLIA-certified, CAP-accredited lab (Foundation Medicine, Cambridge, MA). Actionable GAs were defined as those for which there were FDA-approved agents and/or agents being evaluated in clinical trials.

Results: The patient population had a median age of 4.6 yrs (range 2 - 18 yrs), 13 were males, and 16 had Stage 4 disease (one Stage 3). Specimens were sequenced to an average depth of 861x, and GAs were present in 100% (17/17) of cases. These 17 cases harbored 27 GAs (1.6 alterations per tumor; range 1 to 5). Ninety-four percent of cases harbored at least one actionable GA, with a mean of 1.6 actionable GAs per tumor (range 1 to 5). Previously described GAs in neuroblastoma were present in this series, such as GAs in ALK (5 cases; 29%), MYCN (5 cases; 29%), and ATRX (2 cases; 12%), which occurred in a largely mutually exclusive fashion. Alterations in ALK were predominantly base substitutions (80%) and included F1174L and R1275Q at frequencies of 40% and 20%, respectively. One ALK alteration was a novel fusion gene predicted to be active in vivo and potentially responsive to crizotinib. Another recurrent actionable alteration is potentially targetable by FGFR inhibitors, as two neuroblastoma cases contained the activating base substitution N546K in FGFR1.

Conclusions: Profiling the tumor genomes of 17 high-risk neuroblastoma patients led to the identification of actionable GAs in a high proportion of patients including alterations previously unseen in neuroblastoma. Specifically, novel fusions of ALK and activating alterations in FGFR1 would not be detected by current molecular diagnostic assays employed in neuroblastoma but offer possible immediate benefit from targeted treatment. Such findings suggest the value of rebiopsying progressive or recurrent high-risk neuroblastoma to identify unforeseen avenues for treatment with targeted therapy.

Citation Format: Siraj M. Ali, Matthew J. Hawryluk, Kai Wang, Juliann Chmielecki, Gary A. Palmer, Lazaro Garcia, Emily White, Roman Yelensky, Philip J. Stephens, Jeffrey S. Ross, John M. Maris, Vince A. Miller. Clinical next-generation sequencing (NGS) reveals genomic alterations (GAs) to guide targeted therapy in advanced neuroblastoma patients. [abstract]. In: Proceedings of the AACR Special Conference on Pediatric Cancer at the Crossroads: Translating Discovery into Improved Outcomes; Nov 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2013;74(20 Suppl):Abstract nr A28.

Abstract A27: A noncoding polymorphism in a GATA-containing enhancer element drives the association of LMO1 with neuroblastoma

Background: Our ongoing genome-wide association study (GWAS) in neuroblastoma has identified multiple common and rare polymorphisms highly associated with disease susceptibility and phenotype. SNPs at the LMO1 locus showed one of the most robust associations and were associated with LMO1 overexpression and oncogenicity in preclinical models (Nature, 2011). Here we seek to define the DNA polymorphism(s) responsible for the GWAS association and determine the mechanism by which common variation determines tumor aggressiveness.

Methods: Using 1000 Genomes data, we imputed all known variants within a 500-kilobase window around the LMO1 gene in a discovery set of 2,101 cases and 4,202 controls of European ancestry using the IMPUTE2 algorithm and performed association testing with SNPTEST. We further prioritized significant variants by evolutionary conservation based on comparative genome analysis of 46 mammalian species. Identification of non-coding variant regions with regulatory potential was performed through analysis of neuroblastoma-specific DNase I hypersensitivity mapping and chromatin immunoprecipitation (ChIP) sequencing data generated through the ENCODE consortium. Identification of canonical transcription factor binding motifs was performed using the MATCH-TM algorithm and JASPAR motif database. Independent replication of the top candidate causal SNP was performed by PCR-based genotyping in case series from Italy (420 cases, 751 controls) and the United Kingdom (369 cases, 1,108 controls). For statistical testing, homozygous and heterozygous odds ratios (OR) were computed from a comparison of (TT vs. GG) and (GT vs. GG) genotypes, respectively, and a single chi-squared p-value was computed from the 2x3 contingency table of phenotype vs. genotype.

Results: The most significantly associated SNP at the LMO1 locus (rs2168101, homozygous OR=0.55, heterozygous OR=0.69, p-value=6.18x10-21) resides within an active enhancer region inferred by DNase I sequencing and histone modification ChIP-seq profiling in the SKNSH neuroblastoma cell line. Furthermore, rs2168101 lies within a GATA motif with perfect evolutionary conservation (5′-AGATAA-3′, phastCons score=100% across 46 mammalian species) that robustly binds to GATA2 and GATA3 transcription factors by ChIP-seq profiling. Consistent with an enhancer model, the risk “G” allele preserves the GATA motif and is associated with higher levels of LMO1 expression across a panel of 24 neuroblastoma cell lines (t-test p=0.047). Additionally, primary tumors with heterozygous G/T genotypes exhibit a greater degree of allele-specific expression imbalance relative to homozygous tumors by RNA-sequencing (t-test p=4.42x10-4), consistent with an effect in cis. In follow-up to imputation-based analysis, robust replication of the rs2168101 neuroblastoma association was observed by direct genotyping in an independent Italian cohort (homozygous OR=0.40, heterozygous OR=0.57, chi-squared p=9.94x10-6) and UK cohort (homozygous OR=0.31, heterozygous OR=0.51, chi-squared p=2.44x10-9). Furthermore, rs2168101 genotype was also associated with high-risk neuroblastoma and outcome (homozygous OR=0.67, heterozygous OR=0.74, p-value=2.16x10-4).

Conclusions: Integrative genomic analysis provides mechanistic insight into how germline variation within non-coding DNA can impact neuroblastoma susceptibility and prognosis, supporting the hypothesis that the risk “G” allele at rs2168101 promotes oncogenic LMO1 overexpression through increased GATA transcription factor binding within an active enhancer region. Functional validation experiments are currently underway, including ChIP-PCR of the enhancer locus and targeted genome editing of the GATA binding site.

Citation Format: Derek A. Oldridge, Andrew Wood, Cindy Winter, Maura Diamond, Ian Crimmins, Shile Zhang, Jun Wei, Javed Khan, Mario Capasso, Nazneen Rahman, Sharon J. Diskin, John M. Maris. A noncoding polymorphism in a GATA-containing enhancer element drives the association of LMO1 with neuroblastoma. [abstract]. In: Proceedings of the AACR Special Conference on Pediatric Cancer at the Crossroads: Translating Discovery into Improved Outcomes; Nov 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2013;74(20 Suppl):Abstract nr A27.

Common genetic variants in NEFL influence gene expression and neuroblastoma risk

The genetic etiology of sporadic neuroblastoma is still largely obscure. In a genome-wide association study, we identified single-nucleotide polymorphisms (SNP) associated with neuroblastoma at the CASC15, BARD1, LMO1, DUSP12, HSD17B12, HACE1, and LIN28B gene loci, but these explain only a small fraction of neuroblastoma heritability. Other neuroblastoma susceptibility genes are likely hidden among signals discarded by the multiple testing corrections. In this study, we evaluated eight additional genes selected as candidates for further study based on proven involvement in neuroblastoma differentiation. SNPs at these candidate genes were tested for association with disease susceptibility in 2,101 cases and 4,202 controls, with the associations found replicated in an independent cohort of 459 cases and 809 controls. Replicated associations were further studied for cis-effect using gene expression, transient overexpression, silencing, and cellular differentiation assays. The neurofilament gene NEFL harbored three SNPs associated with neuroblastoma (rs11994014: Pcombined = 0.0050; OR, 0.88; rs2979704: Pcombined = 0.0072; OR, 0.87; rs1059111: Pcombined = 0.0049; OR, 0.86). The protective allele of rs1059111 correlated with increased NEFL expression. Biologic investigations showed that ectopic overexpression of NEFL inhibited cell growth specifically in neuroblastoma cells carrying the protective allele. NEFL overexpression also enhanced differentiation and impaired the proliferation and anchorage-independent growth of cells with protective allele and basal NEFL expression, while impairing invasiveness and proliferation of cells homozygous for the risk genotype. Clinically, high levels of NEFL expression in primary neuroblastoma specimens were associated with better overall survival (P = 0.03; HR, 0.68). Our results show that common variants of NEFL influence neuroblastoma susceptibility and they establish that NEFL expression influences disease initiation and progression.

Abstract 5081: Systematic identification of germline mutations in rhabdomyosarcoma and neuroblastoma using massively paralleled sequencing

Despite improvement of survival using multimodal chemo- and immunotherapy, high mortality and morbidity is still substantial for pediatric patients with metastatic cancers. Recent large-scale sequencing studies of pediatric tumors including rhabdomyosarcoma (RMS) and neuroblastoma (NB) have been focusing on somatic mutations, and revealed a low somatic mutation rate and surprisingly few recurrently somatic mutated genes in these childhood tumors. Currently, only a small portion of pediatric cancer cases can be explained by somatic driver events; whereas the cause for the majority of these diseases remains unknown. Because both these two types of tumors are uncommon, here we hypothesize that infrequent germline mutations (frequency&lt;0.05 in control populations) may play a role in the initiation of sporadically occurring tumor.

To test this hypothesis, we utilized sequencing data from two cancer patient cohorts consisting of RMS (n=133) and NB (n=222) patients, of which latter is a part of the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) initiative for pediatric cancers. First, high-quality protein-coding changing single nucleotide variants (SNVs) were called in both paired germline and tumor genomic DNAs. Then we excluded common variants with frequency &gt;5% in a normal human population using the 1000 Genomes data. Due to our interest in the enriched variants, we further required the frequencies of variants in our rhabdomyosarcoma and neuroblastoma patient cohorts are higher than those in the ESP dataset, a non-cancer control population comprising 6503 individuals. There are 63247 SNVs fulfilled these selection criteria. Among them, 1589 have been reported in these pediatric cancers or in other malignancies in the Cancer Genome Atlas (TCGA) project; and 1178 variants are present in the Human Gene Mutation Database (HGMD). Of these HGMD variants, 49 have been reported in human diseases and 34 of them are known disease-causing mutations for human cancers and genetic disorders including TP53, ALK, CHEK2, and PINK1. Interestingly, the most frequent germline mutations in these pediatric tumors were rarely found in the TCGA project which mostly consists of adult cancers. This observation suggests a very different genetic background of pediatric cancer patients from that of the adult cancers, and warrants a careful examination of germline mutations in these cancers. Furthermore, previous studies have highlighted the importance of expression of variant genes (including tumor suppressor genes) for identification of driver mutations in cancers. Therefore we will use 178 transcriptome sequencing experiments available for these tumors (RMS=84; NB=93) to identify expressed variants in tumor. Statistical and pathway analyses are currently underway to determine potential pathological or casual germline mutations associated with neuroblastoma and rhabdomyosarcoma.

Citation Format: Jun S. Wei, Rajesh Patidar, John Shern, Shile Zhang, Trevor Pugh, Sharon J. Diskin, Sivasish Sindiri, Young K. Song, Hongling Liao, Xinyu Wen, Jianjun Wang, Stephen X. Skapek, James R. Anderson, Frederic G. Barr, Robert C. Seeger, John M. Maris, Douglas S. Hawkins, Javed Khan. Systematic identification of germline mutations in rhabdomyosarcoma and neuroblastoma using massively paralleled sequencing. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5081. doi:10.1158/1538-7445.AM2014-5081

Abstract 2953: Rev-erbα modulates Myc-driven cancer cell growth and altered metabolism

Circadian rhythms are regulated by feedback loops comprising a network of factors that regulate Clock-associated genes. Chronotherapy seeks to take advantage of altered circadian rhythms in some cancers to better time administration of treatments to increase efficacy and reduce toxicity. While many cancers have perturbed expression of core circadian rhythm genes, the molecular basis underlying these perturbations and their functional implications in oncogenesis are still poorly understood, and so it is impossible to predict which cancers have altered circadian rhythms and would best benefit from chronotherapy. We have observed in cancer cell models of osteosarcoma, hepatocellular carcinoma, and neuroblastoma that the c-Myc and N-Myc oncogenic transcription factors disrupt oscillation of the circadian clock by specifically upregulating the circadian rhythm gene and nuclear hormone receptor NR1D1 (Rev-erbα). Interestingly, while Rev-erbα has not been previously recognized as an oncogene, data from The Cancer Genome Atlas revealed that it is amplified in many forms of human cancer, and we also observed that Rev-erbα was upregulated in primary human neuroblastoma and associated with poor prognosis. Therefore, we hypothesized that Rev-erbα is a novel oncogene downstream of Myc and is important for cancer cell growth.

Here we show that Rev-erbα is specifically essential for the growth of Myc-driven hepatocellular carcinoma cells, as the related protein Rev-erbβ did not strongly influence growth. While knockdown of Rev-erbα expression by siRNA slowed growth, it did not cause cell death or canonical cell cycle arrest. Rev-erbα modulates circadian rhythm by downregulating the central circadian regulatory protein Bmal1, but this pathway did not play a central role in Rev-erbα control of cell growth. Additionally, while Rev-erbα has a well-described role in heme metabolism and subsequent support of mitochondria respiration, this pathway was not directly altered in Myc-driven liver cancer cells. Rather, knockdown of Rev-erbα was associated with decreased glycolytic activity characterized by a decrease in intracellular lactate and extracellular lactate production as well as an increase in certain glycolytic intermediates. In addition to these glycolytic changes, the maximum respiratory capacity of cells lacking Rev-erbα increased, as measured by oxygen consumption. These data suggest a novel role for Rev-erbα in promoting the growth of cancer cells through modulation of glucose metabolism and a shift towards increased respiration, and imply that cancers with upregulated Myc and Rev-erbα may be good candidates for chronotherapy.

We thank the following funding sources: NIH R01CA57341, LLS 6106-14.

Citation Format: Brian J. Altman, Annie Hsieh, Arvin M. Gouw, Zachary E. Stine, Anand Venkataraman, David I. Bellovin, Sharon J. Diskin, Wenyun Lu, Sisi Zhang, Dean W. Felsher, John M. Maris, Mitchell A. Lazar, Joshua D. Rabinowitz, John B. Hogenesch, Chi V. Dang. Rev-erbα modulates Myc-driven cancer cell growth and altered metabolism. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2953. doi:10.1158/1538-7445.AM2014-2953

Initial testing (stage 1) of the notch inhibitor PF-03084014, by the pediatric preclinical testing program

PF-03084014, a γ-secretase inhibitor, was tested against the PPTP in vitro cell line panel (1.0 nM to 10 μM) and against the in vivo xenograft panels (administered orally twice daily on Days 1-7 and 15-21). PF-03084014 demonstrated limited in vitro activity, with no cell line achieving ≥50% inhibition. PF-03084014 induced significant differences in EFS distribution in 14 of 35 (40%) solid tumor xenografts, and 1 of 9 ALL xenografts (which lacked a NOTCH1 mutation), but objective responses were not observed. PF-03084014 demonstrated limited single agent activity in vitro and in vivo against the pediatric preclinical models studied.

Initial testing (stage 1) of the investigational mTOR kinase inhibitor MLN0128 by the pediatric preclinical testing program

MLN0128 is an investigational small molecule ATP-competitive inhibitor of the serine/threonine kinase mTOR. MLN0128 was tested against the in vitro panel at concentrations ranging from 0.1 nM to 1 μM and against the PPTP in vivo panels at a dose of 1 mg/kg administered orally daily × 28. In vitro the median relative IC(50) concentration was 19 nM. In vivo MLN0128 induced significant differences in EFS in 24/31 (77%) solid tumor models, but 0/7 ALL xenografts. The modest activity observed for MLN0128 against the PPTP preclinical models is similar to that previously reported for another TOR kinase inhibitor.

Time to disease progression in children with relapsed or refractory neuroblastoma treated with ABT-751: a report from the Children's Oncology Group (ANBL0621)

BACKGROUND

ABT-751, an orally bioavailable sulfonamide binds the colchicine site of beta-tubulin and inhibits microtubule polymerization. Prior phase I studies established the recommended dose in children with solid tumors as 200 mg/m(2) PO daily × 7 days every 21 days and subjects with neuroblastoma experienced prolonged stable disease. We conducted a phase 2 study (NCT00436852) in children and adolescents with progressive neuroblastoma to determine if ABT-751 prolonged the time to progression (TTP) compared to a hypothesized standard based on a historical control population.

PROCEDURE

Children and adolescents (n = 91) with a median (range) age 7.7 (2.3-21.5) years and progressive neuroblastoma were enrolled and stratified by disease status into disease measureable by CT/MRI (n = 47) or disease assessable by (123) I-metaiodobenzylguanine scintigraphy (MIBG, n = 44). Response was evaluated using RECIST for measureable disease and the Curie score for MIBG-avid disease.

RESULTS

ABT-751 was well tolerated. The objective response rate was 7%. The median TTP was 42 days (95% CI: 36, 56) in the measureable disease stratum and 45 days (95% CI: 42, 85) in the MIBG-avid disease stratum. TTP was similar to the historical control group (n = 136, median TTP 42 days). For the combined strata (n = 91), 1-year progression free survival (PFS) was 13 ± 4% and overall survival (OS) was 48 ± 5%.

CONCLUSIONS

The low objective response rate and failure to prolong TTP indicate that ABT-751 is not sufficiently active to warrant further development for neuroblastoma. However, this trial demonstrates the utility of TTP as the primary endpoint in phase 2 trials in children and adolescents with neuroblastoma.