Laura Donovan

CD133 glycosylation is enhanced by hypoxia in cultured glioma stem cells

The cancer stem cell (CSC) marker CD133 is widely expressed in gliomas and employed mostly by use of the CD133/1 antibody which binds the extracellular glycosylated AC133 epitope. CD133 recognition may, however, be affected by its glycosylation pattern and oxygen tension. The present study investigates the effect of oxygen deprivation on CD133 expression and glycosylation status employing a high AC133-expressing glioblastoma multiforme (GBM) cell line, IN699. IN699 cells were cultured under normoxic (21% O2) and hypoxic (3% O2) conditions. CD133 expression was analysed by western blotting (WB), qRT-PCR, immunocytochemistry (ICC) and flow cytometry using the glycosylation-specific antibody CD133/1 and ab19898 which binds the unglycosylated intra-cellular residues of CD133. By flow cytometry, ab19898 detected 94.1% and 96.2% CD133+ cells under normoxia and hypoxia, respectively. Hypoxia significantly increased the percentage of CD133+ cells from 69% to 92% using CD133/1 (p<0.005). Moreover, a significantly higher geomean fluorescence intensity (GMI) was demonstrated by ab19898 (p<0.005) in CD133+ cells. WB and qRT-PCR results were consistent with flow cytometry data. Furthermore, over a period of 72-h incubation under normoxic and hypoxic conditions after autoMACS sorting, an average of 31.8% and 42.2%, respectively, of CD133-negative IN699 cells became positive using CD133/1. Our data show that a) previously reported CD133- cells may have been misidentified using the glycosylation-specific CD133/1 as constitutive expression of CD133 was detected by the intracellular antibody ab19898; b) hypoxia promotes glycosylation status of CD133, indicating possible involvement of glycosylated CD133 in the process of anti-hypoxia-mediated apoptosis.

Childhood cerebellar tumors mirror conserved fetal transcriptional programs

The study of the origin and development of cerebellar tumours has been hampered by the complexity and heterogeneity of cerebellar cells that change over the course of development. We used single-cell transcriptomics to study >60,000 cells from the developing murine cerebellum, and show that different molecular subgroups of childhood cerebellar tumors mirror the transcription of cells from distinct, temporally restricted cerebellar lineages. Sonic Hedgehog medulloblastoma transcriptionally mirrors the granule cell hierarchy as expected, whereas Group 3 medulloblastoma resemble Nestin+ve stem cells, Group 4 medulloblastomas resemble unipolar brush cells, and PFA/PFB ependymoma and cerebellar pilocytic astrocytoma resemble the prenatal gliogenic progenitor cells. Furthermore, single-cell transcriptomics of human childhood cerebellar tumors demonstrates that many bulk tumors contain a mixed population of cells with divergent differentiation. Our data highlight cerebellar tumors as a disorder of early brain development, and provide a proximate explanation for the peak incidence of cerebellar tumors in early childhood.

Abstract 685: GPC2 is an oncogene and immunotherapeutic target in high-risk neuroblastoma

Background: GD2-directed immunotherapeutic strategies have improved outcomes in neuroblastoma; however, the majority of patients treated suffer relapse and GD2 expression on pain fibers causes dose-limiting toxicities. Methods: To identify alternative cell surface immunotherapeutic targets, we compared high-risk neuroblastoma (n=126 tumors) and normal tissue RNA sequencing data (GTEx; n=7859 samples from 31 normal tissues) and prioritized genes by differential and absolute expression and cell surface prediction. Genes were further surveyed for somatic copy number gain and correlative expression with MYCN amplification. Differential protein expression and localization were confirmed in neuroblastoma primary tumors (n=98), patient-derived xenografts (n=32; PDXs), cell lines (n=23), and normal pediatric tissues (n=36). Cell lines were subjected to candidate gene gain and loss of function studies (n=11). Additional pediatric tumor RNA sequencing data was surveyed followed by confirmatory immunohistochemistry (IHC). Finally, candidate specific antibodies were isolated from a human Fab phage library and utilized for antibody-drug conjugate (ADC) engineering followed by cytotoxicity studies. Results: We identified 33 differentially expressed cell surface molecules from which we prioritized glypican-2 (GPC2) for validation given GPC2’s robust differential expression (log-fold change tumor vs. normal tissue = 1.71-9.22; p=1.99 x 10-9-1.88 x10-300), high-level absolute RNA expression (median FPKM=60), and frequent DNA copy number gain associated with higher GPC2 expression (35%, n=182 tumors; p Conclusions: GPC2 is an oncogene and immunotherapeutic target in neuroblastoma and potentially other cancers. Citation Format: Kristopher R. Bosse, Pichai Raman, Maria Lane, Robyn T. Sussman, Jo Lynne Harenza, Daniel Martinez, Sabine Heitzeneder, Zhongyu Zhu, Komal Rathi, Michael Randall, Laura Donovan, Sorana Morrissy, Doncho V. Zhelev, Yang Feng, Jennifer Hwang, Yanping Wang, Bruce Pawel, Tricia Bhatti, Mariarita Santi, Javed Khan, Michael Taylor, Dimiter S. Dimitrov, Crystal Mackall, John M. Maris. GPC2 is an oncogene and immunotherapeutic target in high-risk neuroblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 685. doi:10.1158/1538-7445.AM2017-685

Abstract A019: Chimeric antigen receptors (CARs) as a low-impact treatment of pediatric ependymomas

Ependymoma is the third most common paediatric brain tumor and can occur anywhere along the neuroaxis, the most common location being the posterior fossa (PF). Surgery followed by radiation therapy (>4 years of age) is to date the most effective treatment regimen; chemotherapy is not part of the current standard of care as multiple clinical trials have failed to show any survival benefits. Despite extensive characterization of ependymoma, few credible oncogenes and tumor suppressor genes have been identified, in fact, up to 50% of PF ependymoma cases exhibit a balanced and bland genomic profile. Consequently, actionable mutations are not currently identifiable in the vast majority of cases. We are investigating candidate chimeric antigen receptor (CAR)- strategies to treat posterior fossa-A ependymoma (PFA) — a subtype that has the worst associated prognosis and is found predominately in infants. Probing of our extensive ependymoma gene expression dataset has identified several potential CAR target antigens, including HER2, EPHA2 and IL13Rα2, these have been further verified with tissue microarrays (TMAs). Using our orthotopic xenograft models of PFA ependymoma, we are confident from our preliminary analysis that HER2-positive PFA ependymomas respond to HER2-specific CAR treatment. Furthermore, the use of a TRI-CAR, tailored to target cells expressing EPHA2, IL13Rα2 and HER2, both collectively and independently, increases the efficacy and specificity as a therapy for both primary and recurrent ependymoma. To ensure we are using the most effective negative controls when confirming the therapeutic response of our CARs, we are silencing our genes of interest in our patient-derived ependymoma lines using shRNA and CRISPR-technology for HER2, EPHA2 and IL13Rα2. Whole-genome and whole-exome sequencing has demonstrated, that in comparison to PFB ependymomas, PFA tumors have more methylated CpG sites, and more genes that are transcriptionally silenced by CpG hypermethylation. To reduce this silencing and potentially improve therapeutic response to our CARs, we are using Azacitadine in combination with our CAR therapies. In parallel with our pre-clinical trials, we are performing safety trials to assess the administration of intravenous versus intrathecal HER2 CAR delivery. Patients presenting with a brain tumor frequently present with a leaky blood-CSF and blood-Brain barrier, therefore we aim to observe whether CARs injected intrathecally can be found within the blood and vice versa. Using a HER2 Copy Number Assay, we observed two significant results: firstly, HER2 CARs injected intrathecally, in the presence of a HER2-positive brain tumor, remain within the central nervous and are not found within the blood; secondly, HER2 CARs administered intraventrically in the presence of a HER2-positive brain tumor, migrate to the CSF (P = 0.009). Results from this project have the potential to create a paradigm shift in our approach to the treatment of ependymoma, including the initiation of a clinical trial for children with PFA ependymoma. This technology has the real potential to improve cure rates whilst also dramatically improving the quality of life for surviving patients by reducing the impact that current treatments have on normal brain development. Citation Format: Laura K. Donovan, Kevin J. Bielamowicz, Alex Manno, Nabil Ahmed, Michael D. Taylor. Chimeric antigen receptors (CARs) as a low-impact treatment of pediatric ependymomas [abstract]. In: Proceedings of the Second CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; 2016 Sept 25-28; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(11 Suppl):Abstract nr A019.

Abstract 2384: High-complexity neutral genomic barcoding technology reveals extensive clonal dynamics in multiple human cancer model systems

Increasing evidence of extensive intratumoral heterogeneity, along with advances in high-throughput in vivo functional genetic screening technologies, have together highlighted the need to observe growth in cancer models at the clonal level. To address this, we have designed, constructed and validated multiple high-diversity lentivirally delivered barcode libraries, which utilize next-gen sequencing technology to read out millions of clones in heterogeneous cancer populations. These libraries can be used to address a multitude of biological questions in many cancer model systems. To date, we have completed, sequenced and analyzed three different types of barcoding applications to explore clonal dynamics in a variety of human cancer models. First, we tested the serial limiting dilution analysis (LDA) assay for tumor initiating cells (TICs) in patient-derived colon tumor models. In the LDA assay, a range of cell dilutions, down to a single cell, are transplanted into immunocompromised mice. The TIC frequency is calculated using a single-hit model from the proportion of tumors established at each dose. However, quantifying minimum cell numbers required for tumor formation does not reveal the actual diversity of clonal contribution during tumour engraftment and progression. In fact, recent research suggests that the single-hit model, which assumes a static hierarchy of intrinsically determined initiating cells, may not be biologically relevant as some clones may have the potential to form or contribute to a tumor only in specific environment, or in cooperation with another clone. Our barcoded, serial LDAs show interesting and informative patterns of clonal dynamics. Second, we have performed clonal lineage tracing on established human cancer cell lines in vitro compared to in vivo. Our findings demonstrate the presence of TICs in standard cell lines and serve as precursors to future in vivo genetic screens by defining upper limits of library size. Finally, we used a patient-derived xenograft model of brain tumor metastasis to investigate the presence of pre-existing metastatic clones with site-specific homing abilities. In summary, given the extensive heterogeneity present in cancer models, we propose the use of high-complexity barcoding technology to validate novel cancer targets in xenograft models, including LDAs and metastasis models. Furthermore, we suggest the use of barcodes for careful optimization of the system before genetic screens in animal models. Citation Format: Allison ML Nixon, Kevin R. Brown, Jennifer Haynes, Laura K. Donovan, Michael D. Taylor, Catherine W. O’Brien, Jason Moffat. High-complexity neutral genomic barcoding technology reveals extensive clonal dynamics in multiple human cancer model systems. [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 2384.