KDM3B inhibitors disrupt the oncogenic activity of PAX3-FOXO1 in fusion-positive rhabdomyosarcoma

Fusion-positive rhabdomyosarcoma (FP-RMS) is an aggressive pediatric sarcoma driven primarily by the PAX3-FOXO1 fusion oncogene, for which therapies targeting PAX3-FOXO1 are lacking. Here, we screen 62,643 compounds using an engineered cell line that monitors PAX3-FOXO1 transcriptional activity identifying a hitherto uncharacterized compound, P3FI-63. RNA-seq, ATAC-seq, and docking analyses implicate histone lysine demethylases (KDMs) as its targets. Enzymatic assays confirm the inhibition of multiple KDMs with the highest selectivity for KDM3B. Structural similarity search of P3FI-63 identifies P3FI-90 with improved solubility and potency. Biophysical binding of P3FI-90 to KDM3B is demonstrated using NMR and SPR. P3FI-90 suppresses the growth of FP-RMS in vitro and in vivo through downregulating PAX3-FOXO1 activity, and combined knockdown of KDM3B and KDM1A phenocopies P3FI-90 effects. Thus, we report KDM inhibitors P3FI-63 and P3FI-90 with the highest specificity for KDM3B. Their potent suppression of PAX3-FOXO1 activity indicates a possible therapeutic approach for FP-RMS and other transcriptionally addicted cancers.

Preclinical development of a chimeric antigen receptor T cell therapy targeting FGFR4 in rhabdomyosarcoma

Pediatric patients with relapsed or refractory rhabdomyosarcoma (RMS) have dismal cure rates, and effective therapy is urgently needed. The oncogenic receptor tyrosine kinase fibroblast growth factor receptor 4 (FGFR4) is highly expressed in RMS and lowly expressed in healthy tissues. Here, we describe a second-generation FGFR4-targeting chimeric antigen receptor (CAR), based on an anti-human FGFR4-specific murine monoclonal antibody 3A11, as an adoptive T cell treatment for RMS. The 3A11 CAR T cells induced robust cytokine production and cytotoxicity against RMS cell lines in vitro. In contrast, a panel of healthy human primary cells failed to activate 3A11 CAR T cells, confirming the selectivity of 3A11 CAR T cells against tumors with high FGFR4 expression. Finally, we demonstrate that 3A11 CAR T cells are persistent in vivo and can effectively eliminate RMS tumors in two metastatic and two orthotopic models. Therefore, our study credentials CAR T cell therapy targeting FGFR4 to treat patients with RMS.

Piperacetazine Directly Binds to the PAX3::FOXO1 Fusion Protein and Inhibits Its Transcriptional Activity

The tumor-specific chromosomal translocation product, PAX3::FOXO1, is an aberrant fusion protein that plays a key role for oncogenesis in the alveolar subtype of rhabdomyosarcoma (RMS). PAX3::FOXO1 represents a validated molecular target for alveolar RMS and successful inhibition of its oncogenic activity is likely to have significant clinical applications. Even though several PAX3::FOXO1 function-based screening studies have been successfully completed, a directly binding small-molecule inhibitor of PAX3::FOXO1 has not been reported. Therefore, we screened small-molecule libraries to identify compounds that were capable of directly binding to PAX3::FOXO1 protein using surface plasmon resonance technology. Compounds that directly bound to PAX3::FOXO1 were further evaluated in secondary transcriptional activation assays. We discovered that piperacetazine can directly bind to PAX3::FOXO1 protein and inhibit fusion protein-derived transcription in multiple alveolar RMS cell lines. Piperacetazine inhibited anchorage-independent growth of fusion-positive alveolar RMS cells but not embryonal RMS cells. On the basis of our findings, piperacetazine is a molecular scaffold upon which derivatives could be developed as specific inhibitors of PAX3::FOXO1. These novel inhibitors could potentially be evaluated in future clinical trials for recurrent or metastatic alveolar RMS as novel targeted therapy options.

SIGNIFICANCE

RMS is a malignant soft-tissue tumor mainly affecting the pediatric population. A subgroup of RMS with worse prognosis harbors a unique chromosomal translocation creating an oncogenic fusion protein, PAX3::FOXO1. We identified piperacetazine as a direct inhibitor of PAX3::FOXO1, which may provide a scaffold for designing RMS-specific targeted therapy.

A stem cell epigenome is associated with primary nonresponse to CD19 CAR T cells in pediatric acute lymphoblastic leukemia

CD19 chimeric antigen receptor T-cell therapy (CD19-CAR) has changed the treatment landscape and outcomes for patients with pre-B-cell acute lymphoblastic leukemia (B-ALL). Unfortunately, primary nonresponse (PNR), sustained CD19+ disease, and concurrent expansion of CD19-CAR occur in 20% of the patients and is associated with adverse outcomes. Although some failures may be attributable to CD19 loss, mechanisms of CD19-independent, leukemia-intrinsic resistance to CD19-CAR remain poorly understood. We hypothesize that PNR leukemias are distinct compared with primary sensitive (PS) leukemias and that these differences are present before treatment. We used a multiomic approach to investigate this in 14 patients (7 with PNR and 7 with PS) enrolled in the PLAT-02 trial at Seattle Children's Hospital. Long-read PacBio sequencing helped identify 1 PNR in which 47% of CD19 transcripts had exon 2 skipping, but other samples lacked CD19 transcript abnormalities. Epigenetic profiling discovered DNA hypermethylation at genes targeted by polycomb repressive complex 2 (PRC2) in embryonic stem cells. Similarly, assays of transposase-accessible chromatin-sequencing revealed reduced accessibility at these PRC2 target genes, with a gain in accessibility of regions characteristic of hematopoietic stem cells and multilineage progenitors in PNR. Single-cell RNA sequencing and cytometry by time of flight analyses identified leukemic subpopulations expressing multilineage markers and decreased antigen presentation in PNR. We thus describe the association of a stem cell epigenome with primary resistance to CD19-CAR therapy. Future trials incorporating these biomarkers, with the addition of multispecific CAR T cells targeting against leukemic stem cell or myeloid antigens, and/or combined epigenetic therapy to disrupt this distinct stem cell epigenome may improve outcomes of patients with B-ALL.

Abstract 3538: Endogenous HiBiT-tagging of PAX3-FOXO1 identifies potent suppressors of PAX3-FOXO1 protein levels by high-throughput screening

Background: Oncogenic fusion genes are attractive therapeutic targets due to their tumor-specific expression and driver roles in cancers. PAX3-FOXO1 (P3F) is the dominant oncogenic driver of fusion-positive rhabdomyosarcoma (FP-RMS) with no targeted therapy. We developed methods to directly measure endogenous P3F protein levels amenable to high-throughput drug screens to identify suppressors of P3F.

Methods: HiBiT tag, an 11 amino acid peptide of the small fragment of NanoLuc luciferase, was inserted into the endogenous P3F using CRISPR-Cas9 in FP-RMS cell lines RH4 and SCMC. Western analysis was used for HiBiT tag validation and confirmation of P3F suppression. RNA-seq and ChIP-seq were used to assess transcriptomics and DNA binding of HiBiT-tagged P3F (P3F-HiBiT) respectively. High-throughput drug screen using Nano-Glo luciferase assay was performed using the Mechanism Interrogation PlatE (MIPE 5.0) drug library, which included 2,480 drugs with known mechanisms of action. CellTiter-Glo was used to monitor cell viability. We identified drugs that suppressed P3F by Nano-Glo without acute cytotoxicity by CellTiter-Glo at an early 24-hour timepoint. Mouse xenograft model of FP-RMS was used to investigate in vivo efficacy of top hits.

Results: We validated HiBiT tagging of P3F and not the wild-type FOXO1 by Western analysis. We showed that the HiBiT tag did not change the function of P3F by transducing human fibroblasts with P3F-HiBiT versus unmodified P3F. Gene Set Enrichment Analysis (GSEA) of RNA-seq showed that P3F-HiBiT activated the same downstream target genes as unmodified P3F. ChIP-seq using HiBiT antibody in HiBiT-tagged FP-RMS cell lines RH4 and SCMC matched the genomic locations from ChIP-seq with P3F antibody in parental RH4 and SCMC. Using a cutoff of Area Under the Curve (AUC) of CellTiter-Glo - AUC of Nano-Glo > 90, in both RH4 and SCMC, identified 182 compounds. Filtering for drugs with ≥ 3 hits for the same target identified 14 drug classes that suppressed P3F protein level including HDAC inhibitors (3), mTOR inhibitors (4), CDK inhibitors (8), and BRD4 inhibitors (3). One top hit was the CDK inhibitor TG02 (Zotiraciclib), currently in human trials. TG02 suppressed P3F protein levels by Nano-Glo and Western analysis. We confirmed induction of apoptosis by PARP cleavage in a panel of FP-RMS cell lines. GSEA analysis of RNA-seq after treatment with TG02 showed marked suppression of P3F target gene sets. TG02 also significantly delayed tumor progression of established tumors in a mouse xenograft model of FP-RMS without weight loss.

Conclusion and Future Directions:By HiBiT tagging the fusion oncogene P3F, we identified 182 compounds that suppress P3F levels of which TG02 was a top hit that also showed in vivo efficacy. Drug combination studies are currently underway to identify synergistic suppressors of P3F protein levels that can be translated into clinical trials.

Citation Format: Yong Yean Kim, Robert G. Hawley, Mehal Churiwal, Teresa S. Hawley, Christine N. Evans, Raj Chari, David Milewski, Ranuka Sinniah, Young K. Song, Hsien-Chao Chou, Xinyu Wen, Ying Pang, Jing Wu, Craig J. Thomas, Jun S. Wei, Michele Ceribelli, Javed Khan. Endogenous HiBiT-tagging of PAX3-FOXO1 identifies potent suppressors of PAX3-FOXO1 protein levels by high-throughput screening. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3538.

[Microfocal prostate cancer: a clinicopathological analysis of 206 cases]

Objective: To investigate the clinical and pathological features and prognosis of patients with microfocal prostate adenocarcinoma. Methods: Clinical and pathological data of the patients diagnosed with microfocal adenocarcinoma on prostate biopsy at the West China Hospital from 2013 to 2019 were collected. Microfocal adenocarcinoma was defined as follows: Gleason score of 3+3=6, total number of the cores ≥10, number of the positive cores ≤2, and proportion of the tumor in each positive core<50%. Clinicopathological parameters, treatment plans and follow-up data were collected. Pathological information of the biopsy and radical resection specimens was used to analyze the correlation between pathological parameters in the biopsy report and adverse pathological features of radical resection specimens, including increased Gleason score, capsule invasion, positive surgical margin and perineural invasion. Results: A total of 206 cases of microfocal adenocarcinoma were diagnosed on prostate biopsies from 2013 to 2019, accounting for 6.7% of all adenocarcinoma cases. There were 139 cases of 1 positive core and 67 cases of 2 positive cores. Patients with microfocal adenocarcinoma were younger than those with non-microfocal adenocarcinoma (69 years versus 71 years, P<0.001). Compared with patients with non-microfocal adenocarcinoma, the pre-biopsy total prostate specific antigen (tPSA) and free prostate specific antigen (fPSA) levels in patients with microfocal adenocarcinoma were both lower (11.2 μg/L² versus 23.7 μg/L²; 1.4 μg/L² versus 3.0 μg/L², P<0.001), the fPSA/tPSA level was higher (12.9% versus 10.7%, P<0.05), the prostate volume was larger (38.9 mL versus 34.3 mL, P<0.05), and the PSA density was lower (0.3 μg/L² versus 0.8 μg/L², P<0.001). 130 patients underwent radical prostatectomy, 30 patients chose active monitoring, 31 patients chose endocrine or radiation therapy, and 15 patients were lost to follow-up. Three patients in the active surveillance group underwent radical prostatectomy for disease progression after 21-39 months observation. Biochemical relapses occurred in two patients in the radical prostatectomy group. The remaining patients have no disease progression or recurrence at present. Compared with radical prostatectomy specimens, Gleason score in the biopsy material was increased in 64/115 patients (55.7%). Among resection excision specimens, 14 cases (12.2%) had extraprostatic extension (EPE), 35 cases (30.4%) had perineural invasion, and 16 cases (13.9%) had a positive margin. Univariate and multivariate analyses showed that low fPSA/tPSA ratio and 2 positive cores were independent risk factors for Gleason score increase in the radical prostatectomy specimens. A low fPSA/tPSA ratio was an independent risk factor for perineural invasion. Low fPSA/tPSA ratio and low prostate volume were associated with a positive margin in radical prostatectomy specimens. Conclusions: In this study, patients diagnosed with microfocal adenocarcinoma on prostate biopsy account for a high proportion of the patients with increased Gleason score in the radical prostatectomy specimens, and there is a certain proportion of adverse pathological features in the radical specimens. Therefore, for the patients with only a small amount of low-grade adenocarcinoma found in biopsy, PSA levels and PSA density should be taken into consideration in treatment selection.

Abstract 552: FGFR4 and CD276 dualtargeting CAR-T cells for treating rhabdomyosarcoma and other solid tumors

Background: Chimeric antigen receptor T-cell therapies (CAR-T) have shown success in treating refractory and relapsed leukemia and lymphoma, while they perform poorly in solid tumors due to heterogenous expression of tumor-associated antigens (TAAs), limited T cell persistence and propensity for exhaustion. The receptor tyrosine kinase FGFR4 and immune checkpoint molecule CD276 are highly and heterogeneously expressed in some solid tumors, including Rhabdomyosarcoma (RMS), a most common soft tissue sarcoma of childhood, and human hepatocellular carcinoma (HCC). However, their expression is usually low in normal human tissues. These features make FGFR4 and CD276 promising therapeutic targets for CAR-T therapy for RMS and HCC. We have developed a FGFR4 targeting CAR construct (3A11-BBz) with a CD8 hinge (H) and a transmembrane domain (TM) infused with a 4-1BB intracellular domain (ICD). 3A11-BBz CAR can efficiently eliminate low RMS disease burden in metastatic models, but less effectively for bulky disease in RMS intramuscular (I.M.) xenograft models. Testing of a CD276 targeting CAR T-cells showed significant shrinking of tumors in RMS I.M. xenograft models.

Methods: To improve the CAR-T cells efficacy, we first modified the H/TM and ICD of 3A11-BBz CAR to CD28 (3A11-CD28z). To overcome tumor heterogeneity, we also created Bicistronic CARs (BiCisCARs) combining the complete FGFR4 and CD276 CAR into a single construct allowing co-expression of both constructs on the same T cells. We then tested the efficacy of these CARs in-vitro and in-vivo using intramuscular FP-RMS xenograft (RH30) or HCC intraperitoneal models.

Results and Conclusions: We found either FGFR4 targeting CARs or dual targeting BiCisCARs, showed similar in-vitro cytotoxicity against RMS cells and HCC cells. However, CARs with CD28 ICD released more IL-2 than those with 4-1BB ICD when co-cultured with target cells. In RMS I.M. xenograft model, 3A11-CD28z CAR-T cells shrank and eliminated the tumor in 5/8 mice whereas 3A11-BBz only suppressed tumor growth. Furthermore, 3A11-CD28z BiCisCAR eradicated tumor cells in 8/8 mice, whereas 3A11-BBz BiCisCAR showed very poor efficacy. Moreover, there are more 3A11-CD28z BiCisCAR T-cells persisting in blood and spleen than the other bicistronic or single CAR-T cells, suggesting this BiCisCAR-T cells have prolonged persistence. Therefore, we have developed a potent BiCisCAR dual targeting both FGFR4 and CD276 that overcomes RMS heterogeneity and effectively eliminates tumors in-vivo, which will be developed as a future therapeutic CAR for clinical trials.

Citation Format: Meijie Tian, Adam Cheuk, David Milewski, Jun S. Wei, Hsien-Chao Chou, Yong Yean Kim, Young K. Song, Brad St. Croix, Mitchell Ho, Javed Khan. FGFR4 and CD276 dualtargeting CAR-T cells for treating rhabdomyosarcoma and other solid tumors [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 552.

Abstract 3581: Multi-omic analysis identifies mechanisms of resistance to CD19 CAR T-cell therapy in children with acute lymphoblastic leukemia

Background: Acute lymphoblastic leukemia (ALL) is the most common childhood cancer. Despite the survival rate of 90% for newly diagnosed children with ALL, the outcome for relapsed patients is historically poor with a less than 30% survival. CD19 CAR T-cell therapy (CART19) has shown remarkable response rates, between 80-90% in relapsed/refractory disease. Little is known about antigen-independent factors that predict initial resistance to CART19. We hypothesized that leukemias that are resistant to CART19 are distinct from sensitive leukemias and that these differences can be detected prior to therapy.

Methods: To interrogate differences between resistant and sensitive leukemias, we obtained pre-treatment bone marrow aspirates (BMAs) from patients enrolled in a clinical trial at Seattle Children’s Hospital (PLAT-02). Samples were categorized based on patient response, with non-response defined as not achieving and maintaining minimal residual disease negativity at Day +63. Our study included 7 resistant and 7 sensitive leukemias as controls. We performed whole exome sequencing, bulk RNA-seq, PacBio-seq of the CD19 locus, array-based methylation, ATAC-seq, scRNA-seq, and CyTOF.

Results: We found that non-response to CART19 is independent of leukemic subtype. Despite blasts being CD19+ in all patients by flow cytometry, we identified alternative splicing of CD19 in one non-responder, while the remaining non-responders expressed high levels of wildtype CD19. We discovered a distinctive DNA methylation pattern in the non-responders characterized by hypermethylation of PRC2 targets in embryonic and cancer stem cells (p = 8.15E-25) Furthermore, using gene set enrichment analysis of ATAC-seq data, we found increased accessibility of chromatin at regions associated with stem cell proliferation (NES = 2.31; p &lt; 0.0001) and cell cycling (NES = 2.27; p &lt; 0.0001). We found a greater similarity between accessibility patterns of non-responders to hematopoietic progenitors, including hematopoietic stem cells (p = 0.037) and common myeloid progenitors (p = 0.047). These findings were supported by an increased frequency of cell subpopulations expressing a multi-lineage phenotype (CD19, CD20, CD33, CD34; p = 0.009). Moreover, we find decreased expression of antigen presentation and processing pathways across all leukemic cells relative to responders (p = 0.0001).

Conclusions: This study, one of the most comprehensive multi-omic analyses of samples from patients treated with CAR T-cells, identified resistance mechanisms that can be detected prior to treatment. We report the novel association of a stem cell phenotype, lineage plasticity, and decreased antigen presentation with resistance. These results support further refinement of eligibility for CART19 for children with leukemia and highlights the need for alternative of complimentary approaches for these patients.

Citation Format: Katherine E. Masih, Rebecca Gardner, Hsien-Chao Chou, Abdalla Abdelmaksoud, Young K. Song, Luca Mariani, Vineela Gangalapudi, Berkley E. Gryder, Ashley Wilson, Serifat O. Adebola, Benjamin Z. Stanton, Chaoyu Wang, Xinyu Wen, Gregoire Altan-Bonnet, Michael C. Kelly, Jun S. Wei, Martha L. Bulyk, Michael C. Jensen, Rimas J. Orentas, Javed Khan. Multi-omic analysis identifies mechanisms of resistance to CD19 CAR T-cell therapy in children with acute lymphoblastic leukemia [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 3581.

Dentithecamides A-H, Diacylated Zoanthoxanthin Derivatives with PAX3-FOXO1 Inhibitory Activity from the Hydroid Dentitheca habereri

Chemical investigation of the marine hydroid Dentitheca habereri led to the identification of eight new diacylated zoanthoxanthin alkaloids, named dentithecamides A-H (1-8), along with three previously reported analogues, zoamides B-D (9-11). The structures of compounds 1-11 were elucidated by spectroscopic and spectrometric analyses, including IR, HRESIMS, and NMR experiments, and by comparison with literature data. Compounds 1-11 are the first zoanthoxanthin alkaloids to be reported from a hydroid. Dentithecamides A (1) and B (2) along with zoamides B-D (9-11), which all share a conformationally mobile cycloheptadiene core, inhibited PAX3-FOXO1 regulated transcriptional activity and thus provided a structural framework for the potential development of more potent PAX3-FOXO1 inhibitors.

BAF complexes drive proliferation and block myogenic differentiation in fusion-positive rhabdomyosarcoma

Rhabdomyosarcoma (RMS) is a pediatric malignancy of skeletal muscle lineage. The aggressive alveolar subtype is characterized by t(2;13) or t(1;13) translocations encoding for PAX3- or PAX7-FOXO1 chimeric transcription factors, respectively, and are referred to as fusion positive RMS (FP-RMS). The fusion gene alters the myogenic program and maintains the proliferative state while blocking terminal differentiation. Here, we investigated the contributions of chromatin regulatory complexes to FP-RMS tumor maintenance. We define the mSWI/SNF functional repertoire in FP-RMS. We find that SMARCA4 (encoding BRG1) is overexpressed in this malignancy compared to skeletal muscle and is essential for cell proliferation. Proteomic studies suggest proximity between PAX3-FOXO1 and BAF complexes, which is further supported by genome-wide binding profiles revealing enhancer colocalization of BAF with core regulatory transcription factors. Further, mSWI/SNF complexes localize to sites of de novo histone acetylation. Phenotypically, interference with mSWI/SNF complex function induces transcriptional activation of the skeletal muscle differentiation program associated with MYCN enhancer invasion at myogenic target genes, which is recapitulated by BRG1 targeting compounds. We conclude that inhibition of BRG1 overcomes the differentiation blockade of FP-RMS cells and may provide a therapeutic strategy for this lethal childhood tumor.

Immuno-transcriptomic profiling of extracranial pediatric solid malignancies

We perform an immunogenomics analysis utilizing whole-transcriptome sequencing of 657 pediatric extracranial solid cancer samples representing 14 diagnoses, and additionally utilize transcriptomes of 131 pediatric cancer cell lines and 147 normal tissue samples for comparison. We describe patterns of infiltrating immune cells, T cell receptor (TCR) clonal expansion, and translationally relevant immune checkpoints. We find that tumor-infiltrating lymphocytes and TCR counts vary widely across cancer types and within each diagnosis, and notably are significantly predictive of survival in osteosarcoma patients. We identify potential cancer-specific immunotherapeutic targets for adoptive cell therapies including cell-surface proteins, tumor germline antigens, and lineage-specific transcription factors. Using an orthogonal immunopeptidomics approach, we find several potential immunotherapeutic targets in osteosarcoma and Ewing sarcoma and validated PRAME as a bona fide multi-pediatric cancer target. Importantly, this work provides a critical framework for immune targeting of extracranial solid tumors using parallel immuno-transcriptomic and -peptidomic approaches.

Genomic Classification and Clinical Outcome in Rhabdomyosarcoma: A Report From an International Consortium

PURPOSE

Rhabdomyosarcoma is the most common soft tissue sarcoma of childhood. Despite aggressive therapy, the 5-year survival rate for patients with metastatic or recurrent disease remains poor, and beyond PAX-FOXO1 fusion status, no genomic markers are available for risk stratification. We present an international consortium study designed to determine the incidence of driver mutations and their association with clinical outcome.

PATIENTS AND METHODS

Tumor samples collected from patients enrolled on Children's Oncology Group trials (1998-2017) and UK patients enrolled on malignant mesenchymal tumor and RMS2005 (1995-2016) trials were subjected to custom-capture sequencing. Mutations, indels, gene deletions, and amplifications were identified, and survival analysis was performed.

RESULTS

DNA from 641 patients was suitable for analyses. A median of one mutation was found per tumor. In FOXO1 fusion-negative cases, mutation of any RAS pathway member was found in > 50% of cases, and 21% had no putative driver mutation identified. BCOR (15%), NF1 (15%), and TP53 (13%) mutations were found at a higher incidence than previously reported and TP53 mutations were associated with worse outcomes in both fusion-negative and FOXO1 fusion-positive cases. Interestingly, mutations in RAS isoforms predominated in infants < 1 year (64% of cases). Mutation of MYOD1 was associated with histologic patterns beyond those previously described, older age, head and neck primary site, and a dismal survival. Finally, we provide a searchable companion database (ClinOmics), containing all genomic variants, and clinical annotation including survival data.

CONCLUSION

This is the largest genomic characterization of clinically annotated rhabdomyosarcoma tumors to date and provides prognostic genetic features that refine risk stratification and will be incorporated into prospective trials.

Case Report: Single-Cell Transcriptomic Analysis of an Anaplastic Oligodendroglioma Post Immunotherapy

Glioma is the most common primary malignant brain tumor with a poor prognosis. Immune checkpoint inhibitors have been of great interest in investigation of glioma treatments. Here, we report single-cell transcriptomic analyses of two tumor areas from an oligodendroglioma taken from a patient who had multiple tumor recurrences, following several chemotherapies and radiation treatments. The patient subsequently received nivolumab and was considered have disease progression based on conventional diagnostic imaging after two cycles of treatment. He underwent a debulking surgical resection and pathological diagnosis was recurrent disease. During the surgery, tumor tissues were also collected from the enhancing and non-enhancing areas for a scRNAseq analysis to investigate the tumor microenvironment of these radiographically divergent areas. The scRNAseq analysis reveals a plethora of immune cells, suggesting that the increased mass observed on MRI may be partially a result of immune cell infiltration. The patient continued to receive immunotherapy after a short course of palliative radiation and remained free of disease progression for at least 12 months after the last surgery, suggesting a sustained response to immunotherapy. The scRNAseq analysis indicated that the radiological progression was in large part due to immune cell infiltrate and continued immunotherapy led to a positive clinical outcome in a patient who would have otherwise been admitted to hospice care with halting of immunotherapy. Our study demonstrates the potential of scRNAseq analyses in understanding the tumor microenvironment, which may assist the clinical decision-making process for challenging glioma cases following immunotherapy.

Abstract 3445: Immuno-transcriptomic profiling identifies actionable genomic alterations in pediatric solid malignancies

Malignancy remains the leading cause of disease-related death in children. To identify potential tumor-driving molecular targets and characterize immunogenomic profiles in pediatric cancers, we performed RNA-seq analysis on a cohort of 788 pediatric solid tumors across 14 different diagnoses in conjunction with additional 147 normal tissues for comparison. Sequencing data were analyzed for expressed mutations, fusion events, and expressional patterns, providing therapeutic targets and rich cancer biology for these childhood cancers. Furthermore, we describe a comprehensive and in-depth immunogenomic landscape of these solid tumors including immune cell infiltrate, neoepitope analysis from expressed mutations and fusions, expressional patterns of clinically relevant immune checkpoint genes, expression of tumor-specific genes as potential pharmacological or immunological targets, and T cell receptor repertoire. Across the cohort, we observed a striking correlation between the expressed neoepitope burden in tumors and enrichment of the effector immune signatures. Intriguingly, canonical fusions (e.g. EWS-FLI1) contribute a disproportionally large number of neoepitopes in these typically low mutational tumors. Histology-specific immunogenomic patterns are also apparent. Several of the pediatric cancers such as alveolar soft part sarcoma and osteosarcoma exhibit rich immune cell infiltration and evidence for activated T cell activities, whereas others such as Wilms tumors and synovial sarcoma generally have a very low T cell infiltration. In addition, we demonstrated a significant positive correlation between tumor-infiltrating CD8+ T cells and overall survival in patients with osteosarcoma, revealing the clinical importance of these tumor-infiltrating immune cells in these childhood cancers. Moreover, an orthogonal evaluation of immunopeptidome in osteosarcoma, a cancer type displaying high immune infiltrates, confirmed our transcriptomic findings on potential targetable tumor-specific genes. Finally, we took an adoptive cell therapy-based approach to target a tumor-specific gene PRAME identified by our transcriptomic and immunopeptidomic studies and showed significant in-vitro cytotoxicity using T cells expressing TCRs specifically targeting PRAME in osteosarcoma U2OS cells. Therefore, we demonstrate that RNA-seq is a powerful tool to identify clinically relevant and histology-specific genomic alterations and translationally relevant immunogenomic patterns for pediatric cancers. This study also represents one of the largest of its type to date and provides a framework for future translational efforts in pediatric cancer.

Citation Format: Jun S. Wei, Andrew S. Brohl, Sivasish Sindiri, David Milewski, Young K. Song, Sushma Nagaraj, Vineela Gangalapudi, Xinyu Wen, Marc Ladanyi, Javed Khan. Immuno-transcriptomic profiling identifies actionable genomic alterations in pediatric solid malignancies [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3445.

Abstract A13: Immunogenomic approaches to optimize immunotherapeutic targeting of neuroblastoma

Neuroblastoma (NB) is the most common extracranial solid cancer in children. Although multimodal therapies with differentiating agents and immunotherapy with anti-GD2 antibody and GM-CSF have shown promising results, it remains deadly in approximately 50% of patients with high-risk disease. Chimeric antigen receptor T-cell therapies (CAR-T) have been found to be effective in treating refractory and relapsed leukemia and lymphoma, and two of them have been recently approved by the FDA. However, current CARs frequently lose efficacy due to T-cell exhaustion, and CARs against solid tumor antigens often lack enough specificity due to a low incidence of somatic mutations resulting in a paucity of tumor neoantigens. There have not been effective CAR-T therapies against other solid cancers to date, although many clinical trials are under way. Therefore, we attempted to develop a high-throughput way of identifying optimal CART cell binders that show activation and expansion in the presence of targets but lack of exhaustion. We previously identified two cell surface cancer-associated antigens, GPC2 (Glypican-2) and CD276 (B7-H3), both highly expressed in NB tumor cells but expressed at low or undetectable levels in normal organs. 14 established binders as well as novel binders targeting these two antigens were cloned into CAR lentiviral constructs and then were separately transduced into T cells to develop 14 CAR-T cells using a 2nd-generation design. All 14 CAR-T cells were pooled and cocultured with CD276/GPC2-expressing NB cancer cells (target cells) for 24 hr. To identify the effective GPC2 or CD276-specific targeting CAR-T cells, we utilized a combined proteomics and transcriptomics method for every single CAR-T cell to quantify RNA and protein at the same. Cocultured CAR-T cells were examined for their activation, exhaustion, cytotoxicity state and distinguished different cell types by staining with CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by Sequencing) antibodies, and then molecularly barcoded using 10X Genomics platform for single-cell RNA-sequencing (scRNA-seq). The data are currently being analyzed and will be presented. Using this method, we will be able to identify which of the CARs are enriched and have an activated T-cell signature, and lack exhaustion marks as determined by the CITE-seq and RNAseq analyses. Finally, top candidate binders for each antigen will be developed into “AND” or “OR” CARs and will be tested in in vitro and in vivo models of NB. Thus, we will develop a high-throughput way to identify high-affinity functional binders against tumor cell surface antigens. This study also will provide novel immunogenomics methods of CARs optimization for development of highly effective immunotherapies against NB and other cancers.

Citation Format: Meijie Tian, Adam Tai-Chi Cheuk, Jeetendra Kumar, Young K. Song, Sivasish Sindiri, Nan Li, Christopher M. Dower, Mitchell Ho, Brad St. Croix, Javed Khan. Immunogenomic approaches to optimize immunotherapeutic targeting of neuroblastoma [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr A13.

Abstract PR17: Immunogenomic landscape of pediatric solid malignancies

Malignancy remains the leading cause of disease-related death in children. To identify potential tumor-driving molecular targets and immunogenomic profiles in pediatric cancers, we performed RNA-seq analysis on a cohort of 788 pediatric solid malignant tumors across 14 different diagnoses in conjunction with additional 147 normal tissues for comparison. Sequencing data were analyzed for expressed mutations, fusion events, and expressional patterns, providing therapeutic targets and rich cancer biology for these childhood cancers. Furthermore, we describe immunogenomic features of these solid tumors including immune cell infiltrate, neoantigen expression, expression of immunomodulatory molecules, and T-cell receptor repertoire. Across the cohort, we observed a striking correlation between the expressed neoantigen burden in tumors and enrichment of the effector immune signatures. Histology-specific immunogenomic patterns were also apparent. Several of the pediatric cancers such as alveolar soft part sarcoma and osteosarcoma exhibit rich immune cell infiltration and evidence for activated T-cell activities, whereas others such as Wilms’ tumors and synovial sarcoma generally have a very low T-cell infiltration. We demonstrate that RNA-seq is a powerful tool to identify clinically relevant and histology-specific recurrent mutations, novel oncogenic fusions, and translationally relevant immunogenomic patterns for pediatric cancers. This study also represents one of the largest of its type to date and provides a framework for future translational efforts in pediatric cancer.

This abstract is also being presented as Poster A69.

Citation Format: Jun S. Wei, Andrew S. Brohl, Sivasish Sindiri, Young K. Song, Sushma Najaraj, Vineela Gangalapudi, Xinyu Wen, Marc Ladanyi, Javed Khan. Immunogenomic landscape of pediatric solid malignancies [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr PR17.

Abstract A11: A comprehensive and integrative omic analysis of multiply relapsed refractory pediatric pre-B cell acute lymphoblastic leukemia predicts response to CD19 CAR T-cell therapy

Acute lymphoblastic leukemia (ALL) is the most common childhood cancer with a peak incidence at 3-5 years of age. Despite the improved survival rate of 90% for newly diagnosed children with ALL, the outcome for patients with relapsed disease is poor with a less than 30% overall survival. CD19 CAR T-cell therapy has shown remarkable response rates in relapsed/refractory disease. Long-term survival analysis has shown that initial response rates exceed 80%. However, durable response rates at one year are closer to 40%. Little is known about factors predicting durable response to CAR T therapy. We hypothesize that patients with CD19 CAR T-cell resistant ALL have a distinct disease compared to responders to therapy that can be identified in pretreatment leukemia. Utilizing advanced genomic, epigenetic, proteomic, and single-cell (sc) techniques, we characterized patient bone marrow aspirates (BMA) to identify mechanisms of resistance. Patients enrolled in PLAT-02 at Seattle Children’s Hospital were categorized according to the durability of their response to CD19 CAR T therapy. To characterize the molecular and genomic alterations specific to the therapy-resistant ALLs, we performed comprehensive analyses on pre-treatment therapy-resistant and sensitive BMAs using whole-exome sequencing, RNA- BMAs seq, scRNA-seq, sc B cell receptor (BCR)-seq, methylation array, H3K27ac ChIP-seq, ATAC-seq, and CyTOF. Additionally, we developed murine patient-derived xenografts (PDXs) for future studies. Initial mutation analyses revealed 5 hotspot mutations (ABL1, 2 x KRAS, IKZF1, and EP300) and actionable fusion (2 ABL1, 2 ETV6, 2 ETV5, KMT2A). Interestingly, we identified a KMT2A-AFF1 fusion in a sensitive leukemia, which has been demonstrated to predispose patients to CD19 CAR T resistance through lineage switching. Additionally, we identified a novel CREBBP-fusion in leukemias resistant to CD19 CAR T-induced B-cell aplasia. Alterations of CREBBP have previously been associated with ALL that is refractory to conventional therapies. Integrated gene expression and epigenetic analyses are ongoing to identify genes or pathways associated with resistant disease. scRNA- and scBCR-seq data are being analyzed and integrated with CyTOF analyses to detect mixed lineage and gene expression-based heterogeneity that may predict clonal selection by CAR T pressure. Finally, we developed and genetically analyzed murine PDXs for 64% of the patient samples, establishing a valuable resource for future studies and developing novel therapies for resistant leukemias. This study is one of the most integrative and comprehensive genomic profiling approaches to identify the molecular traits of therapy-resistant ALL in patient samples. We hope to identify and develop crucial biomarkers predicting responsiveness to CAR T-cell therapy.

Citation Format: Katherine E. Masih, Rebecca Gardner, Berkley E. Gryder, Abdalla Abdelmaksoud, Ashley Wilson, Serifat Adebola, Benjamin Z. Stanton, Young K. Song, Justin Lack, Chaoyu Wang, Xinyu Wen, Zachary Rae, Adam Cheuk, Gregoire Altan-Bonnet, Michael Kelly, Jun S. Wei, Michael C. Jensen, Rimas J. Orentas, Javed Khan. A comprehensive and integrative omic analysis of multiply relapsed refractory pediatric pre-B cell acute lymphoblastic leukemia predicts response to CD19 CAR T-cell therapy [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr A11.

Outcome-Related Signatures Identified by Whole Transcriptome Sequencing of Resectable Stage III/IV Melanoma Evaluated after Starting Hu14.18-IL2

PURPOSE

We analyzed whole transcriptome sequencing in tumors from 23 patients with stage III or IV melanoma from a pilot trial of the anti-GD2 immunocytokine, hu14.18-IL2, to identify predictive immune and/or tumor biomarkers in patients with melanoma at high risk for recurrence.

EXPERIMENTAL DESIGN

Patients were randomly assigned to receive the first of three monthly courses of hu14.18-IL2 immunotherapy either before (Group A) or after (Group B) complete surgical resection of all known diseases. Tumors were evaluated by histology and whole transcriptome sequencing.

RESULTS

Tumor-infiltrating lymphocyte (TIL) levels directly associated with relapse-free survival (RFS) and overall survival (OS) in resected tumors from Group A, where early responses to the immunotherapy agent could be assessed. TIL levels directly associated with a previously reported immune signature, which associated with RFS and OS, particularly in Group A tumors. In Group A tumors, there were decreased cell-cycling gene RNA transcripts, but increased RNA transcripts for repair and growth genes. We found that outcome (RFS and OS) was directly associated with several immune signatures and immune-related RNA transcripts and inversely associated with several tumor growth-associated transcripts, particularly in Group A tumors. Most of these associations were not seen in Group B tumors.

CONCLUSIONS

We interpret these data to signify that both immunologic and tumoral cell processes, as measured by RNA-sequencing analyses detected shortly after initiation of hu14.18-IL2 therapy, are associated with long-term survival and could potentially be used as prognostic biomarkers in tumor resection specimens obtained after initiating neoadjuvant immunotherapy.

Abstract B17: MEK inhibition induces myogenic differentiation in RAS-driven rhabdomyosarcoma

Fusion-negative rhabdomyosarcoma (FN-RMS), which lacks PAX3/7 gene rearrangement, arises from skeletal muscle precursor cells that fail to differentiate despite expression of the myogenic master transcription factor, MYOD1. These tumors frequently harbor mutations in RAS isoforms (NRAS, HRAS, or KRAS), but the role of RAS in blocking myogenic differentiation is incompletely understood. In this study, we used a combination of high-throughput drug screening, transcriptomics, and epigenomics approaches to investigate the role of RAS in FN-RMS differentiation and survival. Oncogenic RAS was required for FN-RMS survival and activated the MAPK pathway to block myoblast differentiation. Consistent with these findings, the MEK inhibitor, trametinib, selectively reduced FN-RMS cell viability; upregulated the prodifferentiation myogenic transcription factor, MYOG; and induced myogenic differentiation. Mechanistically, we found that ERK2, a downstream target of MEK, bound to myogenic differentiation genes, including the promoter of MYOG, where it phosphorylated RNA polymerase II, resulting in RNA polymerase II stalling and transcriptional repression. MEK inhibition resulted in release of ERK2 from the MYOG promoter, facilitating MYOG transcription. Accordingly, trametinib treatment also resulted in MYOG-dependent chromatin remodeling, leading to the establishment of super-enhancers at genes required for late myogenic differentiation (including MYH3) and the loss of RAS-dependent super-enhancers at proliferation genes, such as MYC. In vivo, MEK inhibition induced myogenic differentiation FN-RMS cells to suppress their growth as xenografts. We then performed a combinatorial drug screen and identified combinations that might improve the therapeutic efficacy of trametinib. Excitingly, the most synergistic combination in vitro, trametinib and the multikinase inhibitor, BMS-754807, also induced tumor regression in mouse xenograft models of FN- RMS. Synergy was similarly observed between trametinib and the IGF1R monoclonal antibody, ganitumab, establishing the combination of MEK and IGF1R inhibition as synergistic in FN-RMS. Therefore, in addition to uncovering a mechanism by which RAS signaling suppresses MYOG expression to block MYOG-dependent chromatin remodeling and cellular differentiation in FN-RMS, these findings suggest that patients with FN-RMS may benefit from combination therapy with MEK and IGF1R inhibitors.

Citation Format: Marielle E. Yohe, Berkley E. Gryder, Hsien-Chao Chou, Young K. Song, Xiaohu Zhang, Donna Butcher, Kristine A. Isanogle, Christina M. Robinson, Xiaoling Luo, Jin-Qiu Chen, Elijah J. Edmondson, Simone Difilippantionio, Craig J. Thomas, Javed Khan. MEK inhibition induces myogenic differentiation in RAS-driven rhabdomyosarcoma [abstract]. In: Proceedings of the AACR Special Conference on Targeting RAS-Driven Cancers; 2018 Dec 9-12; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(5_Suppl):Abstract nr B17.

Photoemission Spectroscopic Evidence for the Dirac Nodal Line in the Monoclinic Semimetal SrAs_{3}

Topological nodal-line semimetals with exotic quantum properties are characterized by symmetry-protected line-contact bulk band crossings in the momentum space. However, in most of identified topological nodal-line compounds, these topological nontrivial nodal lines are enclosed by complicated topological trivial states at the Fermi energy (E_{F}), which would perplex their identification and hinder further applications. Utilizing angle-resolved photoemission spectroscopy and first-principles calculations, we provide compelling evidence for the existence of Dirac nodal-line fermions in the monoclinic semimetal SrAs_{3}, which possesses a simple nodal loop in the vicinity of E_{F} without the distraction from complicated trivial Fermi surfaces. Our calculations revealed that two bands with opposite parities were inverted around Y near E_{F}, resulting in the single nodal loop at the Γ-Y-S plane with a negligible spin-orbit coupling effect. The band crossings were tracked experimentally and the complete nodal loop was identified quantitatively, which provide a critical experimental support for the existence of nodal-line fermions in the CaP_{3} family of materials. Hosting simple topological nontrivial bulk electronic states around E_{F} and without complication from the trivial states, SrAs_{3} is expected to be a potential platform for topological quantum state investigation and applications.

MEK inhibition induces MYOG and remodels super-enhancers in RAS-driven rhabdomyosarcoma

The RAS isoforms are frequently mutated in many types of human cancers, including PAX3/PAX7 fusion-negative rhabdomyosarcoma. Pediatric RMS arises from skeletal muscle progenitor cells that have failed to differentiate normally. The role of mutant RAS in this differentiation blockade is incompletely understood. We demonstrate that oncogenic RAS, acting through the RAF-MEK [mitogen-activated protein kinase (MAPK) kinase]-ERK (extracellular signal-regulated kinase) MAPK effector pathway, inhibits myogenic differentiation in rhabdomyosarcoma by repressing the expression of the prodifferentiation myogenic transcription factor, MYOG. This repression is mediated by ERK2-dependent promoter-proximal stalling of RNA polymerase II at the MYOG locus. Small-molecule screening with a library of mechanistically defined inhibitors showed that RAS-driven RMS is vulnerable to MEK inhibition. MEK inhibition with trametinib leads to the loss of ERK2 at the MYOG promoter and releases the transcriptional stalling of MYOG expression. MYOG subsequently opens chromatin and establishes super-enhancers at genes required for late myogenic differentiation. Furthermore, trametinib, in combination with an inhibitor of IGF1R, potently decreases rhabdomyosarcoma cell viability and slows tumor growth in xenograft models. Therefore, this combination represents a potential therapeutic for RAS-mutated rhabdomyosarcoma.

Abstract 3653: Immunogenomic landscape of pediatric solid malignancies

Malignancy remains the leading cause of disease-related death in children. To identify potential tumor-driving molecular targets and immunogenomic profiles in pediatric cancers, we performed RNA-seq analysis on a cohort of 792 pediatric solid malignant tumors across 14 different diagnoses in conjunction with additional 147 normal tissues for comparison. Sequencing data was analyzed for expressed mutations, fusion events, and expressional patterns, providing therapeutic targets and rich cancer biology for these childhood cancers. Furthermore, we describe immunogenomic features of the tumors including immune cell infiltrate, neoantigen expression, expression of immunomodulatory molecules, and T cell receptor repertoire. Across the cohort, we observed a striking correlation between the expressed neoantigen burden in tumors and enrichment of the effector immune signatures. Histology-specific immunogenomic patterns were also apparent. Several of the pediatric cancers such as alveolar soft part sarcoma and osteosarcoma exhibit rich immune cell infiltration and evidence for activated T cell activities, whereas others such as Ewing’s sarcoma and yolk sac tumors generally have a very low T cell infiltration. We demonstrate that RNA-seq is a powerful tool to identify clinically relevant and histology-specific recurrent mutations, novel oncogenic fusions, and translationally relevant immunogenomic patterns for pediatric cancers. This study also represents one of the largest of its type to date and provides a framework for future translational efforts in pediatric cancer.

Citation Format: Jun S. Wei, Andrew S. Brohl, Young K. Song, Sushma Najaraj, Vineela Gangalapudi, Ashley Walton, Xinyu Wen, Marc Ladanyi, Javed Khan. Immunogenomic landscape of pediatric solid malignancies [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 3653.

Clinically Relevant Cytotoxic Immune Cell Signatures and Clonal Expansion of T-Cell Receptors in High-Risk MYCN-Not-Amplified Human Neuroblastoma

Purpose: High-risk neuroblastoma is an aggressive disease. DNA sequencing studies have revealed a paucity of actionable genomic alterations and a low mutation burden, posing challenges to develop effective novel therapies. We used RNA sequencing (RNA-seq) to investigate the biology of this disease, including a focus on tumor-infiltrating lymphocytes (TIL).Experimental Design: We performed deep RNA-seq on pretreatment diagnostic tumors from 129 high-risk and 21 low- or intermediate-risk patients with neuroblastomas. We used single-sample gene set enrichment analysis to detect gene expression signatures of TILs in tumors and examined their association with clinical and molecular parameters, including patient outcome. The expression profiles of 190 additional pretreatment diagnostic neuroblastomas, a neuroblastoma tissue microarray, and T-cell receptor (TCR) sequencing were used to validate our findings.Results: We found that MYCN-not-amplified (MYCN-NA) tumors had significantly higher cytotoxic TIL signatures compared with MYCN-amplified (MYCN-A) tumors. A reported MYCN activation signature was significantly associated with poor outcome for high-risk patients with MYCN-NA tumors; however, a subgroup of these patients who had elevated activated natural killer (NK) cells, CD8+ T cells, and cytolytic signatures showed improved outcome and expansion of infiltrating TCR clones. Furthermore, we observed upregulation of immune exhaustion marker genes, indicating an immune-suppressive microenvironment in these neuroblastomas.Conclusions: This study provides evidence that RNA signatures of cytotoxic TIL are associated with the presence of activated NK/T cells and improved outcomes in high-risk neuroblastoma patients harboring MYCN-NA tumors. Our findings suggest that these high-risk patients with MYCN-NA neuroblastoma may benefit from additional immunotherapies incorporated into the current therapeutic strategies. Clin Cancer Res; 24(22); 5673-84. ©2018 AACR.

The robustness of T2 value as a trabecular structural index at multiple spatial resolutions of 7 Tesla MRI

PURPOSE

To evaluate the robustness of MR transverse relaxation times of trabecular bone from spin-echo and gradient-echo acquisitions at multiple spatial resolutions of 7 T.

METHODS

The effects of MRI resolutions to T₂ and T2* of trabecular bone were numerically evaluated by Monte Carlo simulations. T₂ , T2*, and trabecular structural indices from multislice multi-echo and UTE acquisitions were measured in defatted human distal femoral condyles on a 7 T scanner. Reference structural indices were extracted from high-resolution microcomputed tomography images. For bovine knee trabecular samples with intact bone marrow, T₂ and T2* were measured by degrading spatial resolutions on a 7 T system.

RESULTS

In the defatted trabecular experiment, both T₂ and T2* values showed strong ( |r| > 0.80) correlations with trabecular spacing and number, at a high spatial resolution of 125 µm³ . The correlations for MR image-segmentation-derived structural indices were significantly degraded ( |r| < 0.50) at spatial resolutions of 250 and 500 µm³ . The correlations for T2* rapidly dropped ( |r| < 0.50) at a spatial resolution of 500 µm³ , whereas those for T₂ remained consistently high ( |r| > 0.85). In the bovine trabecular experiments with intact marrow, low-resolution (approximately 1 mm³ , 2 minutes) T₂ values did not shorten ( |r| > 0.95 with respect to approximately 0.4 mm³ , 11 minutes) and maintained consistent correlations ( |r| > 0.70) with respect to trabecular spacing (turbo spin echo, 22.5 minutes).

CONCLUSION

T₂ measurements of trabeculae at 7 T are robust with degrading spatial resolution and may be preferable in assessing trabecular spacing index with reduced scan time, when high-resolution 3D micro-MRI is difficult to obtain.

Frequent inactivating germline mutations in DNA repair genes in patients with Ewing sarcoma

Purpose

Ewing sarcoma is a highly malignant small round blue cell tumor that predominantly affects the adolescent and young adult population. It has long been suspected that a genetic predisposition exists for this cancer, but the germline genetic underpinnings of this disease have not been well established.

Methods

We performed germline variant analysis of whole genome or whole exome sequencing of samples from 175 patients affected by Ewing sarcoma.

Results

We discovered pathogenic or likely pathogenic germline mutations in 13.1% of our cohort. Pathogenic mutations were highly enriched for genes involved with DNA damage repair and for genes associated with cancer predisposition syndromes.

Conclusion

Our findings reported here have important clinical implications for patients and families affected by Ewing sarcoma. Genetic counseling should be considered for patients and families affected by this disease to take advantage of existing risk management strategies. Our study also highlights the importance of germline sequencing for patients enrolled on precision medicine protocols.

Aurora B kinase is a potent and selective target in MYCN-driven neuroblastoma

Despite advances in multimodal treatment, neuroblastoma (NB) is often fatal for children with high-risk disease and many survivors need to cope with long-term side effects from high-dose chemotherapy and radiation. To identify new therapeutic targets, we performed an siRNA screen of the druggable genome combined with a small molecule screen of 465 compounds targeting 39 different mechanisms of actions in four NB cell lines. We identified 58 genes as targets, including AURKB, in at least one cell line. In the drug screen, aurora kinase inhibitors (nine molecules) and in particular the AURKB-selective compound, barasertib, were the most discriminatory with regard to sensitivity for MYCN-amplified cell lines. In an expanded panel of ten NB cell lines, those with MYCN-amplification and wild-type TP53 were the most sensitive to low nanomolar concentrations of barasertib. Inhibition of the AURKB kinase activity resulted in decreased phosphorylation of the known target, histone H3, and upregulation of TP53 in MYCN-amplified, TP53 wild-type cells. However, both wild-type and TP53 mutant MYCN-amplified cell lines arrested in G2/M phase upon AURKB inhibition. Additionally, barasertib induced endoreduplication and apoptosis. Treatment of MYCN-amplified/TP53 wild-type neuroblastoma xenografts resulted in profound growth inhibition and tumor regression. Therefore, aurora B kinase inhibition is highly effective in aggressive neuroblastoma and warrants further investigation in clinical trials.

Abstract 126: The transcriptome landscape of high-risk neuroblastoma

Despite the success of multimodal therapies, the mortality and morbidity remains substantial for patients with high-risk neuroblastoma (NBL). Sequencing of paired tumor/normal DNA of NBL has revealed a low somatic mutation burden and few recurrent somatically-mutated genes. Here we hypothesize that the integrated analysis of DNA sequencing with whole transcriptome sequencing (WTS) in patients with high-risk NBL tumor will yield valuable insights into the biology of this disease. We performed WTS of 139 NBLs (118 high-risk stage 4 and 21 stage 4S tumors) which had whole genome sequencing or whole exome sequencing of case-matched tumor/normal pairs through the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) initiative. We identified expressed mutations, fusion genes, and correlations between gene expression and clinical parameters of patients such as survival to provide understandings of high-risk NBL biology.

Out of 1500 protein-coding changing somatic nucleotide variants detected by DNA sequencing, 614 variants (41%) were also detected in the transcriptome. Twenty-four genes known to be recurrently mutated in NBL showed the exact mutations in their transcriptome as seen in the DNA, including ALK (9.4%), ATRX (2.2%) and MYCN (1.4%). Fusion gene analysis identified in-frame fusions involving ALK (n = 2) and FOXR1 genes (n = 4). All tumors positive for ALK- and FOXR1-fusions expressed transcripts containing ALK or FOXR1 sequences at much higher levels (&gt;10 folds) than those without fusion in these respective genes. Consensus clustering using tumor gene expression profiles revealed 4 subgroups with distinct survival probability. Among them, several molecular signatures including MYC activation and tumor microenvironment were observed. Intriguingly, 58% tumors without MYCN-amplification showed a MYC activation signature significantly associated with worse overall survival (p = 0.0017). Further examination of these tumors with the MYC activation signature revealed different somatic alterations including MYCN P44L mutations, high expression of other MYC family members (MYC and MYCL), mutations in the RAS pathway, and FOXR1 fusions. Interestingly, a gene expression signature representing tumor-associated macrophages (TAM) and regulatory T-cells significantly correlated with a worse outcome in NBLs with normal MYCN copy number, similar to that seen in tumors with the MYC activation signature. In contrast, NBL patients with tumors showing a signature of cytotoxic T-cells and B-cells have better outcomes. Furthermore, tumors of the latter subgroup express significantly more somatic SNVs comparing to the other two subgroups of worse outcome with MYC activation or TAM signatures, suggesting that expressed neo-antigens may elevate cytotoxic T-cell response in these tumors. Our study suggests that patients with high-risk neuroblastoma may benefit from immune-based therapies including check point inhibitors in the future trials.

Citation Format: Jun S. Wei, Shile Zhang, Young K. Song, Shahab Asgharzadeh, Sivasish Sindiri, Xinyu Wen, Rajesh Patidar, Jaime M. Guidry Auvil, Daniela S. Gerhard, Robert Seeger, John M. Maris, Javed Khan. The transcriptome landscape of high-risk neuroblastoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 126.

MultiDimensional ClinOmics for Precision Therapy of Children and Adolescent Young Adults with Relapsed and Refractory Cancer: A Report from the Center for Cancer Research

PURPOSE

We undertook a multidimensional clinical genomics study of children and adolescent young adults with relapsed and refractory cancers to determine the feasibility of genome-guided precision therapy.

EXPERIMENTAL DESIGN

Patients with non-central nervous system solid tumors underwent a combination of whole exome sequencing (WES), whole transcriptome sequencing (WTS), and high-density single-nucleotide polymorphism array analysis of the tumor, with WES of matched germline DNA. Clinically actionable alterations were identified as a reportable germline mutation, a diagnosis change, or a somatic event (including a single nucleotide variant, an indel, an amplification, a deletion, or a fusion gene), which could be targeted with drugs in existing clinical trials or with FDA-approved drugs.

RESULTS

Fifty-nine patients in 20 diagnostic categories were enrolled from 2010 to 2014. Ages ranged from 7 months to 25 years old. Seventy-three percent of the patients had prior chemotherapy, and the tumors from these patients with relapsed or refractory cancers had a higher mutational burden than that reported in the literature. Thirty patients (51% of total) had clinically actionable mutations, of which 24 (41%) had a mutation that was currently targetable in a clinical trial setting, 4 patients (7%) had a change in diagnosis, and 7 patients (12%) had a reportable germline mutation.

CONCLUSIONS

We found a remarkably high number of clinically actionable mutations in 51% of the patients, and 12% with significant germline mutations. We demonstrated the clinical feasibility of next-generation sequencing in a diverse population of relapsed and refractory pediatric solid tumors. Clin Cancer Res; 22(15); 3810-20. ©2016 AACR.

Abstract B31: Combined siRNA and small molecule screening identifies Aurora B kinase as an effective target in MYCN-driven neuroblastoma

Despite advances in multimodal treatment, neuroblastoma (NB) is often fatal for children with high-risk disease and many survivors need to cope with long-term side effects from high-dose chemotherapy and radiation. To identify new therapeutic targets, we performed a siRNA screen of the druggable genome combined with a small molecule screen of 465 compounds targeting 39 different mechanisms of actions in four NB cell lines. We identified 58 genes as targets, including AURKB, in at least one cell line. In the drug screen, aurora kinase inhibitors (nine molecules) and in particular the AURKB-selective compound, barasertib, were the most discriminatory with regard to sensitivity for MYCN-amplified cell lines. In an expanded panel of NB cell lines, those with MYCN amplification and wild-type TP53 were the most sensitive to low nanomolar concentrations of barasertib. Inhibition of the AURKB kinase activity resulted in decreased phosphorylation of its known target histone H3, and upregulation of p53 pathway in MYCN-amplified NB cells with wild-type TP53. Both wild-type and p53-mutant MYCN-amplified cell lines arrested in G2/M phase upon AURKB inhibition. Additionally, barasertib induced endoreduplication and apoptosis. Treatment of MYCN-amplified/TP53 wild-type neuroblastoma xenografts resulted in profound growth inhibition and tumor regression. Therefore, aurora B kinase inhibition is highly effective in aggressive neuroblastoma and warrants further investigation in clinical trials.

Citation Format: Dominik Bogen, Jun S. Wei, David O. Azorsa, Pinar Ormanoglu, Eugen Buehler, Rajarshi Guha, Jonathan M. Keller, Lesley A. Mathews Griner, Marc Ferrer, Young K. Song, Hongling Liao, Arnulfo Mendoza, Berkley E. Gryder, Sivasish Sindri, Jianbin He, Xinyu Wen, Xinyu Wen, Shile Zhang, John F. Shern, Marielle E. Yohe, Sabine Taschner-Mandl, Jason Shohet, Craig J. Thomas, Scott E. Martin, Peter F. Ambros, Javed Khan. Combined siRNA and small molecule screening identifies Aurora B kinase as an effective target in MYCN-driven neuroblastoma. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Pediatric Cancer Research: From Mechanisms and Models to Treatment and Survivorship; 2015 Nov 9-12; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(5 Suppl):Abstract nr B31.

MYCN controls an alternative RNA splicing program in high-risk metastatic neuroblastoma

The molecular mechanisms underlying the aggressive behavior of MYCN driven neuroblastoma (NBL) is under intense investigation; however, little is known about the impact of this family of transcription factors on the splicing program. Here we used high-throughput RNA sequencing to systematically study the expression of RNA isoforms in stage 4 MYCN-amplified NBL, an aggressive subtype of metastatic NBL. We show that MYCN-amplified NBL tumors display a distinct gene splicing pattern affecting multiple cancer hallmark functions. Six splicing factors displayed unique differential expression patterns in MYCN-amplified tumors and cell lines, and the binding motifs for some of these splicing factors are significantly enriched in differentially-spliced genes. Direct binding of MYCN to promoter regions of the splicing factors PTBP1 and HNRNPA1 detected by ChIP-seq demonstrates that MYCN controls the splicing pattern by direct regulation of the expression of these key splicing factors. Furthermore, high expression of PTBP1 and HNRNPA1 was significantly associated with poor overall survival of stage4 NBL patients (p ≤ 0.05). Knocking down PTBP1, HNRNPA1 and their downstream target PKM2, an isoform of pro-tumor-growth, result in repressed growth of NBL cells. Therefore, our study reveals a novel role of MYCN in controlling global splicing program through regulation of splicing factors in addition to its well-known role in the transcription program. These findings suggest a therapeutically potential to target the key splicing factors or gene isoforms in high-risk NBL with MYCN-amplification.

Abstract 3218: Transcriptome characterization by RNA sequencing identifies molecular and clinical subgroups in high risk neuroblastoma

Background/objectives: Neuroblastoma (NBL) is characterized with its heterogeneous clinical and biological behavior. Despite improvement of survival rate with multimodal chemo- and immunotherapy, high mortality and morbidity is still substantial for patients with metastatic disease. Previous DNA sequencing studies characterized the genetic basis of the disease and revealed a very low somatic mutation burden and surprisingly few recurrently somatic mutated genes comparing to adult solid tumors. In order to identify the novel molecular therapeutic target and understand the biology of the high-risk neuroblastoma, we investigated gene expression profiles of tumors from a cohort of high-risk neuroblastoma patient using RNA sequencing as an integral part of the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) project.

Methods: We performed RNA sequencing in a cohort of 150 high risk patients (97 survival and 53 death) using polyA selected mRNA. Gene and transcript isoform expression was used to correlate to the clinical parameters for this clinically well-annotated patient cohort. Whole exome sequencing (WES) data was available for 106 of the 150 patients cohort for combined analysis of DNA and RNA sequencing to identify expressed mutation.

Results: On average, we found 12.5% of the human genome, which include 63.7% of exon, 18.0% of intron, and 4.6% of intergenic regions covered by RNA-seq reads in NB samples. Preliminary gene expression analysis showed four molecular subgroups of NB tumors with distinct outcomes (log-ranked p = 0.002). Sixty-two percent of somatic mutations identified by WES was present (&gt;10% VAF) in the RNA transcriptome when the locus was expressed (10X). We found that some of the important pathogenic somatic mutations such as TP53 p.R243W can be only detectable by integrated analysis of the sequencing data of RNA and DNA, possibly due to low tumor purity.

Future directions: We will assess the expressed mutations, fusion genes, mRNA expression, and splicing profiles to provide clinically relevant classification and offer insight into the tumor biology especially for those without detectable oncogenic driver mutation by DNA sequencing.

Citation Format: Shile Zhang, Jun S. Wei, Rajesh Patidar, Young K. Song, Sivasish Sindiri, Xinyu Wen, Shahab Asgharzadeh, Robert C. Seeger, John M. Maris, Jamie M. Guidry Auvil, Daniela S. Gerhard, Javed Khan. Transcriptome characterization by RNA sequencing identifies molecular and clinical subgroups in high risk neuroblastoma. [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 3218. doi:10.1158/1538-7445.AM2015-3218

Abstract 3882: Clinical exome and transcriptome sequencing for identification of actionable cancer targets: A pilot study for children and young adults with relapsed or refractory solid tumors

Background. With technological advances such as next-generation sequencing, recent gains in understanding pediatric cancer can aid in treatment decisions, especially in the setting of relapse. To discover expressed, clinically significant mutations for pediatric patients with relapsed tumors, we performed a pilot trial using a combination of whole exome sequencing (WES) of tumor/normal DNA and whole transcriptome sequencing (WTS) of tumors, complemented by single nucleotide polymorphism (SNP) arrays.

Objectives. We identified 48 pediatric and young adult patients with relapsed or refractory solid tumors with matched tumor/normal samples. Our goals were to determine the feasibility of performing comprehensive genomic analyses in this population, to compare the genomic profile of relapsed tumors to prior reports of primary tumors, and to delineate the percentage of patients with actionable mutations. Actionable changes were defined as reportable germ line mutations determined by the American College of Medical Genetics (ACMG), a change in diagnosis, and somatic changes targetable by FDA approved medications or drugs undergoing clinical trials.

Methods. WES was performed on matched tumor and normal samples to identify germ line and somatic mutations. WTS was performed on tumor samples to identify fusion genes, gene expression profiling, and expressed variants. SNP arrays were performed to identify copy number changes. Sanger validation confirmed reportable mutations.

Results. In the exome, we noted a median of 33 somatic mutations per sample (range 1-375), a higher mutational burden compared to previously reported primary pediatric malignancies. Transcriptome data further refined results to a median of 7 expressed somatic mutations per sample (range 0-95). The majority of patients had one oncogenic driver. Sequencing relapsed tumors at multiple time points showed the continued presence of driver mutations but a shift in passenger mutations. Eleven of the 48 patients (23%) had a targetable mutation, such as ALK, BRAF, GNAQ, GNA11, IDH1, MTOR, PIK3CA, and SKP2. Two patients (4%) had a change in diagnosis due to the presence or absence of diagnostic fusion genes. In the germ line of 5 patients (10%) we discovered mutations in ACMG-reportable genes MUTYH, SCN5A, TP53, and MLH1. A total of 16 patients (33%) had actionable mutations.

Conclusions. Our study showed the feasibility of next-generation sequencing in relapsed pediatric solid tumors, with actionable mutations detected in a third of our patients. We demonstrated the utility in using exome and transcriptome sequencing with SNP arrays. Implementation of these techniques has the potential to change the practice of precision medicine. In summary, we have developed a prototype that will be utilized to design a national Pediatric Match trial in collaboration with the Children's Oncology Group. 

Citation Format: Wen-I Chang, Andrew S. Brohl, Rajesh Patidar, Jack F. Shern, Jun S. Wei, Young K. Song, Hongling Liao, Jimmy Lin, Sivasish Sindiri, Li Chen, Berkley Gryder, Marielle E. Yohe, Shile Zhang, Melinda S. Merchant, Brigitte C. Widemann, Javed Khan. Clinical exome and transcriptome sequencing for identification of actionable cancer targets: A pilot study for children and young adults with relapsed or refractory solid tumors. [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 3882. doi:10.1158/1538-7445.AM2015-3882

The genetics of splicing in neuroblastoma

Regulation of mRNA splicing, a critical and tightly regulated cellular function, underlies the majority of proteomic diversity and is frequently disrupted in disease. Using an integrative genomics approach, we combined both genomic data and exon-level transcriptome data in two somatic tissues (cerebella and peripheral ganglia) from a transgenic mouse model of neuroblastoma, a tumor that arises from the peripheral neural crest. Here, we describe splicing quantitative trait loci associated with differential splicing across the genome that we use to identify genes with previously unknown functions within the splicing pathway and to define de novo intronic splicing motifs that influence splicing from hundreds of bases away. Our results show that these splicing motifs represent sites for functional recurrent mutations and highlight novel candidate genes in human cancers, including childhood neuroblastoma.

SIGNIFICANCE

Somatic mutations with predictable downstream effects are largely relegated to coding regions, which comprise less than 2% of the human genome. Using an unbiased in vivo analysis of a mouse model of neuroblastoma, we have identified intronic splicing motifs that translate into sites for recurrent somatic mutations in human cancers.

Clonality and evolutionary history of rhabdomyosarcoma

To infer the subclonality of rhabdomyosarcoma (RMS) and predict the temporal order of genetic events for the tumorigenic process, and to identify novel drivers, we applied a systematic method that takes into account germline and somatic alterations in 44 tumor-normal RMS pairs using deep whole-genome sequencing. Intriguingly, we find that loss of heterozygosity of 11p15.5 and mutations in RAS pathway genes occur early in the evolutionary history of the PAX-fusion-negative-RMS (PFN-RMS) subtype. We discover several early mutations in non-RAS mutated samples and predict them to be drivers in PFN-RMS including recurrent mutation of PKN1. In contrast, we find that PAX-fusion-positive (PFP) subtype tumors have undergone whole-genome duplication in the late stage of cancer evolutionary history and have acquired fewer mutations and subclones than PFN-RMS. Moreover we predict that the PAX3-FOXO1 fusion event occurs earlier than the whole genome duplication. Our findings provide information critical to the understanding of tumorigenesis of RMS.

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 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 3413: A genetic analysis of splicing in neuroblastoma identifies opposing functions for FUBP1 splice variants in MYC regulation

Neuroblastoma, a tumor of the peripheral neural crest, is the most common cancer of infancy and the most common extracranial solid tumor of childhood. Large scale sequencing efforts have identified recurrent mutations in only a handful of genes in a minority of patients, but these efforts have so far focused on the exome, limiting identification of mutations leading to changes in alternative splicing.

Regulation of alternative splicing is a critical and tightly regulated cellular function involving a complex interplay between cis-acting sequences on the pre-mRNA transcript and accessory trans-acting splicing factors. To elucidate genetic control of splicing, we used a splicing quantitative trait loci (sQTL) analysis in a backcrossed mouse model of neuroblastoma. We utilized Affymetrix Exon Arrays to profile mRNA expression at the exon level for superior cervical ganglia and cerebella (n=102) which we coupled with genotypes at 350 SNP and microsattlelite locations. With whole-genome sequencing data available for the inbred parental strains, our approach provided us with localized sequences for each individual mouse.

In addition to identifying novel candidate trans-acting splicing factors, these sQTL identify novel candidate intronic regulatory sequences critical for splicing and reveal strain-specific splicing events leading to functional consequences in neuroblastoma. Among these, we show that a subtle splicing event within FUBP1 modulates levels of the MYC oncoprotein in human neuroblastoma-derived cell lines and correlates with outcome in children with neuroblastoma.

Citation Format: Justin Chen, Christopher S. Hackett, Shile Zhang, Young K. Song, Annette Molinaro, David A. Quigley, Allan Balmain, William C. Gustafson, Terry A. Van Dyke, Pui-Yan Kwok, Javed Khan, William A. Weiss. A genetic analysis of splicing in neuroblastoma identifies opposing functions for FUBP1 splice variants in MYC regulation. [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 3413. doi:10.1158/1538-7445.AM2014-3413

Ultrafast 3D spin-echo acquisition improves Gadolinium-enhanced MRI signal contrast enhancement

Long scan times of 3D volumetric MR acquisitions usually necessitate ultrafast in vivo gradient-echo acquisitions, which are intrinsically susceptible to magnetic field inhomogeneities. This is especially problematic for contrast-enhanced (CE)-MRI applications, where non-negligible T₂* effect of contrast agent deteriorates the positive signal contrast and limits the available range of MR acquisition parameters and injection doses. To overcome these shortcomings without degrading temporal resolution, ultrafast spin-echo acquisitions were implemented. Specifically, a multiplicative acceleration factor from multiple spin echoes (×32) and compressed sensing (CS) sampling (×8) allowed highly-accelerated 3D Multiple-Modulation-Multiple-Echo (MMME) acquisition. At the same time, the CE-MRI of kidney with Gd-DOTA showed significantly improved signal enhancement for CS-MMME acquisitions (×7) over that of corresponding FLASH acquisitions (×2). Increased positive contrast enhancement and highly accelerated acquisition of extended volume with reduced RF irradiations will be beneficial for oncological and nephrological applications, in which the accurate in vivo 3D quantification of contrast agent concentration is necessary with high temporal resolution.

Comprehensive genomic analysis of rhabdomyosarcoma reveals a landscape of alterations affecting a common genetic axis in fusion-positive and fusion-negative tumors

Despite gains in survival, outcomes for patients with metastatic or recurrent rhabdomyosarcoma remain dismal. In a collaboration between the National Cancer Institute, Children's Oncology Group, and Broad Institute, we performed whole-genome, whole-exome, and transcriptome sequencing to characterize the landscape of somatic alterations in 147 tumor/normal pairs. Two genotypes are evident in rhabdomyosarcoma tumors: those characterized by the PAX3 or PAX7 fusion and those that lack these fusions but harbor mutations in key signaling pathways. The overall burden of somatic mutations in rhabdomyosarcoma is relatively low, especially in tumors that harbor a PAX3/7 gene fusion. In addition to previously reported mutations in NRAS, KRAS, HRAS, FGFR4, PIK3CA, and CTNNB1, we found novel recurrent mutations in FBXW7 and BCOR, providing potential new avenues for therapeutic intervention. Furthermore, alteration of the receptor tyrosine kinase/RAS/PIK3CA axis affects 93% of cases, providing a framework for genomics-directed therapies that might improve outcomes for patients with rhabdomyosarcoma.

SIGNIFICANCE

This is the most comprehensive genomic analysis of rhabdomyosarcoma to date. Despite a relatively low mutation rate, multiple genes were recurrently altered, including NRAS, KRAS, HRAS, FGFR4, PIK3CA, CTNNB1, FBXW7, and BCOR. In addition, a majority of rhabdomyosarcoma tumors alter the receptor tyrosine kinase/RAS/PIK3CA axis, providing an opportunity for genomics-guided intervention.

Comprehensive genomic analysis of rhabdomyosarcoma reveals a landscape of alterations affecting a common genetic axis in fusion-positive and fusion-negative tumors

Despite gains in survival, outcomes for patients with metastatic or recurrent rhabdomyosarcoma remain dismal. In a collaboration between the National Cancer Institute, Children's Oncology Group, and Broad Institute, we performed whole-genome, whole-exome, and transcriptome sequencing to characterize the landscape of somatic alterations in 147 tumor/normal pairs. Two genotypes are evident in rhabdomyosarcoma tumors: those characterized by the PAX3 or PAX7 fusion and those that lack these fusions but harbor mutations in key signaling pathways. The overall burden of somatic mutations in rhabdomyosarcoma is relatively low, especially in tumors that harbor a PAX3/7 gene fusion. In addition to previously reported mutations in NRAS, KRAS, HRAS, FGFR4, PIK3CA, and CTNNB1, we found novel recurrent mutations in FBXW7 and BCOR, providing potential new avenues for therapeutic intervention. Furthermore, alteration of the receptor tyrosine kinase/RAS/PIK3CA axis affects 93% of cases, providing a framework for genomics-directed therapies that might improve outcomes for patients with rhabdomyosarcoma.

SIGNIFICANCE

This is the most comprehensive genomic analysis of rhabdomyosarcoma to date. Despite a relatively low mutation rate, multiple genes were recurrently altered, including NRAS, KRAS, HRAS, FGFR4, PIK3CA, CTNNB1, FBXW7, and BCOR. In addition, a majority of rhabdomyosarcoma tumors alter the receptor tyrosine kinase/RAS/PIK3CA axis, providing an opportunity for genomics-guided intervention.

Massively parallel sequencing reveals an accumulation of de novo mutations and an activating mutation of LPAR1 in a patient with metastatic neuroblastoma

Neuroblastoma is one of the most genomically heterogeneous childhood malignances studied to date, and the molecular events that occur during the course of the disease are not fully understood. Genomic studies in neuroblastoma have showed only a few recurrent mutations and a low somatic mutation burden. However, none of these studies has examined the mutations arising during the course of disease, nor have they systemically examined the expression of mutant genes. Here we performed genomic analyses on tumors taken during a 3.5 years disease course from a neuroblastoma patient (bone marrow biopsy at diagnosis, adrenal primary tumor taken at surgical resection, and a liver metastasis at autopsy). Whole genome sequencing of the index liver metastasis identified 44 non-synonymous somatic mutations in 42 genes (0.85 mutation/MB) and a large hemizygous deletion in the ATRX gene which has been recently reported in neuroblastoma. Of these 45 somatic alterations, 15 were also detected in the primary tumor and bone marrow biopsy, while the other 30 were unique to the index tumor, indicating accumulation of de novo mutations during therapy. Furthermore, transcriptome sequencing on the 3 tumors demonstrated only 3 out of the 15 commonly mutated genes (LPAR1, GATA2, and NUFIP1) had high level of expression of the mutant alleles, suggesting potential oncogenic driver roles of these mutated genes. Among them, the druggable G-protein coupled receptor LPAR1 was highly expressed in all tumors. Cells expressing the LPAR1 R163W mutant demonstrated a significantly increased motility through elevated Rho signaling, but had no effect on growth. Therefore, this study highlights the need for multiple biopsies and sequencing during progression of a cancer and combinatorial DNA and RNA sequencing approach for systematic identification of expressed driver mutations.

Targeting wild-type and mutationally activated FGFR4 in rhabdomyosarcoma with the inhibitor ponatinib (AP24534)

Rhabdomyosarcoma (RMS) is the most common childhood soft tissue sarcoma. Despite advances in modern therapy, patients with relapsed or metastatic disease have a very poor clinical prognosis. Fibroblast Growth Factor Receptor 4 (FGFR4) is a cell surface tyrosine kinase receptor that is involved in normal myogenesis and muscle regeneration, but not commonly expressed in differentiated muscle tissues. Amplification and mutational activation of FGFR4 has been reported in RMS and promotes tumor progression. Therefore, FGFR4 is a tractable therapeutic target for patients with RMS. In this study, we used a chimeric Ba/F3 TEL-FGFR4 construct to test five tyrosine kinase inhibitors reported to specifically inhibit FGFRs in the nanomolar range. We found ponatinib (AP24534) to be the most potent FGFR4 inhibitor with an IC₅₀ in the nanomolar range. Ponatinib inhibited the growth of RMS cells expressing wild-type or mutated FGFR4 through increased apoptosis. Phosphorylation of wild-type and mutated FGFR4 as well as its downstream target STAT3 was also suppressed by ponatinib. Finally, ponatinib treatment inhibited tumor growth in a RMS mouse model expressing mutated FGFR4. Therefore, our data suggests that ponatinib is a potentially effective therapeutic agent for RMS tumors that are driven by a dysregulated FGFR4 signaling pathway.

Abstract 4398: Synthetic lethal siRNA screening to identify novel combinational therapies with Topotecan in neuroblastoma

Despite advances in multimodal treatment, the outcome of neuroblastoma (NB) is still often fatal for children with advanced-stage disease. The topoisomerase-1 inhibitor topotecan is currently a mainstay for both up-front and salvage regimens for NB patients. In order to improve efficacy of single agent therapy, we used high throughput loss of function siRNA screens to identify genes whose inhibition sensitizes cell lines to topotecan treatment. The translation of these silenced-gene-drug interactions into potent synergistic drug-drug combinations for cancer therapy is the ultimate goal.

We screened with the QIAgen human druggable genome kit containing 13910 siRNAs targeting 6878 genes in four NB cell lines, two MYCN-amplified (IMR5 and IMR32) and two non-amplified (SKNAS and NBEB) lines. To reduce the false positive rate mainly due to off-target binding of the seed region of siRNAs (2nd -8th base) to multiple gene transcripts, we performed common seed analysis to eliminate siRNA exhibiting this effect. We then ranked the siRNAs by their activity applying the Redundant siRNA activity (RSA) algorithm and identified 150 genes whose silencing caused a significant decrease in cell survival in combination with topotecan in any of the four cell lines. This list was further filtered to contain only curated drug targets for potential drug combination therapies.

Furthermore, Haystack analysis allowed us to predict target genes based on the siRNA off-target effects in our screens. Using this method, 39 additional transcripts whose 3’-UTR regions contain off-target binding sites for the seeds of multiple, active siRNAs were identified. Additionally, we picked transcription factors predicted by Ingenuity Pathway Analysis (IPA) to regulate our target genes. These hits were verified with three additional siRNAs per gene. In 12-point drug dosage response screens, we evaluated 634 siRNAs targeting 213 genes for significant decrease of the IC50 concentration of topotecan. As expected, the prime target genes for therapeutical intervention are within the DNA double-strand breakage repair pathway. In addition, we also identified other biologically interesting targets ranking high on the list. Based on this hit list, we are now selecting the appropriate drugs targeting a particular gene or an affiliated pathway to test them for synergy with topotecan in the four cell lines. Furthermore, expression profiles are generated for the cell lines in the presence of a low and a high topotecan concentration to examine the biology behind the killing mechanism of the drug. A good correlation of an up-regulated expression with a strong sensitizing effect in the siRNA screens will further validate the significance of our target genes.

Citation Format: Dominik Bogen, Eugen C. Buehler, Pinar Tuzmen, Rajesh Patidar, David Azorsa, Young K. Song, Hongling Liao, Catherine A. Tolman, Xinyu Wen, Jianbin N. He, Scott E. Martin, Jun S. Wei, Javed Khan. Synthetic lethal siRNA screening to identify novel combinational therapies with Topotecan in neuroblastoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4398. doi:10.1158/1538-7445.AM2013-4398

Abstract 2619: Whole genome and transcriptome sequencing identifies an activating mutation of LPAR1 in a patient with metastatic neuroblastoma

Neuroblastoma is the most common extra-cranial solid tumor of childhood, and is one of the most genomically heterogeneous malignances studied to date. Despite advance of multimodal therapies, the current overall survival rate for patient with metastatic neuroblastoma is &lt;40%, and the molecular events that drive the disease are not fully understood. To systematically identify expressed driver oncogenes, we performed whole genome and transcriptome sequencing on an index liver metastasis of neuroblastoma from a young adult patient. Additional transcriptome sequencing was performed on tumor cells from bone marrow taken at diagnosis and from the adrenal primary taken at the time of primary surgical resection. Whole genome sequencing of the index tumor identified 44 somatic small variant mutations in 42 genes and a large hemizygous deletion in the ATRX gene which has been recently implicated in neuroblastoma. Of these 45 somatic alterations, 15 genes including ATRX were found commonly mutated in all three tumors and transcriptome sequencing showed 3 of them (LPAR1, GATA2, and NUFIP1) had high level of expression of the mutant alleles, suggesting potential oncogenic driver roles for these mutated genes. Among these commonly mutated expressed genes, the druggable G-protein coupled receptor LPAR1 was expressed at the highest level in all tumors. Cells expressing the LPAR1 mutant resulted in a significant increase in motility, but had no effect on growth. Further biochemical characterization demonstrated that elevated Rho signaling was responsible for the increased cell mobility mediated by the LPAR1 mutant. Therefore, parallel whole genome and transcriptome sequencing identified a cell motility driver mutation in the LPAR1 gene, and this combinatorial approach may be leveraged for identification of expressed driver mutations in cancer patients for precision therapy.

Citation Format: Jun S. Wei, Peter Johansson, Li Chen, Young K. Song, Catherine Tolman, Samuel Li, Laura Hurd, Rajesh Patidar, Xinyu Wen, Thomas C. Badgett, Adam Cheuk, Jean-Claude Marshall, Patricia Steeg, José Pedro Vaqué Díez, J Silvio Gutkind, Javed Khan. Whole genome and transcriptome sequencing identifies an activating mutation of LPAR1 in a patient with metastatic neuroblastoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2619. doi:10.1158/1538-7445.AM2013-2619

Development of peptide nucleic acid probes for detection of the HER2 oncogene

Peptide nucleic acids (PNAs) have gained much interest as molecular recognition tools in biology, medicine and chemistry. This is due to high hybridization efficiency to complimentary oligonucleotides and stability of the duplexes with RNA or DNA. We have synthesized 15/16-mer PNA probes to detect the HER2 mRNA. The performance of these probes to detect the HER2 target was evaluated by fluorescence imaging and fluorescence bead assays. The PNA probes have sufficiently discriminated between the wild type HER2 target and the mutant target with single base mismatches. Furthermore, the probes exhibited excellent linear concentration dependence between 0.4 to 400 fmol for the target gene. The results demonstrate potential application of PNAs as diagnostic probes with high specificity for quantitative measurements of amplifications or over-expressions of oncogenes.

Synthetic lethal screen identifies NF-κB as a target for combination therapy with topotecan for patients with neuroblastoma

Background

Despite aggressive multimodal treatments the overall survival of patients with high-risk neuroblastoma remains poor. The aim of this study was to identify novel combination chemotherapy to improve survival rate in patients with high-risk neuroblastoma.

Methods

We took a synthetic lethal approach using a siRNA library targeting 418 apoptosis-related genes and identified genes and pathways whose inhibition synergized with topotecan. Microarray analyses of cells treated with topotecan were performed to identify if the same genes or pathways were altered by the drug. An inhibitor of this pathway was used in combination with topotecan to confirm synergism by in vitro and in vivo studies.

Results

We found that there were nine genes whose suppression synergized with topotecan to enhance cell death, and the NF-κB signaling pathway was significantly enriched. Microarray analysis of cells treated with topotecan revealed a significant enrichment of NF-κB target genes among the differentially altered genes, suggesting that NF-κB pathway was activated in the treated cells. Combination of topotecan and known NF-κB inhibitors (NSC 676914 or bortezomib) significantly reduced cell growth and induced caspase 3 activity in vitro. Furthermore, in a neuroblastoma xenograft mouse model, combined treatment of topotecan and bortezomib significantly delayed tumor formation compared to single-drug treatments.

Conclusions

Synthetic lethal screening provides a rational approach for selecting drugs for use in combination therapy and warrants clinical evaluation of the efficacy of the combination of topotecan and bortezomib or other NF-κB inhibitors in patients with high risk neuroblastoma.

Murine rhabdomyosarcoma is immunogenic and responsive to T-cell-based immunotherapy

BACKGROUND

Immunotherapies targeting cellular immunity are currently approved for treatment of melanoma, renal cell carcinoma, and prostate cancer. Studies on the immunogenicity and immune responsiveness of pediatric tumors are limited, therefore, it remains unclear to what extent T-cell-based immunotherapy holds promise for pediatric solid tumors.

PROCEDURE

A new rhabdomyosarcoma cell line (M3-9-M) was derived from an embryonal rhabdomyosarcoma (ERMS) occurring in a C57BL/6 mouse transgenic for hepatocyte growth factor and heterozygous for mutated p53. Primary tumors and metastases derived from M3-9-M were studied for similarities to human ERMS, and for immunogenicity and immune responsiveness.

RESULTS

Primary and metastatic tumors develop after orthotopic injection of M3-9-M into immunocompetent C57BL/6 mice, which mirror human ERMS with regard to histology, gene expression, and metastatic behavior. Whole cell vaccination using irradiated M3-9-M cells or M3-9-M-pulsed dendritic cells (DC)-induced tumor-specific T-cell responses that prevent tumor growth following low-dose tumor injection, and slow tumor growth following higher doses. Administration of anti-CD25 moAbs to deplete CD4(+)CD25(+)FOXP3(+) regulatory T cells prior to tumor vaccination enhanced the potency of the ERMS tumor vaccine. Adoptive immunotherapy with M3-9-M primed T cells plus DC-based vaccination resulted in complete eradication of day 10 M3-9-M derived tumors.

CONCLUSIONS

M3-9-M derived murine ERMS is immunogenic and immunoresponsive; regulatory T cells contribute to immune evasion by murine rhabdomyosarcoma. Adoptive immunotherapy with DC vaccination can eradicate low tumor burdens. Future work will seek to identify the tumor-associated antigens that mediate protective and therapeutic immunity in this model.

Magnetic field anisotropy based MR tractography

Non-invasive measurements of structural orientation provide unique information regarding the connectivity and functionality of fiber materials. In the present study, we use a capillary model to demonstrate that the direction of fiber structure can be obtained from susceptibility-induced magnetic field anisotropy. The interference pattern between internal and external magnetic field gradients carries the signature of the underlying anisotropic structure and can be measured by MRI-based water diffusion measurements. Through both numerical simulation and experiments, we found that this technique can determine the capillary orientation within 3°. Therefore, susceptibility-induced magnetic field anisotropy may be useful for an alternative tractography method when diffusion anisotropy is small at higher magnetic field strength without the need to rotate the subject inside the scanner.