STEM-11. POLYAMINE METABOLISM AND INFLAMMATORY STATE CONTROL A VIRAL MIMICRY-DRIVEN QUIESCENT PHENOTYPE IN GLIOMA STEM CELLS (GSCS)

The rate limiting enzyme of the polyamine pathway, SAT1, is significantly upregulated in non-cycling GSCs. However, higher SAT1 expression predicts poorer survival in GBM suggesting a role in quiescence and recurrence post-treatment. Treating GSCs with N1N11-Diethylnorspermine (DENSpm) recapitulates SAT1 upregulation and triggers a chemoprotective, long-term reversible growth arrest, while not affecting expression of stem, differentiation, nor senescence-associated markers. Remarkably, DENSpm strongly induces double-stranded RNA in GSCs. Interestingly, S-Adenosyl methionine (SAM) is an essential aminopropyl donor for polyamine biosynthesis. We found a significant correlation between DNA methylation, SAM, and polyamines across GSCs suggesting that SAM depletion may cause epigenetic and post-transcriptional alterations leading to re-activation of endogenous retroviral elements (ERVs) and viral mimicry-driven quiescence. However, while we confirmed DENSpm-induced SAM depletion, we did not detect DNA, histone, nor RNA demethylation. Noteworthy, ERVs are the most accessible transposable elements in GSCs indicative of a poised state. Furthermore, the correlation between expression of ERVs and interferon stimulated genes reveals a spectrum of viral mimicry amongst GSCs. Using a larger cohort of GSCs and hfNSCs, we identified three DENSpm response subgroups. A resistant subgroup comprised of cells able to proliferate through treatment, a reversible one whereby cells become quiescent and readily re-enter cell cycle post-treatment, and an irreversible consisting of cells that enter a deep quiescent state which they cannot escape. Importantly, we found that DENSpm response correlates with the cell's basal inflammatory state and the activity of viral defense pathways. These results indicate that a viral mimicry-driven quiescence may be specific to slower-growing neurodevelopmental GSCs, while more proliferative, inflammatory-poised GSCs are impervious to these additional cues. We propose that polyamine metabolism, glioma stem cell hierarchy and tumour inflammatory context play a central role in regulating quiescence and have important clinical implications in the initial response to treatment, aggressiveness, and ultimately recurrence of GBM.

Single-cell chromatin accessibility profiling of glioblastoma identifies an invasive cancer stem cell population associated with lower survival

Chromatin accessibility discriminates stem from mature cell populations, enabling the identification of primitive stem-like cells in primary tumors, such as glioblastoma (GBM) where self-renewing cells driving cancer progression and recurrence are prime targets for therapeutic intervention. We show, using single-cell chromatin accessibility, that primary human GBMs harbor a heterogeneous self-renewing population whose diversity is captured in patient-derived glioblastoma stem cells (GSCs). In-depth characterization of chromatin accessibility in GSCs identifies three GSC states: Reactive, Constructive, and Invasive, each governed by uniquely essential transcription factors and present within GBMs in varying proportions. Orthotopic xenografts reveal that GSC states associate with survival, and identify an invasive GSC signature predictive of low patient survival, in line with the higher invasive properties of Invasive state GSCs compared to Reactive and Constructive GSCs as shown by in vitro and in vivo assays. Our chromatin-driven characterization of GSC states improves prognostic precision and identifies dependencies to guide combination therapies.

Live-Cell Imaging Assays to Study Glioblastoma Brain Tumor Stem Cell Migration and Invasion

Glioblastoma (GBM) is an aggressive brain tumor that is poorly controlled with the currently available treatment options. Key features of GBMs include rapid proliferation and pervasive invasion into the normal brain. Recurrence is thought to result from the presence of radio- and chemo-resistant brain tumor stem cells (BTSCs) that invade away from the initial cancerous mass and, thus, evade surgical resection. Hence, therapies that target BTSCs and their invasive abilities may improve the otherwise poor prognosis of this disease. Our group and others have successfully established and characterized BTSC cultures from GBM patient samples. These BTSC cultures demonstrate fundamental cancer stem cell properties such as clonogenic self-renewal, multi-lineage differentiation, and tumor initiation in immune-deficient mice. In order to improve on the current therapeutic approaches for GBM, a better understanding of the mechanisms of BTSC migration and invasion is necessary. In GBM, the study of migration and invasion is restricted, in part, due to the limitations of existing techniques which do not fully account for the in vitro growth characteristics of BTSCs grown as neurospheres. Here, we describe rapid and quantitative live-cell imaging assays to study both the migration and invasion properties of BTSCs. The first method described is the BTSC migration assay which measures the migration toward a chemoattractant gradient. The second method described is the BTSC invasion assay which images and quantifies a cellular invasion from neurospheres into a matrix. The assays described here are used for the quantification of BTSC migration and invasion over time and under different treatment conditions.

ING5 activity in self-renewal of glioblastoma stem cells via calcium and follicle stimulating hormone pathways

Stem cell-like brain tumor initiating cells (BTICs) cause recurrence of glioblastomas, with BTIC 'stemness' affected by epigenetic mechanisms. The ING family of epigenetic regulators (ING1-5) function by targeting histone acetyltransferase (HAT) or histone deacetylase complexes to the H3K4me3 mark to alter histone acetylation and subsequently, gene expression. Here we find that ectopic expression of ING5, the targeting subunit of HBO1, MOZ and MORF HAT complexes increases expression of the Oct4, Olig2 and Nestin stem cell markers, promotes self-renewal, prevents lineage differentiation and increases stem cell pools in BTIC populations. This activity requires the plant homeodomain region of ING5 that interacts specifically with the H3K4me3 mark. ING5 also enhances PI3K/AKT and MEK/ERK activity to sustain self-renewal of BTICs over serial passage of stem cell-like spheres. ING5 exerts these effects by activating transcription of calcium channel and follicle stimulating hormone pathway genes. In silico analyses of The Cancer Genome Atlas data suggest that ING5 is a positive regulator of BTIC stemness, whose expression negatively correlates with patient prognosis, especially in the Proneural and Classical subtypes, and in tumors with low SOX2 expression. These data suggest that altering histone acetylation status and signaling pathways induced by ING5 may provide useful clinical strategies to target tumor resistance and recurrence in glioblastoma.

Abstract 2524: STAT3 is a key regulator of an “EMT-like” process mediated by Slug in GBM

Glioblastoma Multiforme (GBM) is the most aggressive subtype of adult brain tumor with a median survival of 15 months. Despite a combination of maximal safe resection, radiation and chemotherapy, GBM invariably recurs, highlighting the need to better delineate the basis of recurrent disease and develop novel, more targeted and effective therapies. The Signal Transducer and Activator of Transcription 3 (STAT3) has been implicated in a proneural to mesenchymal shift associated with the emergence of a more aggressive, more resistant GBM phenotype at recurrence. Brain Tumor Initiating Cells (BTICs), defined by the key features of self-renewal, multipotency and tumorigenic potential, are integral players of recurrence post-treatment and represent a “reservoir of disease” that needs to be specifically targeted if GBM outcome is to be improved. Analysis of GBM patient transcriptomic data from The Cancer Genome Atlas (TCGA) shows that an Epithelial to Mesenchymal Transition (EMT) gene signature is particularly enriched in the mesenchymal subtype, tightly correlates with STAT3 activity and is associated with shorter survival. The key EMT transcription factor Slug is also highly expressed in mesenchymal samples and associated with poorer prognosis. Interestingly, we found stronger expression of EMT transcription factors Snail, Slug and Twist in faster proliferating, more aggressive BTIC lines. Noteworthy, Slug was more highly expressed in both BTICs and parental tumors compared to Snail and Twist and positively correlated with pSTAT3. We also found that Slug expression correlates with faster growth in vitro and shorter survival in orthotopic xenografts. Conversely, higher E-cadherin expression correlates with slower growth and longer survival of xenografted mice. While Slug is not a known STAT3 target gene (unlike Twist and Snail), we show that Slug expression is decreased after pharmacological inhibition of STAT3 signaling in BTICs. In contrast, activation of the STAT3 pathway via growth factor/cytokine treatment (EGF, OSM), as well as expression of a constitutively active form of STAT3 promotes Slug expression. We have identified a potential STAT3 consensus binding site in the Slug promoter and preliminary Chromatin Immuno Precipitation (ChIP) experiments suggest that Slug is a novel direct transcriptional target of STAT3. Over-expression of Slug in BTIC lines triggered down-regulation of E-cadherin and resulted in increased Cyclin D1 and pRB protein levels. However, we found that Cyclin D1 RNA levels remain unchanged suggesting that overexpression of Slug leads to the post-transcriptional stabilization of Cyclin D1 potentially via repression of UbcH5C. To conclude, STAT3 is a key regulator of an EMT-like process in GBM BTICs, mediated at least in part by Slug. Our results suggest that STAT3 and the key regulator Slug may be involved in the promotion of a more aggressive GBM phenotype and represent interesting therapeutic targets in GBM.

Citation Format: Charles Chesnelong, H. Artee Luchman, J. Gregory Cairncross, Samuel Weiss. STAT3 is a key regulator of an “EMT-like” process mediated by Slug in GBM. [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 2524.

Hyperpolarized (13)C MR imaging detects no lactate production in mutant IDH1 gliomas: Implications for diagnosis and response monitoring

Metabolic imaging of brain tumors using (13)C Magnetic Resonance Spectroscopy (MRS) of hyperpolarized [1-(13)C] pyruvate is a promising neuroimaging strategy which, after a decade of preclinical success in glioblastoma (GBM) models, is now entering clinical trials in multiple centers. Typically, the presence of GBM has been associated with elevated hyperpolarized [1-(13)C] lactate produced from [1-(13)C] pyruvate, and response to therapy has been associated with a drop in hyperpolarized [1-(13)C] lactate. However, to date, lower grade gliomas had not been investigated using this approach. The most prevalent mutation in lower grade gliomas is the isocitrate dehydrogenase 1 (IDH1) mutation, which, in addition to initiating tumor development, also induces metabolic reprogramming. In particular, mutant IDH1 gliomas are associated with low levels of lactate dehydrogenase A (LDHA) and monocarboxylate transporters 1 and 4 (MCT1, MCT4), three proteins involved in pyruvate metabolism to lactate. We therefore investigated the potential of (13)C MRS of hyperpolarized [1-(13)C] pyruvate for detection of mutant IDH1 gliomas and for monitoring of their therapeutic response. We studied patient-derived mutant IDH1 glioma cells that underexpress LDHA, MCT1 and MCT4, and wild-type IDH1 GBM cells that express high levels of these proteins. Mutant IDH1 cells and tumors produced significantly less hyperpolarized [1-(13)C] lactate compared to GBM, consistent with their metabolic reprogramming. Furthermore, hyperpolarized [1-(13)C] lactate production was not affected by chemotherapeutic treatment with temozolomide (TMZ) in mutant IDH1 tumors, in contrast to previous reports in GBM. Our results demonstrate the unusual metabolic imaging profile of mutant IDH1 gliomas, which, when combined with other clinically available imaging methods, could be used to detect the presence of the IDH1 mutation in vivo.

Lactate dehydrogenase A silencing in IDH mutant gliomas

BACKGROUND

Mutations of the isocitrate dehydrogenase 1 and 2 gene (IDH1/2) were initially thought to enhance cancer cell survival and proliferation by promoting the Warburg effect. However, recent experimental data have shown that production of 2-hydroxyglutarate by IDH mutant cells promotes hypoxia-inducible factor (HIF)1α degradation and, by doing so, may have unexpected metabolic effects.

METHODS

We used human glioma tissues and derived brain tumor stem cells (BTSCs) to study the expression of HIF1α target genes in IDH mutant ((mt)) and IDH wild-type ((wt)) tumors. Focusing thereafter on the major glycolytic enzyme, lactate dehydrogenase A (LDHA), we used standard molecular methods and pyrosequencing-based DNA methylation analysis to identify mechanisms by which LDHA expression was regulated in human gliomas.

RESULTS

We found that HIF1α-responsive genes, including many essential for glycolysis (SLC2A1, PDK1, LDHA, SLC16A3), were underexpressed in IDH(mt) gliomas and/or derived BTSCs. We then demonstrated that LDHA was silenced in IDH(mt) derived BTSCs, including those that did not retain the mutant IDH1 allele (mIDH(wt)), matched BTSC xenografts, and parental glioma tissues. Silencing of LDHA was associated with increased methylation of the LDHA promoter, as was ectopic expression of mutant IDH1 in immortalized human astrocytes. Furthermore, in a search of The Cancer Genome Atlas, we found low expression and high methylation of LDHA in IDH(mt) glioblastomas.

CONCLUSION

To our knowledge, this is the first demonstration of downregulation of LDHA in cancer. Although unexpected findings, silencing of LDHA and downregulation of several other glycolysis essential genes raise the intriguing possibility that IDH(mt) gliomas have limited glycolytic capacity, which may contribute to their slow growth and better prognosis.

DNA hypermethylation and 1p Loss silence NHE-1 in oligodendroglioma

Oligodendroglioma is characterized by mutations of IDH and CIC, 1p/19q loss, and slow growth. We found that NHE-1 on 1p is silenced in oligodendrogliomas secondary to IDH-associated hypermethylation and 1p allelic loss. Silencing lowers intracellular pH and attenuates acid load recovery in oligodendroglioma cells. Others have shown that rapid tumor growth cannot occur without NHE-1-mediated neutralization of the acidosis generated by the Warburg glycolytic shift. Our findings show for the first time that the pH regulator NHE-1 can be silenced in a human cancer and also suggest that pH deregulation may contribute to the distinctive biology of human oligodendroglioma.

An in vivo patient-derived model of endogenous IDH1-mutant glioma

Somatic mutations in the catalytic domain of isocitrate dehydrogenase (IDH) 1/2 and accumulation of the oncometabolite 2-hydroxyglutarate (2-HG) appear to be among the earliest events in gliomagenesis and may contribute to malignant transformation. The lack of cell lines with endogenous mutations has been one of the major challenges in studying IDH1/2-mutant glioma and developing novel therapeutics for these tumors. Here, we describe the isolation of a glioma brain tumor stem cell line (BT142) with an endogenous R132H mutation in IDH1, aggressive tumor-initiating capacity, and 2-HG production. The neurosphere culture method was used to establish a brain tumor stem cell line from an IDH1-mutant anaplastic oligoastrocytoma sample, and an orthotopic xenograft system was developed to allow its rapid expansion. Production of 2-HG by glioma cells with endogenous IDH1 mutations was confirmed by mass spectrometry. BT142 retained an endogenous R132H IDH1 mutation in culture and possessed aggressive tumor-initiating capacity, allowing it to be readily propagated in orthotopic xenografts of nonobese diabetic/severe combined immune deficiency (NOD SCID) mice. Endogenous 2-HG production by BT142 was detectable in both cell culture medium and xenograft animal serum. BT142 is the first brain tumor cell line with an endogenous IDH1 mutation and detectable 2-HG production both in vitro and in vivo, which thus provides a unique model for studying the biology of IDH1-mutant glioma and in vivo validation of compounds targeting IDH1-mutant cells.

Concurrent CIC mutations, IDH mutations, and 1p/19q loss distinguish oligodendrogliomas from other cancers

Oligodendroglioma is characterized by unique clinical, pathological, and genetic features. Recurrent losses of chromosomes 1p and 19q are strongly associated with this brain cancer but knowledge of the identity and function of the genes affected by these alterations is limited. We performed exome sequencing on a discovery set of 16 oligodendrogliomas with 1p/19q co-deletion to identify new molecular features at base-pair resolution. As anticipated, there was a high rate of IDH mutations: all cases had mutations in either IDH1 (14/16) or IDH2 (2/16). In addition, we discovered somatic mutations and insertions/deletions in the CIC gene on chromosome 19q13.2 in 13/16 tumours. These discovery set mutations were validated by deep sequencing of 13 additional tumours, which revealed seven others with CIC mutations, thus bringing the overall mutation rate in oligodendrogliomas in this study to 20/29 (69%). In contrast, deep sequencing of astrocytomas and oligoastrocytomas without 1p/19q loss revealed that CIC alterations were otherwise rare (1/60; 2%). Of the 21 non-synonymous somatic mutations in 20 CIC-mutant oligodendrogliomas, nine were in exon 5 within an annotated DNA-interacting domain and three were in exon 20 within an annotated protein-interacting domain. The remaining nine were found in other exons and frequently included truncations. CIC mutations were highly associated with oligodendroglioma histology, 1p/19q co-deletion, and IDH1/2 mutation (p < 0.001). Although we observed no differences in the clinical outcomes of CIC mutant versus wild-type tumours, in a background of 1p/19q co-deletion, hemizygous CIC mutations are likely important. We hypothesize that the mutant CIC on the single retained 19q allele is linked to the pathogenesis of oligodendrogliomas with IDH mutation. Our detailed study of genetic aberrations in oligodendroglioma suggests a functional interaction between CIC mutation, IDH1/2 mutation, and 1p/19q co-deletion.