Germline pathogenic variants in neuroblastoma patients are enriched in BARD1 and predict worse survival

BACKGROUND

Neuroblastoma is an embryonal cancer of the developing sympathetic nervous system. The genetic contribution of rare pathogenic or likely pathogenic germline variants in patients without a family history remains unclear.

METHODS

Germline DNA sequencing was performed on 786 neuroblastoma patients. The frequency of rare cancer predisposition gene pathogenic or likely pathogenic variants in patients was compared with 2 cancer-free control cohorts. Matched tumor DNA sequencing was evaluated for second hits, and germline DNA array data from 5585 neuroblastoma patients and 23 505 cancer-free control children were analyzed to identify rare germline copy number variants. Patients with germline pathogenic or likely pathogenic variants were compared with those without to test for association with clinical characteristics, tumor features, and survival.

RESULTS

We observed 116 pathogenic or likely pathogenic variants involving 13.9% (109 of 786) of neuroblastoma patients, representing a statistically significant excess burden compared with cancer-free participants (odds ratio [OR] = 1.60, 95% confidence interval [CI] = 1.27 to 2.00). BARD1 harbored the most statistically significant enrichment of pathogenic or likely pathogenic variants (OR = 32.30, 95% CI = 6.44 to 310.35). Rare germline copy number variants disrupting BARD1 were identified in patients but absent in cancer-free participants (OR = 29.47, 95% CI = 1.52 to 570.70). Patients harboring a germline pathogenic or likely pathogenic variant had a worse overall survival compared with those without (P = 8.6 x 10-3).

CONCLUSIONS

BARD1 is an important neuroblastoma predisposition gene harboring both common and rare germline pathogenic or likely pathogenic variations. The presence of any germline pathogenic or likely pathogenic variant in a cancer predisposition gene was independently predictive of worse overall survival. As centers move toward paired tumor-normal sequencing at diagnosis, efforts should be made to centralize data and provide an infrastructure to support cooperative longitudinal prospective studies of germline pathogenic variation.

A proteogenomic surfaceome study identifies DLK1 as an immunotherapeutic target in neuroblastoma

Cancer immunotherapies have produced remarkable results in B-cell malignancies; however, optimal cell surface targets for many solid cancers remain elusive. Here, we present an integrative proteomic, transcriptomic, and epigenomic analysis of tumor specimens along with normal tissues to identify biologically relevant cell surface proteins that can serve as immunotherapeutic targets for neuroblastoma, an often-fatal childhood cancer of the developing nervous system. We apply this approach to human-derived cell lines (N=9) and cell/patient-derived xenograft (N=12) models of neuroblastoma. Plasma membrane-enriched mass spectrometry identified 1,461 cell surface proteins in cell lines and 1,401 in xenograft models, respectively. Additional proteogenomic analyses revealed 60 high-confidence candidate immunotherapeutic targets and we prioritized Delta-like canonical notch ligand 1 (DLK1) for further study. High expression of DLK1 directly correlated with the presence of a super-enhancer spanning the DLK1 locus. Robust cell surface expression of DLK1 was validated by immunofluorescence, flow cytometry, and immunohistochemistry. Short hairpin RNA mediated silencing of DLK1 in neuroblastoma cells resulted in increased cellular differentiation. ADCT-701, a DLK1-targeting antibody-drug conjugate (ADC), showed potent and specific cytotoxicity in DLK1-expressing neuroblastoma xenograft models. Moreover, DLK1 is highly expressed in several adult cancer types, including adrenocortical carcinoma (ACC), pheochromocytoma/paraganglioma (PCPG), hepatoblastoma, and small cell lung cancer (SCLC), suggesting potential clinical benefit beyond neuroblastoma. Taken together, our study demonstrates the utility of comprehensive cancer surfaceome characterization and credentials DLK1 as an immunotherapeutic target.

Highlights

Plasma membrane enriched proteomics defines surfaceome of neuroblastomaMulti-omic data integration prioritizes DLK1 as a candidate immunotherapeutic target in neuroblastoma and other cancersDLK1 expression is driven by a super-enhancer DLK1 silencing in neuroblastoma cells results in cellular differentiation ADCT-701, a DLK1-targeting antibody-drug conjugate, shows potent and specific cytotoxicity in DLK1-expressing neuroblastoma preclinical models.

Integrative Genomic Analyses Identify LncRNA Regulatory Networks across Pediatric Leukemias and Solid Tumors

Long noncoding RNAs (lncRNA) play an important role in gene regulation and contribute to tumorigenesis. While pan-cancer studies of lncRNA expression have been performed for adult malignancies, the lncRNA landscape across pediatric cancers remains largely uncharted. Here, we curated RNA sequencing data for 1,044 pediatric leukemia and extracranial solid tumors and integrated paired tumor whole genome sequencing and epigenetic data in relevant cell line models to explore lncRNA expression, regulation, and association with cancer. A total of 2,657 lncRNAs were robustly expressed across six pediatric cancers, including 1,142 exhibiting histotype-elevated expression. DNA copy number alterations contributed to lncRNA dysregulation at a proportion comparable to protein coding genes. Application of a multidimensional framework to identify and prioritize lncRNAs impacting gene networks revealed that lncRNAs dysregulated in pediatric cancer are associated with proliferation, metabolism, and DNA damage hallmarks. Analysis of upstream regulation via cell type-specific transcription factors further implicated distinct histotype-elevated and developmental lncRNAs. Integration of these analyses prioritized lncRNAs for experimental validation, and silencing of TBX2-AS1, the top-prioritized neuroblastoma-specific lncRNA, resulted in significant growth inhibition of neuroblastoma cells, confirming the computational predictions. Taken together, these data provide a comprehensive characterization of lncRNA regulation and function in pediatric cancers and pave the way for future mechanistic studies.

SIGNIFICANCE

Comprehensive characterization of lncRNAs in pediatric cancer leads to the identification of highly expressed lncRNAs across childhood cancers, annotation of lncRNAs showing histotype-specific elevated expression, and prediction of lncRNA gene regulatory networks.

Germline pathogenic variants in 786 neuroblastoma patients

Importance

Neuroblastoma accounts for 12% of childhood cancer deaths. The genetic contribution of rare pathogenic germline variation in patients without a family history remains unclear.

Objective

To define the prevalence, spectrum, and clinical significance of pathogenic germline variation in cancer predisposition genes (CPGs) in neuroblastoma patients.

Design Setting and Participants

Germline DNA sequencing was performed on the peripheral blood from 786 neuroblastoma patients unselected for family history. Rare variants mapping to CPGs were evaluated for pathogenicity and the percentage of cases harboring pathogenic (P) or likely pathogenic (LP) variants was quantified. The frequency of CPG P-LP variants in neuroblastoma cases was compared to two distinct cancer-free control cohorts to assess enrichment. Matched tumor DNA sequencing was evaluated for "second hits" at CPGs and germline DNA array data from 5,585 neuroblastoma cases and 23,505 cancer-free control children was analyzed to identify rare germline copy number variants (CNVs) affecting genes with an excess burden of P-LP variants in neuroblastoma. Neuroblastoma patients with germline P-LP variants were compared to those without P-LP variants to test for association with clinical characteristics, tumor features, and patient survival.

Main Outcomes and Measures

Rare variant prevalence, pathogenicity, enrichment, and association with clinical characteristics, tumor features, and patient survival.

Results

We observed 116 P-LP variants in CPGs involving 13.9% (109/786) of patients, representing a significant excess burden of P-LP variants compared to controls (9.1%; P = 5.14 × 10-5, Odds Ratio: 1.60, 95% confidence interval: 1.27-2.00). BARD1 harbored the most significant burden of P-LP variants compared to controls (1.0% vs. 0.03%; P = 8.18 × 10-7; Odds Ratio: 32.30, 95% confidence interval: 6.44-310.35). Rare germline CNVs disrupting BARD1 were also identified in neuroblastoma patients (0.05%) but absent in controls (P = 7.08 × 10-3; Odds Ratio: 29.47, 95% confidence interval: 1.52 - 570.70). Overall, P-LP variants in DNA repair genes in this study were enriched in cases compared to controls (8.1% vs. 5.7%; P = 0.01; Odds Ratio: 1.45, 95% confidence interval: 1.08-1.92). Neuroblastoma patients harboring a germline P-LP variant had a worse overall survival when compared to patients without P-LP variants (P = 8.6 × 10-3), and this remained significant in a multivariate Cox proportional-hazards model (P = 0.01).

Conclusions and Relevance

Neuroblastoma patients harboring germline P-LP variants in CPGs have worse overall survival and BARD1 is an important predisposition gene affected by both common and rare pathogenic variation. Germline sequencing should be performed for all neuroblastoma patients at diagnosis to inform genetic counseling and support future longitudinal and mechanistic studies. Patients with a germline P-LP variant should be closely monitored, regardless of risk group assignment.

Abstract A009: Proteogenomic prioritization of immunotherapeutic targets in rhabdomyosarcoma nominate MEGF10 for preclinical development

Background: Rhabdomyosarcoma (RMS) has a high unmet need in terms of precision therapy development as there are currently no approved immunotherapies or targeted therapies, and few in the developmental pipeline. Here we sought to identify cell surface oncoproteins as a target for novel RMS-directed immunotherapies. Methods: We first performed plasma membrane enrichment followed by mass spectrometry to define the cell surface landscape of 7 fusion(+) and 14 fusion(-) RMS patient-derived xenograft (PDX) models. The surfaceome data was filtered to only “high confidence” surface proteins by querying protein localization databases, Compartments (https://compartments.jensenlab.org/) and CIRFESS (https://gundrylab.shinyapps.io/cirfess/). We then developed a prioritization algorithm that uses a rank-product approach to score surface proteins. The input to the algorithm is a matrix that integrates multiple datasets to score the surface proteins based on their suitability to be an optimal immunotherapeutic target. In addition to the surfaceome data generated here, we also integrated matched RNA-sequencing data from eleven of the RMS PDX models, RNA-sequencing data from GTEx (n=15,253) and a recently developed normal tissue proteomics dataset (n=201) [Jiang. Cell. 2020], a list from Gene Ontology that included genes involved in muscle development pathways, and the gene dependency list for RMS in DepMap (https://depmap.org/portal/). Results: A total of 913 and 937 high confidence surface proteins were annotated from the mass spectrometry data for fusion(+) and fusion(−) samples, respectively. A dendrogram separated the surface protein profiles into two clusters based on fusion(+) and fusion(−) RMS subtypes, thus the algorithm was run separately on each subtype. Within the top 50% of prioritized targets, 88% and 86% of the targets overlapped and 12% and 14% were identified exclusively in fusion(+) and fusion(−) subtypes, respectively. ALK, a previously putative protein marker in fusion(+) RMS, scored in the top 10% of the fusion(+) targets based on the algorithm, and surprisingly we saw abundant ALK expression in 6/14 fusion(−) PDX samples. MEGF10, a novel target, was ranked as the top target for both fusion(+) and fusion(−) RMS. MEGF10 plays a role in cell adhesion, motility, and proliferation. It scored as a significant dependency in DepMap for RMS (p-value=0.0002). Based on RNA-sequencing and proteomics, MEGF10 shows no expression in most healthy tissues surveyed, with several orders of magnitude lower expression detected in RNASeq in muscle and brain tissue, but not in the proteomic datasets. Conclusion: Here, we defined the surfaceome of RMS, and found substantial overlap in surface proteins between fusion(+) and fusion(−) RMS subtypes. We validated previous observations that ALK is expressed in RMS, here verifying that the protein is expressed on the plasma membrane. MEGF10 appears to be a strong novel candidate target for RMS immunotherapies, and ongoing work to validate our proteogenomic findings will be reported.

Citation Format: Rawan Shraim, Amber K. Weiner, Karina L. Conkrite, Alexander B. Radaoui, John M. Maris, Yael P. Mosse, Sharon J. Diskin, Ahmet Sacan, Benjamin A. Garcia, Peter J. Houghton, Raushan T. Kurmasheva, Poul Sorensen, Gregg B. Morin, Brian Mooney. Proteogenomic prioritization of immunotherapeutic targets in rhabdomyosarcoma nominate MEGF10 for preclinical development [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr A009.

Abstract 2725: Molecular mechanisms of aberrant splicing in pediatric high grade gliomas

Pediatric brain cancer is the number one cause of disease-related death in children. While much of the somatic mutation variation in these tumors have been profiled, there have been few studies exploring their transcriptional splicing programs. Here, we characterize aberrant alternative splicing across pediatric brain tumors. We identified three splicing-based clusters that spanned across seven broad histological tumor classifications. Patients in clusters 1 and 2 had significantly lower overall survival (p < 0.001) than those in cluster 3. High-grade gliomas (HGGs) displayed the greatest splicing heterogeneity, spanning all three clusters. We focused on midline HGGs (n = 84), identifying 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. We also identified several splicing factor genes, including SRSF11, that were differentially expressed (p < 0.05), suggesting a potential tumor-specific novel mechanism of splicing dysregulation. Strikingly, 27% (5,157) of these splicing events resulted in either a gain or loss of a functional site in 3,294 genes: disulfide bonding (n = 391), localization signaling (n = 216), modifications, such as phosphorylation sites (n = 1,670), and other, such as ion-binding sites (n = 4,245). We prioritized splice variants affecting targetable kinases and found that mRNAs encoding CDC-like kinase 1 (CLK1), a known modulator of the SR family of master splicing regulators, exhibit significantly increased exon 4 inclusion. This leads to a gain of two known phosphorylation sites in CLK1, increased protein expression, and hyper-phosphorylation of SR proteins, inducing cooperative binding of SR proteins to RNA. To assess the impact of this CLK1 event, we compared splicing in tumors with high exon 4 inclusion (n = 5) to those with low exon 4 inclusion (n = 5) and discovered 862 differential splicing events (DSE). Samples with high CLK1 exon 4 inclusion had significantly lower percent spliced in events, suggesting that increased activity of CLK1 resulting from the gain of the exon 4 promotes overall exon skipping. Additionally, more than 80% of the DSE (n = 695), including those in known brain tumor oncogenes such as CDC27 and E2H2, were recurrently mis-spliced in midline HGG tumors, suggesting that CLK1 splicing dysregulation leads to a global aberrant splicing phenotype in HGGs. Finally, we determined a subset of events significantly associated with prolonged survival, suggesting that stratification of patients based on splicing phenotypes can be utilized as a prognostic indicator. In summary, we demonstrate aberrant splicing in pediatric HGGs as an alternative mechanism driving tumorigenesis and future work will focus on urgently needed therapeutic targeting of these pathways toward our overall goal of improving survival outcomes in children with brain tumors.

Citation Format: Ammar S. Naqvi, Brian Ennis, Run Jin, Karina L. Conkrite, Komal S. Rathi, Adam A. Kraya, Poonam Sonawane, Phillip B. Storm, Adam C. Resnick, Jo Lynne Rokita. Molecular mechanisms of aberrant splicing in pediatric high grade gliomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2725.

Abstract 3028: Integrative genomics reveals lncRNAs associated with pediatric cancer

Background: Long non-coding RNAs (lncRNAs) have emerged as key components of transcriptional and post-transcriptional gene regulation. Dysregulation of lncRNA expression has been widely observed in cancer and several lncRNAs are known to influence tumor initiation and progression. Despite this, the lncRNA landscape and regulatory networks across pediatric cancers remain relatively uncharted.

Methods: To characterize the lncRNA landscape of pediatric cancers, we first curated RNA sequencing data for 1,044 pediatric leukemia and solid tumors from the Therapeutically Applicable Research To Generate Effective Treatments (TARGET) project to identify known and novel expressed lncRNAs. This data set included: 280 acute myeloid leukemia (AML), 190 acute B-cell leukemia (B-ALL), 244 acute T-cell leukemia (T-ALL), 121 Wilm's tumor (WT), 48 rhabdoid tumors (RT), and 161 neuroblastoma (NBL). Histotype-specific expression was assessed using the tau score. Whole genome sequencing (WGS) from 826 matched normal-tumor pairs was integrated to identify somatic copy number alterations (SCNAs) disrupting lncRNA expression. To further implicate cancer-relevant drivers of lncRNA expression, we used a unique combination of epigenetic data in pediatric cell lines, including ChIP-sequencing for cancer-specific transcription factors and genome-scale chromatin capture data. A global analysis of lncRNA function was performed using the lncMod method, in which expression data is modelled to identify lncRNA modulators that perturb transcription factor regulation of target genes. Functional prioritization of lncRNAs was obtained through integration of analyses per cancer. Biochemical assays in human-derived cell line models were utilized to validate the function of the top prioritized lncRNA in NBL.

Results: We report a total of 2,657 robustly expressed lncRNAs across six pediatric cancers, including 1,142 lncRNAs exhibiting histotype-specific expression. SCNAs contributed to lncRNA dysregulation at a proportion comparable to protein coding genes. There were 207 (28%) lncRNAs in regions with SCNA that had significant expression dysregulation. LncMod analysis across the cancers revealed context-specific transcriptional gene networks per dysregulated lncRNA and enrichment for proliferation, metabolic, and DNA damage hallmarks. We further identified 547 cancer-associated lncRNAs in NBL based on upstream regulation via oncogenic transcription factors. The top-prioritized lncRNA, TBX2-AS1, was predicted to impact proliferation in NBL. Silencing of TBX2-AS1 using siRNAs achieved >90% knockdown in NBL cells and resulted in 46.6% decreased cell growth (p = 8.1 x 10-4).

Conclusion: This study defines the lncRNA landscape across six pediatric cancers and provides a detailed catalog of how lncRNAs impact regulatory gene networks. These data serve as a robust resource for future hypothesis-driven mechanistic studies.

Citation Format: Apexa Modi, Gonzalo Lopez, Karina L. Conkrite, Tsz Ching Leung, Sathvik Ramanan, Daphne Cheung, Chun Su, Matthew E. Johnson, Elisabetta Manduchi, Samantha Gadd, Jinghui Zhang, Malcolm A. Smith, Jaime M. Guidry Auvil, Daniela S. Gerhard, Soheil Meshinchi, Elizabeth J. Perlman, Stephen P. Hunger, John M. Maris, Andrew D. Wells, Struan F. Grant, Sharon J. Diskin. Integrative genomics reveals lncRNAs associated with pediatric cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 3028.

Somatic structural variation targets neurodevelopmental genes and identifies SHANK2 as a tumor suppressor in neuroblastoma

Neuroblastoma is a malignancy of the developing sympathetic nervous system that accounts for 12% of childhood cancer deaths. Like many childhood cancers, neuroblastoma shows a relative paucity of somatic single-nucleotide variants (SNVs) and small insertions and deletions (indels) compared to adult cancers. Here, we assessed the contribution of somatic structural variation (SV) in neuroblastoma using a combination of whole-genome sequencing (WGS) of tumor-normal pairs (n = 135) and single-nucleotide polymorphism (SNP) genotyping of primary tumors (n = 914). Our study design allowed for orthogonal validation and replication across platforms. SV frequency, type, and localization varied significantly among high-risk tumors. MYCN nonamplified high-risk tumors harbored an increased SV burden overall, including a significant excess of tandem duplication events across the genome. Genes disrupted by SV breakpoints were enriched in neuronal lineages and associated with phenotypes such as autism spectrum disorder (ASD). The postsynaptic adapter protein-coding gene, SHANK2, located on Chromosome 11q13, was disrupted by SVs in 14% of MYCN nonamplified high-risk tumors based on WGS and 10% in the SNP array cohort. Expression of SHANK2 was low across human-derived neuroblastoma cell lines and high-risk neuroblastoma tumors. Forced expression of SHANK2 in neuroblastoma cells resulted in significant growth inhibition (P = 2.6 × 10-2 to 3.4 × 10-5) and accelerated neuronal differentiation following treatment with all-trans retinoic acid (P = 3.1 × 10-13 to 2.4 × 10-30). These data further define the complex landscape of somatic structural variation in neuroblastoma and suggest that events leading to deregulation of neurodevelopmental processes, such as inactivation of SHANK2, are key mediators of tumorigenesis in this childhood cancer.

Telomere Maintenance Mechanisms Define Clinical Outcome in High-Risk Neuroblastoma

Neuroblastoma is a childhood cancer with heterogeneous clinical outcomes. To comprehensively assess the impact of telomere maintenance mechanism (TMM) on clinical outcomes in high-risk neuroblastoma, we integrated the C-circle assay [a marker for alternative lengthening of telomeres (ALT)], TERT mRNA expression by RNA-sequencing, whole-genome/exome sequencing, and clinical covariates in 134 neuroblastoma patient samples at diagnosis. In addition, we assessed TMM in neuroblastoma cell lines (n = 104) and patient-derived xenografts (n = 28). ALT was identified in 23.4% of high-risk neuroblastoma tumors and genomic alterations in ATRX were detected in 60% of ALT tumors; 40% of ALT tumors lacked genomic alterations in known ALT-associated genes. Patients with high-risk neuroblastoma were classified into three subgroups (TERT-high, ALT+, and TERT-low/non-ALT) based on presence of C-circles and TERT mRNA expression (above or below median TERT expression). Event-free survival was similar among TERT-high, ALT+, or TERT-low/non-ALT patients. However, overall survival (OS) for TERT-low/non-ALT patients was significantly higher relative to TERT-high or ALT patients (log-rank test; P < 0.01) independent of current clinical and molecular prognostic markers. Consistent with the observed higher OS in patients with TERT-low/non-ALT tumors, continuous shortening of telomeres and decreasing viability occurred in low TERT-expressing, non-ALT patient-derived high-risk neuroblastoma cell lines. These findings demonstrate that assaying TMM with TERT mRNA expression and C-circles provides precise stratification of high-risk neuroblastoma into three subgroups with substantially different OS: a previously undescribed TERT-low/non-ALT cohort with superior OS (even after relapse) and two cohorts of patients with poor survival that have distinct molecular therapeutic targets. SIGNIFICANCE: These findings assess telomere maintenance mechanisms with TERT mRNA and the ALT DNA biomarker C-circles to stratify neuroblastoma into three groups, with distinct overall survival independent of currently used clinical risk classifiers.

Epigenomic profiling of neuroblastoma cell lines

Understanding the aberrant transcriptional landscape of neuroblastoma is necessary to provide insight to the underlying influences of the initiation, progression and persistence of this developmental cancer. Here, we present chromatin immunoprecipitation sequencing (ChIP-Seq) data for the oncogenic transcription factors, MYCN and MYC, as well as regulatory histone marks H3K4me1, H3K4me3, H3K27Ac, and H3K27me3 in ten commonly used human neuroblastoma-derived cell line models. In addition, for all of the profiled cell lines we provide ATAC-Seq as a measure of open chromatin. We validate specificity of global MYCN occupancy in MYCN amplified cell lines and functional redundancy of MYC occupancy in MYCN non-amplified cell lines. Finally, we show with H3K27Ac ChIP-Seq that these cell lines retain expression of key neuroblastoma super-enhancers (SE). We anticipate this dataset, coupled with available transcriptomic profiling on the same cell lines, will enable the discovery of novel gene regulatory mechanisms in neuroblastoma.

Abstract LB-B04: A multi-omic surfaceome study identifies DLK1 as an epigenetically regulated protein and immunotherapeutic target in neuroblastoma

Background: Neuroblastoma (NB) is an embryonal tumor of the sympathetic nervous system that accounts for 12% of childhood cancer deaths. While the introduction of GD2 immunotherapy provides an improvement in time to progression, the therapy is toxic and impact on overall survival is minimal, supporting an urgent need for novel immunotherapies. To date, the cell surface landscape (surfaceome) of NB remains undefined, hindering the identification of immunotherapeutic targets. Methods: To identify NB surfaceome proteins, we performed plasma membrane protein extraction using sucrose gradient ultracentrifugation coupled to mass spectrometry (nLC-MS/MS) in NB cell lines (n=12) and patient derived xenografts (PDX; n=10). These data were integrated with existing RNA-sequencing (NB=153; Normal=7859) and H3K27ac chromatin immunoprecipitation (ChIP)-sequencing data (from overlapping NB cell lines) to evaluate extracellular proteins differentially expressed in NB compared to normal tissues. Candidate targets were validated by immunohistochemistry on NB tumor and normal tissue microarrays (TMAs), flow cytometry and immunofluorescence. In-vitro functional studies were performed following genetic manipulation of candidate targets to assess cell proliferation, differentiation and viability. Finally, we tested ADCT-701 (a DLK1-directed antibody drug conjugate [ADC] with a pyrrolobenzodiazepine [PBD] warhead) in eight PDX models (study ongoing, total of 12 models initiated) with varying levels of DLK1 expression. At enrollment, two mice were each treated with a single dose of saline or 1mg/kg of B12-PL1601 (non-targeting PBD-conjugated ADC) or 1mg/kg ADCT-701 and mice were evaluated for 100 days or until tumor reached 2.0cm3. Results: We yielded on average 66% (range:60-68%) membrane protein enrichment with high reproducibility between biological replicates (80%; range:78-84%) and identified 4826 unique membrane proteins. Our approach confirmed known cell surface proteins in development as immunotherapeutic targets in NB (ALK, GPC2, NCAM1, DLL3 and CD276). Here, we prioritized DLK1 for further evaluation due to it being the only candidate with expression directly associated with a super enhancer element (P=6.09X10-5). RNA-sequencing and tissue microarray analysis of NB and normal tissues showed DLK1 to be overexpressed in a large subset of high-risk NB with minimal expression in normal tissues, excepting adrenal medulla and pituitary. Flow cytometry and immunofluorescence confirmed cell surface expression of DLK1 in a panel of NB cell lines. Genetic depletion of DLK1 using shRNA resulted in neurite outgrowth (P=7.26X10-5) and terminal differentiation. Full proteome analysis of DLK1 knockdown and control cell lines using MS showed regulation of proteins that control outgrowth of neurites (P=3.37X10-3) and development of neurons (P=3.76X10-3). To date, ADCT-701 treatment resulted in maintained complete response (N=2), complete response (N=3) and stable disease (N=1) in models with high DLK1 expression, while those with low/no expression showed disease progression (N=2). Conclusion: DLK1 is an epigenetically regulated immunotherapeutic target in neuroblastoma. ADCT-701 shows potent activity in preclinical models of NB and should be prioritized for clinical development.

Citation Format: Amber K. Weiner, Alexander B. Radaoui, Matthew Tsang, Dan Martinez, Simone Sidoli, Karina L. Conkrite, Alberto Delaidelli, Jo Lynne Rokita, Maria V. Lane, Zalman Vaksman, Komal S. Rathi, Pichai Raman, Jennifer Pogoriler, Tricia Bhatti, Bruce Pawel, Beverly Teicher, Stephen W. Erickson, Poul Sorensen, Yael P. Mosse, Kateryna Krytska, Francesca Zammarchi, Patrick H. van Berkel, Malcolm A. Smith, Benjamin A. Garcia, John M. Maris, Sharon J. Diskin. A multi-omic surfaceome study identifies DLK1 as an epigenetically regulated protein and immunotherapeutic target in neuroblastoma [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr LB-B04. doi:10.1158/1535-7163.TARG-19-LB-B04

Abstract 3650: Integrative mass spectrometry and RNA-sequencing identifies DLK1 as a candidate immunotherapeutic target in neuroblastoma

BACKGROUND. Neuroblastoma (NB) is an embryonal tumor of the sympathetic nervous system that accounts for 12% of childhood cancer deaths. Despite multimodal therapy, survival probability for high-risk NB patients remains below 50% and relapsed NB is largely incurable. To date, the cell surface landscape (surfaceome) of NB remains poorly defined. An unbiased survey of these proteins will facilitate the identification of candidate immunotherapeutic targets for preclinical validation.

METHODS. To identify proteins on the cell surface of NB cells, we performed plasma membrane protein extraction utilizing a sucrose density gradient methodology followed by nano-liquid chromatography coupled to mass spectrometry (nLC-MS/MS) in NB cell lines (n=12) and patient derived xenografts (PDX; n=10). We next integrated MS data with RNA-sequencing (NB=153; Normal=7859) data to evaluate proteins with an annotated extracellular domain differentially expressed in NB compared to normal tissues. Candidate immunotherapeutic targets were validated by immunohistochemistry on NB tumor and normal tissue microarray (TMA) and in-vitrofunctional studies were performed following genetic manipulation of candidate targets to assess cell proliferation, differentiation and viability.

RESULTS. We yielded on average 66% (range:60-68%) membrane protein enrichment with high reproducibility between biological replicates (80%; range:78-84%) and identified 4826 unique membrane proteins. Our approach confirmed known cell surface proteins in development as immunotherapeutic targets in NB (ALK, GPC2, NCAM1, DLL3 and CD276). We prioritized DLK1 for further evaluation due to it being the only candidate with expression directly associated with a super enhancer element (P=6.09X10-5). Genetic depletion of DLK1 resulted in neurite outgrowth suggesting induction of terminal differentiation (P=7.26X10-5). Full proteome analysis of DLK1 knockdown and control using MS showed regulation of proteins that promote outgrowth of neurites (P=3.37X10-3) and development of neurons (P=3.76X10-3).

CONCLUSION. We have developed the first MS-based surfaceome of NB. DLK1 is an epigenetically regulated oncoprotein in a large subset of high-risk NBs. We are currently developing antibody drug conjugate therapeutics designed for NBs with proven overexpression of DLK1.

Citation Format: Amber K. Weiner, Alexander B. Radaoui, Nathan M. Kendsersky, Jo Lynne Harenza-Rokita, Simone Sidoli, Karina L. Conkrite, Zalman Vaksman, Komal Rathi, Pichai Raman, Daniel Martinez, Tricia Bhatti, Matthew Tsang, Bruce Pawel, Benjamin A. Garcia, John M. Maris, Sharon J. Diskin. Integrative mass spectrometry and RNA-sequencing identifies DLK1 as a candidate immunotherapeutic target in neuroblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3650.

Common variants upstream of MLF1 at 3q25 and within CPZ at 4p16 associated with neuroblastoma

Neuroblastoma is a cancer of the developing sympathetic nervous system that most commonly presents in young children and accounts for approximately 12% of pediatric oncology deaths. Here, we report on a genome-wide association study (GWAS) in a discovery cohort or 2,101 cases and 4,202 controls of European ancestry. We identify two new association signals at 3q25 and 4p16 that replicated robustly in multiple independent cohorts comprising 1,163 cases and 4,396 controls (3q25: rs6441201 combined P = 1.2x10^-11, Odds Ratio 1.23, 95% CI:1.16–1.31; 4p16: rs3796727 combined P = 1.26x10^-12, Odds Ratio 1.30, 95% CI: 1.21–1.40). The 4p16 signal maps within the carboxypeptidase Z (CPZ) gene. The 3q25 signal resides within the arginine/serine-rich coiled-coil 1 (RSRC1) gene and upstream of the myeloid leukemia factor 1 (MLF1) gene. Increased expression of MLF1 was observed in neuroblastoma cells homozygous for the rs6441201 risk allele (P = 0.02), and significant growth inhibition was observed upon depletion of MLF1 (P < 0.0001) in neuroblastoma cells. Taken together, we show that common DNA variants within CPZ at 4p16 and upstream of MLF1 at 3q25 influence neuroblastoma susceptibility and MLF1 likely plays an important role in neuroblastoma tumorigenesis.

Neuroblastoma is an embryonal tumor of the developing sympathetic nervous system that accounts for 12% of childhood cancer deaths. Approximately 1–2% of cases are inherited in an autosomal dominant fashion. These familial cases often harbor germline mutations in ALK or PHOX2B. However, the vast majority of neuroblastomas appear to arise sporadically. We are studying sporadic neuroblastoma through an ongoing genome-wide association study (GWAS). To date, this effort has identified single nucleotide polymorphisms (SNPs) within or upstream of CASC15 and CASC14, BARD1, LMO1, DUSP12, HSD17B12, DDX4/IL31RA, HACE1, LIN28B, and TP53, along with a common copy number variation (CNV) within NBPF23 at chromosome 1q21.1, each being highly associated with neuroblastoma. Here, we report on genome-wide association study (GWAS) comprising 3,264 neuroblastoma patients and 8,598 control subjects. We identify two new association signals at 3q25 and 4p16 (3q25: rs6441201 combined P = 1.2x10^-11, Odds Ratio 1.23, 95% CI:1.16–1.31; 4p16: rs3796727 combined P = 1.26x10^-12, Odds Ratio 1.30, 95% CI: 1.21–1.40). The 3q25 signal resides upstream of the MLF1 gene and the 4p16 signal maps to the CPZ gene. We further demonstrate that neuroblastoma cells homozygous for the risk allele at 3q25 express higher levels of MLF1 and that silencing of MLF1 in neuroblastoma cells results in significant growth inhibition.

A LIN28B-RAN-AURKA Signaling Network Promotes Neuroblastoma Tumorigenesis

A more complete understanding of aberrant oncogenic signaling in neuroblastoma, a malignancy of the developing sympathetic nervous system, is paramount to improving patient outcomes. Recently, we identified LIN28B as an oncogenic driver in high-risk neuroblastoma. Here, we identify the oncogene RAN as a LIN28B target and show regional gain of chromosome 12q24 as an additional somatic alteration resulting in increased RAN expression. We show that LIN28B influences RAN expression by promoting RAN Binding Protein 2 expression and by directly binding RAN mRNA. Further, we demonstrate a convergence of LIN28B and RAN signaling on Aurora kinase A activity. Collectively, these findings demonstrate that LIN28B-RAN-AURKA signaling drives neuroblastoma oncogenesis, suggesting that this pathway may be amenable to therapeutic targeting.

Transaldolase is essential for maintenance of the mitochondrial transmembrane potential and fertility of spermatozoa

Fertility of spermatozoa depends on maintenance of the mitochondrial transmembrane potential (Deltapsi(m)), which is generated by the electron-transport chain and regulated by an oxidation-reduction equilibrium of reactive oxygen intermediates, pyridine nucleotides, and glutathione (GSH). Here, we report that male mice lacking transaldolase (TAL)(-/-) are sterile because of defective forward motility. TAL(-/-) spermatozoa show loss of Deltapsi(m) and mitochondrial membrane integrity because of diminished NADPH, NADH, and GSH. Mitochondria constitute major Ca(2+) stores; thus, diminished mitochondrial mass accounts for reduced Ca(2+) fluxing, defective forward motility, and infertility. Reduced forward progression of TAL-deficient spermatozoa is associated with diminished mitochondrial reactive oxygen intermediate production and Ca(2+) levels, intracellular acidosis, and compensatory down-regulation of carbonic anhydrase IV and overexpression of CD38 and gamma-glutamyl transferase. Microarray analyses of gene expression in the testis, caput, and cauda epididymidis of TAL(+/+), TAL(+/-), and TAL(-/-) littermates confirmed a dominant impact of TAL deficiency on late stages of sperm-cell development, affecting the electron-transport chain and GSH metabolism. Stimulation of de novo GSH synthesis by oral N-acetyl-cysteine normalized the low fertility rate of TAL(+/-) males without affecting the sterility of TAL(-/-) males. Whereas TAL(-/-) sperm failed to fertilize TAL(+/+) oocytes in vitro, sterility of TAL(-/-) sperm was circumvented by intracytoplasmic sperm injection, indicating that TAL deficiency influenced the structure and function of mitochondria without compromising the nucleus and DNA integrity. Collectively, these data reveal an essential role of TAL in sperm-cell mitochondrial function and, thus, male fertility.

Efficient syntheses of four stable-isotope labeled (1R)-menthyl (1S,2S)-(+)-2-phenylcyclopropanecarboxylates

Many carbenoid cyclopropanation reactions promoted by chiral catalysts give product mixtures reflecting impressive diastereo- and enantioselectivities. Few provide a single chiral product efficiently. This limitation has been overcome in cyclopropanations of styrene and isotopically labeled styrenes with alpha-diazoacetates. Convenient syntheses on a 20 g scale of each of four chiral isotopically labeled (1R)-menthyl (1S,2S)-2-phenylcyclopropanecarboxylates (the 1-d-3-(13)C, 1,(3S)-d2, 1,2,(3S)-d3, and 1,3,3-d3 isotopomers) of better than 99% ee have been realized.