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Supplementary Figures S1-S3 from BRAF Activation Induces Transformation and Then Senescence in Human Neural Stem Cells: A Pilocytic Astrocytoma Model

Purpose: BRAF is frequently activated by gene fusion or point mutation in pilocytic astrocytoma, the most common pediatric brain tumor. We investigated the functional effect of constitutive BRAF activation in normal human neural stem and progenitor cells to determine its role in tumor induction in the brain.Experimental Design: The constitutively active BRAFV600E allele was introduced into human neurospheres, and its effects on MAPK (mitogen-activated protein kinase) signaling, proliferation, soft agarose colony formation, stem cell phenotype, and induction of cellular senescence were assayed. Immunohistochemistry was used to examine p16INK4a levels in pilocytic astrocytoma.Results: BRAFV600E expression initially strongly promoted colony formation but did not lead to significantly increased proliferation. BRAFV600E-expressing cells subsequently stopped proliferating and induced markers of oncogene-induced senescence including acidic β-galactosidase, PAI-1, and p16INK4a whereas controls did not. Onset of senescence was associated with decreased expression of neural stem cell markers including SOX2. Primary pilocytic astrocytoma cultures also showed induction of acidic β-galactosidase activity. Immunohistochemical examination of 66 pilocytic astrocytomas revealed p16INK4a immunoreactivity in the majority of cases, but patients with tumors negative for p16INK4a had significantly shorter overall survival.Conclusions: BRAF activation in human neural stem and progenitor cells initially promotes clonogenic growth in soft agarose, suggesting partial cellular transformation, but oncogene-induced senescence subsequently limits proliferation. Induction of senescence by BRAF may help explain the low-grade pathobiology of pilocytic astrocytoma, whereas worse clinical outcomes associated with tumors lacking p16INK4a expression could reflect failure to induce senescence or an escape from oncogene-induced senescence. Clin Cancer Res; 17(11); 3590–9. ©2011 AACR.

Genome instability and immune evasion are both defining hallmarks of cancer. Tumorigenesis is frequently initiated when there is DNA damage to a proto-oncogene or tumor suppressor gene and DNA repair mechanisms are lost or insufficient to correct the damage; immune evasion then prevents the host immune system from recognizing these transformed cells. Therapies targeting genomic instability and immune evasion have been effectively used to treat cancer. Genotoxic therapies such as chemoradiation have been employed in cancer treatments for several decades, while immunotherapy is a relatively new class of cancer therapy that has led to disease regression even in patients with advanced cancer. Several recent studies have shown synergy between both classes of therapy targeting these two defining hallmarks of cancer, and different mechanisms are proposed to be involved. Here, we review the different classes of DNA damage, their links to cancer, and their contribution to immunotherapy responses, as well as the different models that are currently being used to study tumor–immune interactions.

Malignant phyllodes tumors (PT) are rare aggressive fibroepithelial neoplasms with high metastatic potential and lack effective therapy. We established a patient-derived xenograft (PDX) and cell line model (designated MPT-S1) of malignant PT which demonstrated clinical response to pazopanib. Whole exome sequencing identified somatic mutations in TP53, RB1, MED12, and KMT2D. Immunohistochemistry and genomic profiles of the tumor, PDX and cell line were concordant. In keeping with clinical observation, pazopanib reduced cell viability in a dose-dependent manner and evoked apoptosis, and led to significant abrogation of in vivo tumor growth. Whole transcriptomic analysis revealed that pazopanib decreased expression of genes involved in oncogenic and apoptosis signaling. We also observed decreased expression of ENPP1, with known roles in cancer invasion and metastasis, as well as STING pathway upregulation. Accordingly, pazopanib induced micronuclei formation, and evoked phospho-TBK1 and PD-L1 expression. In an additional cohort of malignant PT (n = 14), six (42.9%) showed comparable or higher levels of ENPP1 relative to MPT-S1, highlighting its potential role as a therapeutic target. In conclusion, we established MPT-S1, a new PDX and cell line model, and provided evidence for the clinical efficacy of pazopanib in malignant PT.

We have previously shown that glioblastoma stem cells (GSCs) are enriched in the hypoxic tumor microenvironment, and that monocarboxylate transporter-4 (MCT4) is critical for mediating GSC signaling in hypoxia. Basigin is involved in many physiological functions during early stages of development and in cancer and is required for functional plasma membrane expression of MCT4. We sought to determine if disruption of the MCT-Basigin interaction may be achieved with a small molecule. Using a cell-based drug-screening assay, we identified Acriflavine (ACF), a small molecule that inhibits the binding between Basigin and MCT4. Surface plasmon resonance and cellular thermal-shift-assays confirmed ACF binding to basigin in vitro and in live glioblastoma cells, respectively. ACF significantly inhibited growth and self-renewal potential of several glioblastoma neurosphere lines in vitro, and this activity was further augmented by hypoxia. Finally, treatment of mice bearing GSC-derived xenografts resulted in significant inhibition of tumor progression in early and late-stage disease. ACF treatment inhibited intratumoral expression of VEGF and tumor vascularization. Our work serves as a proof-of-concept as it shows, for the first time, that disruption of MCT binding to their chaperon, Basigin, may be an effective approach to target GSC and to inhibit angiogenesis and tumor progression.

Ubiquitin-specific proteases (USPs) constitute the largest family of deubiquitinating enzymes, whose catalytic competency is often modulated by their binding partners through unknown mechanisms. Here we report a series of crystallographic and biochemical analyses of an evolutionarily conserved deubiquitinase, USP12, which is activated by two β-propeller proteins, UAF1 and WDR20. Our structures reveal that UAF1 and WDR20 interact with USP12 at two distinct sites far away from its catalytic center. Without increasing substrate affinity of USP12, the two β-propeller proteins potentiate the enzyme through different allosteric mechanisms. UAF1 docks at the distal end of the USP12 Fingers domain and induces a cascade of structural changes that reach to a critical ubiquitin-contacting loop adjacent to the catalytic cleft. By contrast, WDR20 anchors at the base of this loop and remotely modulates the catalytic center of the enzyme. Our results provide a mechanistic example for allosteric activation of USPs by their regulatory partners.

BRCA1 deficient tumor cells have defects in homologous-recombination repair and in replication fork stability, resulting in PARP inhibitor sensitivity. Here, we demonstrate that a deubiquitinase, USP1, is upregulated in tumors with mutations in BRCA1. Knockdown or inhibition of USP1 resulted in replication fork destabilization and decreased viability of BRCA1 deficient cells, revealing a synthetic lethal relationship. USP1 binds to and is stimulated by fork DNA. A truncated form of USP1, lacking its DNA binding region, was not stimulated by DNA and failed to localize and protect replication forks. Persistence of monoubiquitinated PCNA at the replication fork was the mechanism of cell death in the absence of USP1. Taken together, USP1 exhibits DNA-mediated activation at the replication fork, protects the fork, and promotes survival in BRCA1 deficient cells. Inhibition of USP1 may be a useful treatment for a subset of PARP inhibitor resistant BRCA1 deficient tumors with acquired replication fork stabilization.

INTRODUCTION: More than 50% of high-grade serous ovarian cancers (HGSOC) are deficient in Homologous Recombination (HR) DNA repair, predominantly due to inactivation of BRCA1 or BRCA2 genes. HR-deficient cancers are sensitive to inhibitors of Poly-ADP Ribose Polymerase (PARP), and PARP inhibitors (PARPi's) have shown promising efficacy in the treatment of HGSOC. However, the majority of HGSOC patients will eventually develop resistance to PARPi's, and no overall survival benefit has been reported. Clinically, best characterized mechanism of PARPi resistance is restoration of BRCA1/2 protein expression accounting for 20-50% of clinical cases. Recently, emerging preclinical evidence has emphasized the role of replication fork protection in PARPi resistance. In addition, transcriptional regulation of the DNA damage response (DDR) proteins, including 53BP1, have been shown to contribute to PARPi resistance. However, the lack of understanding on the functional heterogeneity of the different PARP inhibitor resistance mechanisms has hampered the clinical targeting and development of biomarkers for acquired PARPi resistance in HGSOC. RESULTS: To understand the dynamics and origin of PARPi resistance, we generated a TP53-/- and BRCA1-/- deficient epithelial (RPE) cell line using the CRISPR/Cas9 system. These cells are deficient in HR, and therefore are hypersensitive to PARPi in vitro. Using cyclic exposure of increasing concentrations of the PARPi Niraparib, we selected a cell population that were resistant to high concentrations (µM range) of the drug. We next isolated single cell clones from the resistant pool and performed deep functional profiling. As expected, the clones were resistant to multiple PARPi, including Niraparib, Olaparib and Talazoparib, and showed decreased DNA damage after PARPi treatment. However, none of the clones has restored BRCA1 protein expression. In functional assays, some clones had different levels of restored HR, and others showed a predominantly fork-stable, non HR-restored phenotype. Upon cytogenetic analyses, the parental RPETP53-/-BRCA1-/- cells exhibited high clonal heterogeneity in terms of ploidy, whereas the PARPi resistant clones are mostly triploid. Interestingly, the HR-restored clones have lower levels of baseline chromosomal aberrations; however, mitomycin C induced chromosomal breaks in all the clones. In flow cytometry-based cell cycle profiling, the clones retained the G2/M accumulation upon PARPi treatment, similar to the parental RPETP53-/-BRCA1-/- cells. Interestingly, all PARPi resistant clones show decreased levels of the DDR protein KAP1, and divergent expression levels of other DDR proteins, such as 53BP1. Importantly, the clones show significant heterogeneity in terms of sensitivity to cisplatin, as well as to DDR targeting agents, such as inhibitors of ATR and CHK1. CONCLUSIONS: We have engineered BRCA1- deficient cells that are resistant to PARPi, and show that subclones of from these cells have significant functional heterogeneity in DNA repair dynamics, and are differentially vulnerable to DDR targeting agents. Importantly, our model system suggests that acquired PARP inhibitor resistance involves the adoption of several distinct resistance mechanisms that are potentially linked to DDR regulation. To enable clinical translation of our findings, we are in the process of performing genomic and transcriptomic profiling to discover the genomic evolution, common vulnerabilities, and novel biomarkers for acquired PARPi resistance in HGSOC. Citation Format: Anniina Färkkilä, Alfredo Rodriquez, Jaana Olkkonen, Larissa Sambel, Julieta Dominiquez, Niraj Joshi, Connor Clairmont, Jia Zhou, Kah-Suan Lim, Sampsa Hautaniemi, and Alan D'Andrea. FUNCTIONAL HETEROGENEITY OF ACQUIRED PARP INHIBITOR RESISTANCE IN BRCA1-DEFICIENT CELLS [abstract]. In: Proceedings of the 12th Biennial Ovarian Cancer Research Symposium; Sep 13-15, 2018; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2019;25(22 Suppl):Abstract nr NT-092.

Hypoxic regions are frequent in glioblastoma (GBM), the most common type of malignant adult brain tumor, and increased levels of tumor hypoxia have been associated with worse clinical outcomes. To unmask genes important in hypoxia, we treated GBM neurospheres in hypoxia and identified monocarboxylate transporter-4 (MCT4) as one of the most upregulated genes. To investigate the clinical importance of MCT4 in GBM, we examined clinical outcomes and found that MCT4 overexpression is associated with shorter patient survival. Consistent with this, MCT4 upregulation correlated with the aggressive mesenchymal subset of GBM, and MCT4 downregulation correlated with the less aggressive G-CIMP (Glioma CpG Methylator Phenotype) subset of GBM. Immunohistochemical analysis of tissue microarrays confirmed that MCT4 protein levels were increased in high-grade as compared with lower-grade astrocytomas, further suggesting that MCT4 is a clinically relevant target. To test the requirement for MCT4 in vitro, we transduced neurospheres with lentiviruses encoding short-hairpin RNAs (shRNAs) against MCT4, resulting in growth inhibition of 50–80% under hypoxia in two lines. MCT4 knockdown was associated with a decreased percentage of cells expressing the stem-cell marker CD133 and increased apoptotic fraction. We also found that flow-sorted CD133-positive cells had almost sixfold higher MCT4 levels than CD133-negative cells, suggesting that the stem-like population might have a greater requirement for MCT4. Most importantly, MCT4 silencing also slowed GBM intracranial xenograft growth in vivo. Interestingly, whereas MCT4 is a well-characterized lactate exporter, we found that both intracellular and extracellular lactate levels did not change following MCT4 silencing, suggesting a novel lactate export-independent mechanism for growth inhibition in GBMs. To identify this potential mechanism, we performed microarray analysis on control and shMCT4-expressing neurospheres and found a dramatic reduction in the expression of multiple Hypoxia-Inducible Factor (HIF)-regulated genes following MCT4 knockdown. The overall reduction in HIF transcriptional response was further validated using a hypoxia response element (HRE)-dependent green-fluorescent protein (GFP) reporter line.

Pediatric low-grade astrocytomas are the most common brain tumors in children. They can have similar microscopic and clinical features, making accurate diagnosis difficult. For patients whose tumors are in locations that do not permit full resection, or those with an intrinsically aggressive biology, more effective therapies are required. Until recently, little was known about the molecular changes that drive the initiation and growth of pilocytic and other low-grade astrocytomas beyond the association of a minority of cases, primarily in the optic nerve, with neurofibromatosis type 1. Over the past several years, a wide range of studies have implicated the BRAF oncogene and other members of this signaling cascade in the pathobiology of pediatric low-grade astrocytoma. In this review, we attempt to summarize this rapidly developing field and discuss the potential for translating our growing molecular knowledge into improved diagnostic and prognostic biomarkers and new targeted therapies.

Inhaled oligonucleotide is an emerging therapeutic modality for various common respiratory diseases, including obstructive airway diseases like asthma and chronic obstructive pulmonary disease (COPD) and restrictive airway diseases like idiopathic pulmonary fibrosis (IPF). The advantage of direct accessibility for oligonucleotide molecules to the lung target sites, bypassing systemic administration, makes this therapeutic approach promising with minimized potential systemic side effects. Asthma, COPD, and IPF are common chronic respiratory diseases, characterized by persistent airway inflammation and dysregulated tissue repair and remodeling, although each individual disease has its unique etiology. Corticosteroids have been widely prescribed for the treatment of asthma, COPD, and IPF. However, the effectiveness of corticosteroids as an anti-inflammatory drug is limited by steroid resistance in severe asthma, the majority of COPD cases, and pulmonary fibrosis. There is an urgent medical need to develop target-specific drugs for the treatment of these respiratory conditions. Oligonucleotide therapies, including antisense oligonucleotide (ASO), small interfering RNA (siRNA), and microRNA (miRNA) are now being evaluated both pre-clinically and clinically as potential therapeutics. The mechanisms of action of ASO and siRNA are highly target mRNA specific, ultimately leading to target protein knockdown. miRNA has both biomarker and therapeutic values, and its knockdown by a miRNA antagonist (antagomir) has a broader but potentially more non-specific biological outcome. This review will compile the current findings of oligonucleotide therapeutic targets, verified in various respiratory disease models and in clinical trials, and evaluate different chemical modification approaches to improve the stability and potency of oligonucleotides for the treatment of respiratory diseases.

Homologous-recombination (HR) deficient tumors with BRCA1 and BRCA2 mutations exhibit replication fork stability defects. To date, PARP inhibitors are the only targeted therapy available in the clinic against HR deficient tumors, and alternative therapies are needed. In this study, we found a deubiquitinase, USP1, to be significantly upregulated in tumors with mutations in BRCA1. SiRNA mediated silencing or small molecule inhibition of USP1 activity resulted in replication fork destabilization and decreased viability of BRCA1 deficient cells, revealing a synthetic lethal relationship between USP1 and BRCA1. The cofactor of USP1, UAF1, had previously been shown to have DNA-binding activity. We observed that USP1 independently binds to and is stimulated by fork DNA. It is therefore the first known deubiquitinase (DUB) to be directly regulated by DNA binding. A truncated form of USP1, lacking its DNA binding region, was not stimulated by DNA and failed to localize and protect the replication fork. Persistence of monoubiquitinated PCNA at the replication fork was the mechanism of fork destabilization and cell death in the absence of USP1. Loss of monoubiquitinated PCNA, resulting from RAD18 knockdown, rescued the sensitivity and replication fork instability induced by USP1 inhibition. USP1 therefore is the first DUB enzyme exhibiting DNA-mediated activation at the replication fork, and is required for fork protection in BRCA1 deficient cells. We propose small molecule inhibitors against USP1 as a therapeutic option for BRCA1 deficient cancers. Citation Format: Kah Suan Lim, Heng Li, Emma A. Roberts, Emily F. Gaudiano, Connor Clairmont, Karthikeyan Ponnienselvan, Jessica C. Liu, Kalindi Parmar, Ning Zheng, Alan D'Andrea. USP1 is required for replication fork stability in BRCA1-deficient tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 333.

Monocarboxylate transporters, constitute a family (SLC16) of proton-linked plasma membrane transporters that carry molecules containing a single carboxylate group across biological membranes. Basigin (CD147), is involved in many physiological functions during early stages of development and in cancer. Basigin has been shown to be required for functional plasma membrane expression of Monocarboxylate transporter-1 and Monocarboxylate transporter-4. Using a cell-based screening assay, we identified acriflavine, a small molecule that inhibits the binding between Basigin and Monocarboxylate transporters in vitro and in vivo. Surface Plasmon Resonance analysis confirmed direct binding of acriflavine to Basigin’s immunoglobulin extracellular domain with a low binding constant (kD) of 0.16µM. Acriflavine inhibits normoxic growth of glioma stem cells in vitro and this activity is augmented by hypoxia or by expression of oxygen-stable mutant forms of HIF-1α or HIF-2α. Treatment of mice bearing established glioma stem cell-derived xenografts resulted in inhibition of tumor growth. Acriflavine treatment inhibited intratumoral expression of the angiogenic cytokine vascular endothelial growth factor and tumor vascularization. Our work shows that disruption of monocarboxylate transporter binding to Basigin is an effective approach to target glioma stem cells. Citation Format: Raffaella Spina, Dillon M. Voss, Kah Suan Lim, Constance J. Jeffery, Eli E. Bar. Disruption of Monocarboxylate transporter-4 Basigin interaction as an effective strategy to inhibit hypoxic response, tumor growth and vascularization, and stem cell phenotype in human glioblastoma in vitro and in vivo [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 5023. doi:10.1158/1538-7445.AM2017-5023

The transcriptional response promoted by hypoxia-inducible factors has been associated with metastatic spread of uveal melanoma. We found expression of hypoxia-inducible factor 1α (HIF-1α) protein in well-vascularized tumor regions as well as in four cell lines grown in normoxia, thus this pathway may be important even in well-oxygenated uveal melanoma cells. HIF-1α protein accumulation in normoxia was inhibited by rapamycin. As expected, hypoxia (1% pO2) further induced HIF-1α protein levels along with its target genes VEGF and LOX. Growth in hypoxia significantly increased cellular invasion of all 5 uveal melanoma lines tested, as did the introduction of an oxygen-insensitive HIF-1α mutant into Mel285 cells with low HIF-1α baseline levels. In contrast, HIF-1α knockdown using shRNA significantly decreased growth in hypoxia, and reduced by more than 50% tumor invasion in four lines with high HIF-1α baseline levels. Pharmacologic blockade of HIF-1α protein expression using digoxin dramatically suppressed cellular invasion both in normoxia and in hypoxia. We found that Notch pathway components, including Jag1-2 ligands, Hes1-Hey1 targets and the intracellular domain of Notch1, were increased in hypoxia, as well as the phosphorylation levels of Erk1-2 and Akt. Pharmacologic and genetic inhibition of Notch largely blocked the hypoxic induction of invasion as did the pharmacologic suppression of Erk1-2 activity. In addition, the increase in Erk1-2 and Akt phosphorylation by hypoxia was partially reduced by inhibiting Notch signaling. Our findings support the functional importance of HIF-1α signaling in promoting the invasive capacity of uveal melanoma cells in both hypoxia and normoxia, and suggest that pharmacologically targeting HIF-1α pathway directly or through blockade of Notch or Erk1-2 pathways can slow tumor spread.

Effective pharmacological intervention of advanced hepatocellular carcinoma (HCC) is currently lacking. Despite the use of tyrosine kinase inhibitors (TKIs) for the targeted therapy of several malignancies, no agent has been developed to specifically interfere with the oncogenic tyrosine kinase signaling aberrations found in HCC. Therefore, we adopted an orthogonal biological phenotypic screening approach to uncover candidate compounds: based on a potent cytotoxicity toward HCC-derived cell lines, and minimal toxicity toward normal liver cells. Given the success of indolinone as a chemical scaffold in deriving potent multi-kinase inhibitors (e.g. sunitinib), we screened a group of newly synthesized benzylidene-indolinones. Among the candidates, E/Z 6-Chloro-3-(3-trifluoromethyl-benzyliden)-1,3-dihydroindol-2-one (compound 47 ) exhibited potent anti-proliferative, anti-migratory, pro-apoptotic properties and good safety profile as compared to known multi-targeted tyrosine kinase inhibitors sunitinib and sorafenib. Additionally, an accompanying suppression of alpha-fetoprotein (AFP) transcription, an HCC tumor marker, implies a favorable selectivity and efficacy on HCC. The in vivo efficacy was demonstrated in an HCC xenograft where 47 was administered once weekly (60 mg/kg) and suppressed tumor burden to the same extent as sorafenib (30 mg/kg daily). A receptor tyrosine kinase (RTK) array study revealed promising inhibition of multiple tyrosine kinases such as IGF-1R, Tyro3 and EphA2 phosphorylation. Gene silencing of these targets ameliorated the cytotoxic potential of 47 on the HuH7 cell line, thereby implicating their contribution to the tumorigenicity of HCC. Hence, 47 exhibits potent anti-cancer effects on HCC cell lines, and is a suitable lead for developing multi-targeted kinase inhibitors of relevance to HCC.

Purpose: BRAF is frequently activated by gene fusion or point mutation in pilocytic astrocytoma, the most common pediatric brain tumor. We investigated the functional effect of constitutive BRAF activation in normal human neural stem and progenitor cells to determine its role in tumor induction in the brain. Experimental Design: The constitutively active BRAFV600E allele was introduced into human neurospheres, and its effects on MAPK (mitogen-activated protein kinase) signaling, proliferation, soft agarose colony formation, stem cell phenotype, and induction of cellular senescence were assayed. Immunohistochemistry was used to examine p16INK4a levels in pilocytic astrocytoma. Results: BRAFV600E expression initially strongly promoted colony formation but did not lead to significantly increased proliferation. BRAFV600E-expressing cells subsequently stopped proliferating and induced markers of oncogene-induced senescence including acidic β-galactosidase, PAI-1, and p16INK4a whereas controls did not. Onset of senescence was associated with decreased expression of neural stem cell markers including SOX2. Primary pilocytic astrocytoma cultures also showed induction of acidic β-galactosidase activity. Immunohistochemical examination of 66 pilocytic astrocytomas revealed p16INK4a immunoreactivity in the majority of cases, but patients with tumors negative for p16INK4a had significantly shorter overall survival. Conclusions: BRAF activation in human neural stem and progenitor cells initially promotes clonogenic growth in soft agarose, suggesting partial cellular transformation, but oncogene-induced senescence subsequently limits proliferation. Induction of senescence by BRAF may help explain the low-grade pathobiology of pilocytic astrocytoma, whereas worse clinical outcomes associated with tumors lacking p16INK4a expression could reflect failure to induce senescence or an escape from oncogene-induced senescence. Clin Cancer Res; 17(11); 3590–9. ©2011 AACR.

MTR-03. ATRX REDUCTION PROMOTES ALKYLATING AGENT RESISTANCE AND XENOGRAFT GROWTH IN A SUBSET OF GLIOMAS Ming Yuan, Ping An, Kah Suan Lim, Isabella Taylor, Fausto Rodriguez, Eric Raabe, and Charles Eberhart; Johns Hopkins University, Baltimore, MD, USA BACKGROUND:Loss ofATRXfunctionhas been implicated inalternative lengthening of telomeres (ALT) and is common in IDH mutant astrocytoma of varying grades. However, the functional effects of ATRX loss on glioma growth are not clear, although it has been suggested that it can modulate response to ATR inhibitors such as VE-821. METHODS: We evaluated the ALT-positive GBM neurosphere line JHH-GBM14, which retains ATRX expression in a subset of cells, the ALT-negative neurosphere line 040821 and LN229 cells. Two distinct shRNA were used to suppress ATRX protein expression. RESULTS: ATRX knockdown had no effect on the overall in vitro growth of the three lines, but GBM14 cells became resistant to temozolamide and hydroxyurea after ATRX knockdown, while the two ALT-negative lines did not. A modest, non-significant increase in radiation resistance was also noted. Sensitivity to the ATR inhibitor VE-821 was not affected by decreased ATRX levels in any of the three lines. Interestingly, clonogenic growth of GBM14, theexpression of several stemcellmarkers, aswellas its ability togenerate large flank and intracranial xenografts was increased by ATRX knockdown, while these effects were not seen in 040821 GBM neurospheres. CONCLUSIONS: While ATRX knockdown had little effect on in vitro tumor growth, it dramatically affected the treatment response, clonogenicity and in vivo growth of ALT-positive GBM14 cells, but not two GBM models lacking ALT. These data suggest that in some GBM, ATRX can modulate growth and treatment sensitivity as well as affecting telomere biology. Neuro-Oncology 17:v124–v129, 2015. doi:10.1093/neuonc/nov219.3 Published by Oxford University Press on behalf of the Society for Neuro-Oncology 2015.

Glioblastomas (GBM) contain a hypoxic core surrounded by proliferative cells. Our group and others have shown that GBM stem cells favor a hypoxic microenvironment, and it is believed that many reside in the tumor core. Conventional therapies target the tumor bulk, but may spare stem cells in the hypoxic niche. To patch this therapeutic loophole, we sought to target the GBM stem cell microenvironment by identifying genes that are important for survival in hypoxia. We identified monocarboxylate transporter 4 (MCT4) as one of the most upregulated genes in our GBM neurosphere lines in response to hypoxia. Clinically, GBM patients with a two-fold or more upregulation of MCT4 have a significantly shorter survival (p = 0.036) than patients with intermediate expression. Consistent with this data, MCT4 upregulation correlated with the aggressive mesenchymal subset of GBM (p Citation Format: Kah Suan Lim, Kah Jing Lim, Brent A. Orr, Antoinette C. Price, Charles G. Eberhart, Eli E. Bar. Silencing MCT4 inhibits GBM growth, HIF response, and CD133-positive fraction in a lactate-independent fashion. [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 2930. doi:10.1158/1538-7445.AM2013-2930

Melanomas arising from the uveal tract of the eye represent the most frequent primary intraocular malignancy in adults and are the second most common type of melanoma. Uveal melanomas are prone to disseminate hematogenously to the liver, and have an overall survival rate of approximately 50%. Hypoxia-inducible factor 1α (HIF1α), a master transcriptional regulator of the hypoxic response, is strongly associated with aggressive uveal melanomas. Elevated expression of one of the HIF target gene lysyl oxidase (LOX) has been found at the invasive front of primary tumors, and is associated with shorter metastasis-free survival. Here we investigated the mechanism responsible for the prometastatic effect of HIF1α in uveal melanoma. Western blot examination of HIF1α and HIF2α proteins in uveal melanoma cell lines grown in normoxia (21% pO2) and in hypoxia (1% pO2) revealed HIF2α to be low. In contrast, HIF1α protein was relatively abundant in the OCM1, OCM3, OMM1, Mel290 and 92.1 uveal melanoma lines grown in normoxia, and was further induced by up to 5 fold in hypoxia. The mRNA levels of VEGF and LOX, two transcriptional targets of HIF1α, were also induced by 2 to 4 fold in hypoxia. Interestingly, while hypoxia reduced the growth of these lines as measured by MTS assay, low oxygen tension increased the ability of uveal melanoma cells to invade Matrigel by 2 to 5 fold. Genetic suppression of HIF1α expression through shRNA in OCM1 and 92.1 cells significantly decreased cellular growth in hypoxia (p Citation Format: Laura Asnaghi, Michael H. Lin, Kah Suan Lim, Kah Jing Lim, Eli E. Bar, Charles G. Eberhart. Hypoxia-inducible factor 1α (HIF1α) has a prometastatic effect in uveal melanoma . [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 3776. doi:10.1158/1538-7445.AM2013-3776

Glioblastomas (GBM) are the most common adult malignant brain tumors and contain a hypoxic/necrotic core surrounded by proliferative cells. To unmask genes important in hypoxia, we exposed 2 GBM neurosphere lines, HSR-GBM1 and JHH-GBM10, to 1% and 21% oxygen levels for 24 hours and compared gene expression using Agilent oligonucleotide microarrays. We identified SLC16A3 (Monocarboxylate transporter-4, MCT4) as one of the most upregulated genes in response to hypoxia. To investigate the clinical importance of MCT4 in GBM, we examined the Kaplan-Meier survival curves of glioma patients using public databases. We found that patients with upregulation of MCT4 (≥2.0X) have a significantly shorter survival (p Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3483. doi:1538-7445.AM2012-3483

Pilocytic astrocytomas are the most common pediatric brain tumor. They are low grade neoplasms, and in some cases can spontaneously stop growing or regress. The recent discovery of constitutive BRAF activation in the majority of pilocytic astrocytomas, due either to gene duplication/fusion or point mutation, suggests a possible molecular basis for this relatively benign pathobiology. Oncogenic BRAF-induced senescence has previously been identified in benign melanocytic nevi and colonic polyps, but whether it also occurs in pilocytic astrocytomas is not clear. To investigate this, we examined the senescence marker acidic beta-galactosidase in low passage pilocytic astrocytoma cultures established from freshly resected tumors. Two of these cultures, tested at passages 2 to 3, were derived from tumors that contained KIAA1549:BRAF fusions, and both expressed the senescence marker in over half of the cells. Another culture tested at passage 3 was also strongly positive for acidic beta-galactosidase, but the genetic status of its parent tumor is not known. A final culture came from a pilocytic astrocytoma lacking the KIAA1549:BRAF fusion, or an activating V600E BRAF point mutation, and was negative for the senescence marker, but was tested at passage 10. To help confirm these effects in vivo, we immunostained a tissue microarray containing 78 pilocytic astrocytoma for p16 and p53, both of which have been implicated in oncogene-induced senescence in other tumor types. The majority of pilocytic astrocytoma expressed p16, but the 13% of tumors lacking this senescence marker were associated with significantly shorter overall survival (p = 0.0002). Patients whose pilocytic astrocytomas lacked p16 were also older (mean age 25 years) as compared to those with intermediate (mean age 12 years) or high expressing tumors (mean age 7 years). Immunohistochemical analysis of p53 revealed much weaker staining, and only 18 tumors were positive, but expression correlated positively with that of p16 (Spearman r = 0.45, p = 0.0001). Our data suggest that the low-grade phenotype of pilocytic astrocytomas may be due to oncogene-induced senescence driven by KIAA1549:BRAF fusions or BRAF V600E point mutations, and that expression of senescence markers in vivo is associated with younger age at presentation and better clinical outcomes. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3459. doi:10.1158/1538-7445.AM2011-3459

In pilocytic astrocytomas, the primary molecular alteration is BRAF activation occurring via gene duplication/fusion or V600E point mutation. To investigate the mechanisms by which BRAF activation leads to transformation, BRAF V600E was introduced into cortical and cerebellar human fetal neural stem and progenitor cells. Overexpression of BRAF V600E did not lead to increases in cellular proliferation compared to controls, but did promote colony forming ability in soft agar. However, after initially growing well, BRAF V600E expressing cells subsequently showed decreased proliferation as compared to control cells, though they remained viable visually. Because constitutive BRAF activation in melanocytes usually leads to cellular senescence, with only rare lesions progressing to melanoma, we examined if senescent markers were induced in our system. Overexpression of BRAF V600E led to an increase in markers of oncogene-induced senescence, such as acidic beta-galactosidase and p16. FISH analysis revealed no differences in telomere length in BRAF over-expressing cells compared to GFP-transduced control cells, indicating that this phenotype was not due to telomere shortening. The pattern of initial transformation followed by senescence is similar to the frequently indolent course of pilocytic astrocytoma, suggesting that overexpressing constitutively active BRAF in human neural stem and progenitor cells phenocopies the behavior of this tumor. To further investigate the mechanism of oncogene-induced senescence, we examined SOX2 expression. This human somatic cell reprogramming factor is an important neurodevelopmental gene and is known to prevent the induction of cellular senescence. However, the functional role of SOX2 in gliomas is poorly understood. We found that although SOX2 was expressed in control GFP transduced neurospheres, high-level expression of BRAFV600E led to downregulation of SOX2 in association with senescence. Our data support the concept that BRAF oncogene-induced senescence plays a role in the pathobiology of pilocytic astrocytoma, and suggest that modulation of SOX2 may play an important role in this process. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3303. doi:10.1158/1538-7445.AM2011-3303

Background Notch and Hedgehog signaling have been implicated in the pathogenesis and stem-like characteristics of glioblastomas, and inhibitors of the pathways have been suggested as new therapies for these aggressive tumors. It has also been reported that targeting both pathways simultaneously can be advantageous in treating glioblastoma neurospheres, but this is difficult to achieve in vivo using multiple agents. Since arsenic trioxide has been shown to inhibit both Notch and Hedgehog in some solid tumors, we examined its effects on these pathways and on stem cell phenotype in glioblastoma. Results We found that arsenic trioxide suppresses proliferation and promotes apoptosis in three stem-like glioblastoma neurospheres lines, while inhibiting Notch and Hedgehog target genes. Importantly, arsenic trioxide markedly reduced clonogenic capacity of the tumor neurospheres, and the stem-like CD133-positive fraction was also diminished along with expression of the stem cell markers SOX2 and CD133. Conclusions Our results suggest that arsenic trioxide may be effective in targeting stem-like glioblastoma cells in patients by inhibiting Notch and Hedgehog activity.