HGG-54. CLK1 aberrant splicing in pediatric high-grade gliomas disrupts key oncogenic transcriptional programs

While much of the somatic coding variation underlying the oncogenic transformation of pediatric high-grade gliomas (HGGs) has been profiled, transcriptional splicing programs of these tumors remain under-explored. Here, we characterize aberrant alternative splicing in pediatric midline HGGs (n = 84). We identified 19,275 recurrent and significant (20% change from control, P < 0.05, FDR < 0.05) aberrant splicing events in 8,587 genes compared to non-diseased brainstem controls. Of those, 27% (n = 5,157) resulted in either a gain or loss of a known protein functional site within 3,294 genes. We prioritized splice variants affecting targetable kinases and found that mRNAs encoding CDC-like kinase 1 (CLK1), a known modulator of master splicing regulators, exhibit significantly increased exon 4 inclusion in midline HGGs. This leads to a gain of two known phosphorylation sites in CLK1, increased CLK1 protein expression and hyper-phosphorylation of Serine-rich splicing factors. To assess the impact of this event, we performed differential splicing and expression analyses, comparing tumors with the highest (n= 5) and lowest (n = 5) exon 4 inclusion. We discovered 3,037 genes to be differentially up-regulated in high exon 4 inclusion tumors with an enrichment of cancer-related pathways, including DNA repair, mitotic spindle, myogenesis and EMT. We next integrated these gene signatures with protein-protein interaction networks of kinase and transcription factors and show that increased CLK1 exon 4 inclusion disrupts critical regulatory networks, such as those involving FOXM1, which is implicated in cell cycle and proliferation processes. In summary, we describe aberrant splicing in pediatric HGGs as an additional mechanism that could drive tumorigenesis. Future work will focus on molecular validation and therapeutic targeting of CLK1 in available HGG models. Characterizing tumor-specific splicing variation has the potential to open new therapeutic strategies and understand mechanisms of treatment resistance in children with central nervous system tumors.

Abstract 4881: Dissecting telomere maintenance mechanisms in neuroblastoma

Background. Telomere maintenance is a major cancer hallmark and has recently attracted attention as an oncogenic mechanism in the pediatric malignancy, neuroblastoma (NBL), due to detection of frequent structural rearrangements near the telomerase (TERT) gene. NBLs display substantial clinical and molecular heterogeneity; tumors with MYCN amplification and TERT-associated rearrangements define separate groups of high-risk patients with active TERT. ATRX mutations are frequent in non-TERT active high-risk tumors, indicating use of alternative lengthening of telomeres (ALT) as a maintenance mechanism. Furthermore, the 4S low-risk NBLs display an elevated rate of spontaneous regression and overall good prognosis; it has been hypothesized that lacking a telomere maintenance mechanism (“telomere crisis”) may be behind this phenomenon.

Methods. To gain mechanistic insight behind these phenomena, we introduce an integrative analysis of a cohort comprising 104 high-risk (32 MYCN-amplified) and 23 4S tumors with matched blood/tumor whole genome sequencing, CpG methylation, and RNA-seq data from the TARGET consortium.

Here, we preformed structural variant (SV), allelic specific expression (ASE), and differential CpG methylation analyses. Additionally, we introduce a novel approach to measure relative telomere DNA abundance from short-read WGS measured as the ratio between tumor and blood telomeric reads (containing canonical repeats TTAGGG/CCCTAA) per million (TBrpm).

Results. We identified 26 tumors harboring TERT rearrangements (25% of all high risk tumors) and 3 tumors with ATRX mutations. We define 4 groups of high-risk NBL with different telomere maintenance mechanisms: 1) Tumors with MYCN amplification or elevated MYC/N activity, TERT gene body hyper-methylation (β-value≅0.8), and expression of biallelic TERT; 2) Tumors harboring TERT associated SVs, hemi-methylation (β-value≅0.5), and expression of mono-allelic TERT, 3) Tumors without TERT expression, including ATRX mutants with hypo-methylated TERT (β-value≅0.3), 4) tumors with abnormally high telomeric DNA abundance (TBrpm > 1.5), hypo-methylation (β-value≅0.3), and no expression of TERT. Intriguingly, while groups 1-3 show telomeric loss (TBrpm ≅ 0.7-0.9), 4S tumors show conservation of telomere abundance between tumor and blood (TBrpm ≅ 1); hence no indication of telomere crisis, perhaps due to early timing of biopsy at diagnosis.

Conclusion. We have used ASE status and gene body methylation of TERT in order to understand and validate mechanisms underlying TERT activation; we extend MYCN-driven TERT activation to tumors with high MYC/MYCN activity in the absence of MYCN amplification. Our telomere analysis suggests that different ALT mechanisms might take place in NBLs. Defining the mechanism of 4S NBL spontaneous regression requires further investigation.

Citation Format: Gonzalo Lopez, Karina Conkrite, Kendra Hong, Jo Lynne Harenza, John M. Maris, Sharon Diskin. Dissecting telomere maintenance mechanisms in neuroblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4881. doi:10.1158/1538-7445.AM2017-4881

Abstract 4734: A LIN28B/RAN/AURKA signaling network promotes neuroblastoma tumorigenesis

Background: Neuroblastoma, a childhood cancer of the sympathetic nervous system, accounts for approximately 10-15% of pediatric oncology deaths. The genetic basis of neuroblastoma has grown clearer, with genome-wide association studies performed by our laboratory uncovering CASC15, BARD1, NBPF23, LMO1, HACE1, TP53 and LIN28B as susceptibility genes, with many (if not all) playing a major role in tumorigenesis. Here we focus on LIN28B, which binds mRNAs directly and is a master regulator of the let-7 family of tumor suppressor microRNAs, as we previously showed that high LIN28B expression is associated with advanced stage disease and worse patient outcome.

Methods: To discover LIN28B-associated pathways in neuroblastoma, we performed gene set enrichment analysis (GSEA) on mRNA expression datasets and analyzed SNP-array based DNA copy number datasets. We used siRNAs, shRNAs, and microRNA mimetics to perturb transcripts of interest in neuroblastoma cells and measured effects on downstream signaling, protein-protein interactions, and proliferation.

Results: We applied GSEA to mRNA expression profiles from 250 neuroblastoma tumors and found LIN28B expression to be robustly correlated with several biologically relevant gene sets, including “RAN signaling.” We focused on RAN signaling as RAN is a member of the Ras family of GTPases implicated in the pathogenesis of several malignancies and we demonstrated a strong positive correlation between LIN28B and RAN expression, most strikingly in the MYCN-amplified context (p = 2.2×10−10). We next analyzed 374 high-risk neuroblastoma tumors and found that 28% of them displayed recurrent somatic copy number gain of chromosome 12q24, the genomic location of RAN, which was associated with increased RAN expression (p = 0.0004) and was inversely related to MYCN amplification (p = 0.0021). Increased RAN expression was associated with stage 4 disease (p = 0.0047) and decreased overall survival (p = 0.0002). To further dissect the LIN28B-RAN relationship, we depleted LIN28B using shRNAs, showing that it reduced RAN RNA and protein levels. LIN28B directly bound RAN mRNA, likely enhancing its translation. As RAN promotes the phosphorylation and activation of Aurora kinase A (AURKA), we then demonstrated that LIN28B leads to AURKA activation via RAN. Moreover, we demonstrated that AURKA is a direct let-7 target, defining a separate mechanism by which LIN28B/let-7 influences AURKA expression. Finally, we showed that RAN depletion resulted in decreased neuroblastoma proliferation, phenocopying LIN28B depletion.

Conclusions: These results demonstrate that enhanced LIN28B expression and chromosome 12q24 gain each independently promote RAN expression and that LIN28B and RAN signaling further converge on AURKA. Collectively, our studies support LIN28B as a master regulator of multiple oncogenes implicated in neuroblastoma pathogenesis, nominating it as a candidate for therapeutic targeting.

Citation Format: Robert W. Schnepp, Priya Khurana, Edward F. Attiyeh, Sara Chodosh, Pichai Raman, Derek A. Oldridge, Maria E. Gagliardi, Karina Conkrite, Shahab Asgharzadeh, Robert C. Seeger, Blair Madison, Anil Rustgi, John M. Maris, Sharon J. Diskin. A LIN28B/RAN/AURKA signaling network promotes neuroblastoma tumorigenesis. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4734. doi:10.1158/1538-7445.AM2015-4734

Rare variants in TP53 and susceptibility to neuroblastoma

TP53 is the most frequently mutated gene in human malignancies; however, de novo somatic mutations in childhood embryonal cancers such as neuroblastoma are rare. We report on the analysis of three independent case-control cohorts comprising 10290 individuals and demonstrate that rs78378222 and rs35850753, rare germline variants in linkage disequilibrium that map to the 3' untranslated region (UTR) of TP53 and 5' UTR of the Δ133 isoform of TP53, respectively, are robustly associated with neuroblastoma (rs35850753: odds ratio [OR] = 2.7, 95% confidence interval [CI] = 2.0 to 3.6, P combined = 3.43×10(-12); rs78378222: OR = 2.3, 95% CI = 1.8 to 2.9, P combined = 2.03×10(-11)). All statistical tests were two-sided. These findings add neuroblastoma to the complex repertoire of human cancers influenced by the rs78378222 hypomorphic allele, which impairs proper termination and polyadenylation of TP53 transcripts. Future studies using whole-genome sequencing data are likely to reveal additional rare variants with large effect sizes contributing to neuroblastoma tumorigenesis.

PTEN is a potent suppressor of small cell lung cancer

Small cell lung carcinoma (SCLC) is a highly metastatic tumor type with neuroendocrine features and a dismal prognosis. PTEN mutations and PIK3CA activating mutations have been reported in SCLC but the functional relevance of this pathway is unknown. The PTEN/PIK3CA pathway was interrogated using an AdenoCre-driven mouse model of SCLC harboring inactivated Rb and p53. Inactivation of one allele of PTEN in Rb/p53-deleted mice led to accelerated SCLC with frequent metastasis to the liver. In contrast with the high mutation burden reported in human SCLC, exome analyses revealed a low number of protein-altering mutations in mouse SCLC. Inactivation of both alleles of PTEN in the Rb/p53-deleted system led to nonmetastatic adenocarcinoma with neuroendocrine differentiation. This study reveals a critical role for the PTEN/PI3K pathway in both SCLC and lung adenocarcinoma and provides an ideal system to test the phosphoinositide 3-kinase (PI3K) pathway inhibitors as targeted therapy for subsets of patients with SCLC.

IMPLICATIONS

The ability of PTEN inactivation to accelerate SCLC in a genetic mouse model suggests that targeting the PTEN pathway is a therapeutic option for a subset of human patients with SCLC. VISUAL OVERVIEW: http://mcr.aacrjournals.org/content/early/2014/04/28/1541-7786.MCR-13-0554/F1.large.jpg.

Cooperation between Rb and Arf in suppressing mouse retinoblastoma

Retinoblastoma is a pediatric cancer that has served as a paradigm for tumor suppressor gene function. Retinoblastoma is initiated by RB gene mutations, but the subsequent cooperating mutational events leading to tumorigenesis are poorly characterized. We investigated what these additional genomic alterations might be using human retinoblastoma samples and mouse models. Array-based comparative genomic hybridization studies revealed deletions in the CDKN2A locus that include ARF and P16INK4A, both of which encode tumor suppressor proteins, in both human and mouse retinoblastoma. Through mouse genetic analyses, we found that Arf was the critical tumor suppressor gene in the deleted region. In mice, inactivation of one allele of Arf cooperated with Rb and p107 loss to rapidly accelerate retinoblastoma, with frequent loss of heterozygosity (LOH) at the Arf locus. Arf has been reported to exhibit p53-independent tumor suppressor roles in other systems; however, our results showed no additive effect of p53 and Arf coinactivation in promoting retinoblastoma. Moreover, p53 inactivation completely eliminated any selection for Arf LOH. Thus, our data reveal important insights into the p53 pathway in retinoblastoma and show that Arf is a key collaborator with Rb in retinoblastoma suppression.

miR-17~92 cooperates with RB pathway mutations to promote retinoblastoma

The miR-17~92 cluster is a potent microRNA-encoding oncogene. Here, we show that miR-17~92 synergizes with loss of Rb family members to promote retinoblastoma. We observed miR-17~92 genomic amplifications in murine retinoblastoma and high expression of miR-17~92 in human retinoblastoma. While miR-17~92 was dispensable for mouse retinal development, miR-17~92 overexpression, together with deletion of Rb and p107, led to rapid emergence of retinoblastoma with frequent metastasis to the brain. miR-17~92 oncogenic function in retinoblastoma was not mediated by a miR-19/PTEN axis toward apoptosis suppression, as found in lymphoma/leukemia models. Instead, miR-17~92 increased the proliferative capacity of Rb/p107-deficient retinal cells. We found that deletion of Rb family members led to compensatory up-regulation of the cyclin-dependent kinase inhibitor p21Cip1. miR-17~92 overexpression counteracted p21Cip1 up-regulation, promoted proliferation, and drove retinoblastoma formation. These results demonstrate that the oncogenic determinants of miR-17~92 are context-specific and provide new insights into miR-17~92 function as an RB-collaborating gene in cancer.

Murine bilateral retinoblastoma exhibiting rapid-onset, metastatic progression and N-myc gene amplification

Human retinoblastoma is a pediatric cancer initiated by RB gene mutations in the developing retina. We have examined the origins and progression of retinoblastoma in mouse models of the disease. Retina-specific inactivation of Rb on a p130-/- genetic background led to bilateral retinoblastoma with rapid kinetics, whereas on a p107-/- background Rb mutation caused predominantly unilateral tumors that arose with delayed kinetics and incomplete penetrance. In both models, retinoblastomas arose from cells at the extreme periphery of the murine retina. Furthermore, late retinoblastomas progressed to invade the brain and metastasized to the cervical lymph nodes. Metastatic tumors lacking Rb and p130 exhibited chromosomal changes revealed by representational oligonucleotide microarray analysis including high-level amplification of the N-myc oncogene. N-myc was found amplified in three of 16 metastatic retinoblastomas lacking Rb and p130 as well as in retinoblastomas lacking Rb and p107. N-myc amplification ranged from 6- to 400-fold and correlated with high N-myc-expression levels. These murine models closely resemble human retinoblastoma in their progression and secondary genetic changes, making them ideal tools for further dissection of steps to tumorigenesis and for testing novel therapies.

Study of transaldolase deficiency in urine samples by capillary LC-MS/MS

Transaldolase (TAL) is a key enzyme of the pentose phosphate pathway (PPP). TAL deficiency is a newly recognized cause of liver cirrhosis. We have developed an ion-pair LC separation combined with negative ion electrospray MS/MS detection method to assess PPP metabolites in urine samples from TAL-deficient mice. Sedoheptulose 7-phosphate (S7P), C5-polyols D-arabitol and D-ribitol, and 6-phosphogluconate (6PG) levels were markedly increased in urine of TAL-deficient mice with respect to those of wild-type and heterozygote littermates. The detection limits of S7P, D-arabitol, and 6PG were 0.15 +/- 0.015 pmol, 3.5 +/- 0.41 pmol, and 0.61 +/- 0.055 pmol, respectively. The limit of quantitation was 0.4 +/- 0.024 nmol/ml for S7P, 1.6 +/- 0.11 nmol/ml for 6PG and 10 +/- 0.7 nmol/ml for D-arabitol. Additional metabolites, hexose 6-phosphates (m/z 259), D-ribose 5-phosphate and D-xylulose 5-phosphate (m/z 229), D-fructose 1,6-diphosphate (m/z 339), C6-polyols (m/z 181) and GSSG (m/z 611), that have been positively identified in mouse urine, showed similar levels in control and TAL-deficient mice.