Sereduk, Chris

Abstract Diffuse gliomas represent the most common type of primary adult malignant brain tumor historically diagnosed and graded from histologic criteria alone. Gliomas harboring isocitrate dehydrogenase (IDH) 1 or 2 mutations are associated with lower grade tumors and portend a favorable prognosis relative to IDH-wildtype glioma. However, the loss of CDKN2A/B in IDH-mutant astrocytoma confers an aggressive high grade phenotype and is the strongest implicated molecular alteration associated poor clinical survival, thus is now sufficient to define a grade 4 tumor regardless of histologic grade. However, there remains no effective therapies targeted at molecular subgroups in aggressive gliomas to date. Here, we sought to elucidate the biologic pathways and functional outcomes associated with the acquisition of high-grade behavior under loss of CDKN2A/B in IDH-mutant astrocytoma to inform future therapeutic strategies. We analyzed a cohort of patient IDH-mutant astrocytomas with RNA sequencing data and found the increased expression of regulators of embryonic nervous system development and signaling concurrent with CDKN2A/B loss. Using grade 4 IDH-mutant astrocytoma patient-derived (PDX) and cell-lines harboring CDKN2A/B homozygous deletion, we stably re-expressed p14ARF, p15INK4B, and p16INK4A using a Tet-inducible system. IDH-mutant cell lines with re-expression of p14, p15, or p16 displayed differential transcription factor activation, impaired neurosphere capability, decreased colony formation, and lower neurosphere proliferation. Intriguingly, RNA-seq data revealed CUX2, a transcription factor known to control neuronal precursor behavior, as the likely candidate regulating the differential expression profile across CDKN2A/B status. We observed increased CUX2 expression in cell lines stably re-expressing p14, p15, and p16. We validated the CUX2 signature across publicly available datasets of IDH-mutant astrocytoma where CUX2 expression negatively correlated with loss of CDKN2A/B in patient tumors. Together our work suggests CUX2 deficiency in IDH-mutant astrocytoma with CDKN2A/B deletion enables an increased neuronal stem-like phenotype in these grade 4 tumors.

Abstract BACKGROUND High-grade glioma (HGG) is the most common and aggressive form of primary brain cancer. Standard of care surgery employs Magnetic Resonance Imaging to identify the contrast enhancing (CE) core for resection, leaving a non-enhancing (NE) invasive rim of tumor which contributes to recurrence. The hypoxic tumor microenvironment is thought to drive invasion into healthy brain, and understanding cellular responses to hypoxia may provide insight into combatting recurrence. Here, we apply a graph network to integrate regionally heterogeneous data from a unique dataset of spatially-localized CE and NE biopsies from a large cohort of patients with HGG to identify gene networks regulating hypoxia response and invasion. METHODS RNA-sequencing of 1159 differentially expressed genes across 159 IDH-wt biopsies (74 patients) from NE/CE regions were represented as nodes in a Neo4j graph network. Candidate genes for network random walks occurred exclusively within NE communities detected by modularity optimization and were localized by cell-type using single-cell RNA-sequencing (scRNAseq). CSF2RA was selected as source (walk length = 5; 10,000 walks/source node). Frequently occurring genes (one-tailed test) in walks were ranked by correlation with CSF2RA expression in NE samples and analyzed by gene set enrichment analysis for biological processes (clusterProfiler). CSF2RA and hypoxia gene expression were visualized with DoHeatmap in composite NE/CE scRNAseq profiles. RESULTS CSF2RA, an immune receptor, was upregulated (logFC = 0.789) in NE samples, scRNAseq myeloid populations, and Glycolytic/Plurimetabolic glioma subtype. CSF2RA random walk genes (n=46) enriched metabolic/proliferative signatures. CSF2RA expression correlated negatively with hypoxia genes globally and regionally (NE/CE), while NE/CE scRNAseq revealed distinct cellular expression patterns of CSF2RA and hypoxia response genes. CONCLUSION CSF2RA expression may prime NE glioma cells for invasion by altering hypoxia response. The genetic network bridging CSF2RA and hypoxia response may be a targetable mechanism of tumor recurrence.

Abstract BACKGROUND High-grade glioma (HGG) is the most common and aggressive form of primary brain cancer. Standard of care surgery employs Magnetic Resonance Imaging to identify the contrast enhancing (CE) core for resection, leaving a non-enhancing (NE) invasive rim of tumor which contributes to recurrence. Recent multi-omics analyses identified predominant neuronal and immune signatures within NE tumor. Here, we apply a graph network to integrate regionally heterogeneous data from a unique dataset of spatially-localized CE and NE biopsies from a large cohort of patients with HGG. METHODS RNA-sequencing of 1159 differentially expressed genes across 159 IDH-wt biopsies (74 patients) from NE/CE regions were represented as nodes in a Neo4j network. Candidate genes for network random walks occurred exclusively within NE communities detected by modularity optimization and localized by cell-type using single-cell RNA-sequencing (scRNAseq). CSF2RA and RBFOX1 were selected as sources (walk length = 5; 10,000 walks/source node). Frequently occurring genes (one-tailed test) in walks were ranked by correlation with CSF2RA/RBFOX1 expression in NE samples and analyzed by gene set enrichment analysis for biological processes (clusterProfiler). Random walk genes were visualized (DoHeatmap) against composite NE/CE scRNAseq profiles. RESULTS CSF2RA and RBFOX1 were upregulated in NE samples (logFC = 0.789, 1.85). Upregulation of CSF2RA, an immune receptor, in the Glycolytic/Plurimetabolic and RBFOX1, a neurodevelopmental regulator, in the Neuronal glioma subtypes were observed in NE samples (ANOVA p < 0.05). CSF2RA walk genes (n=46) enriched metabolic/proliferative signatures, while RBFOX1 walk genes (n=201) showed neurodevelopmental upregulation. scRNAseq localized CSF2RA to monocytes/macrophages while RBFOX1 was expressed in distinct astrocyte/neuroepithelial populations. CONCLUSION CSF2RA and RBFOX1’s gene networks modulate immune and neurodevelopmental processes influencing glioma progression in NE tumor. Understanding the region-specific roles of these networks may offer strategies for targeting cells in the invasive glioma rim.

Abstract BACKGROUND High-grade glioma (HGG) is the most common and aggressive form of primary brain cancer with poor prognosis. Standard of care surgery employs Magnetic Resonance Imaging (MRI) to identify the contrast enhancing (CE) core for resection, leaving behind an unresected non-enhancing (NE) invasive rim of tumor which borders healthy brain tissue and invariably contributes to recurrence. Recent multi-omic analyses identified predominant neuronal and immune signatures within NE tumor; understanding these signatures could provide key insights to combatting recurrence and improving patient outcomes. To this end, we utilized a novel graph database method to integrate multi-omic data from a unique dataset of multi-regional spatially-localized biopsies from the CE core and invasive NE rim from a large cohort of patients with HGG. MATERIAL AND METHODS 159 IDH-wildtype tumor biopsy samples from the NE and CE regions of 74 glioma patients were profiled by bulk RNA sequencing. Differentially expressed genes (DEG) (n=1159) across NE and CE samples were selected using EdgeR. Samples were hierarchically clustered (method = median) for each DEG and represented as nodes in a Neo4j graph network. Edges were generated between nodes sharing ≥ 1 sample. Modularity optimization was used to identify communities of densely connected nodes. Genes occurring exclusively within NE communities were localized by cell type using external single-cell RNA sequencing datasets and selected as candidate source nodes for NE network random walks. RBFOX1 was selected as a source (walk length = 5; 10,000 walks/source node). Random walks traversing samples with significantly elevated RBFOX1 expression (one-tailed test) were kept for analysis. Genes occurring at significantly high frequency (one-tailed test) within random walks were ranked by correlation with RBFOX1 expression in NE samples and analyzed by gene set enrichment analysis (GSEA) for biological processes using clusterProfiler. RESULTS RBFOX1, a neurodevelopmental regulator, was upregulated (logFC = 1.85) in NE samples and uniquely occurred in NE communities. We show RBFOX1 is differential expressed in the aggressive Neuronal glioma subtype and enriched in neuroepithelial/astrocyte subpopulations across single cell HGG datasets. NE network random walks identified 201 DEGs associated with RBFOX1. GSEA revealed upregulation of neurodevelopmental signatures and downregulation of proliferative pathways amongst RBFOX1’s network. CONCLUSION RBFOX1’s genetic network within NE tumor represents neurodevelopmental processes potentially underlying glioma invasiveness within the NE region. As such, understanding the mechanistic role of key genes within the RBFOX1 network may provide insight into novel strategies for targeting these invasive cells within an aggressive subtype of glioma in the NE rim.

Abstract BACKGROUND High-grade glioma (HGG) is the most common and aggressive form of primary brain cancer with poor prognosis. Standard of care surgery employs Magnetic Resonance Imaging to identify the contrast enhancing (CE) core for resection, typically leaving behind a non-enhancing (NE) invasive rim of tumor which invariably contributes to recurrence. Recent multi-omics analyses identified predominant neuronal and immune signatures within NE tumor, which could provide key insights for combatting recurrence. We present the novel application of graph network analyses to integrate multi-omic data from a unique dataset of multi-regional spatially-localized CE and NE biopsy samples from a large cohort of patients with HGG. MATERIAL AND METHODS 159 IDH-wildtype tumor biopsy samples from NE and CE regions of 74 glioma patients were profiled by RNA sequencing. Differentially expressed genes (DEGs) across NE and CE samples (n = 1159) were determined using the EdgeR package, and represented as nodes within a Neo4j graph network. Samples were hierarchically clustered for each gene (method = median), and edges were generated between gene nodes sharing ≥ 1 sample. Modularity optimization was used to identify communities of densely connected nodes. Genes occurring exclusively within NE communities were localized by cell type using external single-cell RNA sequencing datasets and identified as source node candidates for NE network random walks. These were performed with CSF2RA nodes as source (walk length = 5; 10,000 walks/source node). Random walks traversing samples with significantly elevated CSF2RA expression (one-tailed test) were kept for analysis. Genes occurring at high frequency (one-tailed test) within random walks were ranked by correlation with CSF2RA expression in NE samples and analyzed by gene set enrichment analysis (GSEA) for biological processes using clusterProfiler. RESULTS CSF2RA, an immune signaling receptor gene, was upregulated (logFC = 0.789) in NE samples and uniquely occurred within NE communities. We show its differential expression within the immune-enriched Glycolytic/Plurimetabolic (GPM) glioma subtype and confirm its enrichment in myeloid populations across single cell HGG datasets. NE network random walks identified 46 DEGs associated with CSF2RA. GSEA revealed upregulation of proliferative and metabolic signatures and downregulation of signaling pathways within CSF2RA’s network. CONCLUSION CSF2RA’s genetic network in NE tumor represents a potential mechanism for immunologic facilitation of glioma progression within this region. Given the expression of CSF2 ligand by glioma cells, which plays a crucial role in recruiting myeloid cells during peripheral cancer progression, modulating the expression of key genes in the CSF2RA network may be a promising approach for perturbing the crosstalk signals between immune and tumor cells in the NE region.

Glioblastoma (GBM) is the most common primary malignant brain tumor in adults, with few effective treatments. EGFR alterations, including expression of the truncated variant EGFRvIII, are among the most frequent genomic changes in these tumors. EGFRvIII is known to preferentially signal through STAT5 for oncogenic activation in GBM, yet targeting EGFRvIII has yielded limited clinical success to date. In this study, we employed patient-derived xenograft (PDX) models expressing EGFRvIII to determine the key points of therapeutic vulnerability within the EGFRvIII-STAT5 signaling axis in GBM. Our findings reveal that exogenous expression of paralogs STAT5A and STAT5B augments cell proliferation and that inhibition of STAT5 phosphorylation in vivo improves overall survival in combination with temozolomide (TMZ). STAT5 phosphorylation is independent of JAK1 and JAK2 signaling, instead requiring Src family kinase (SFK) activity. Saracatinib, an SFK inhibitor, attenuates phosphorylation of STAT5 and preferentially sensitizes EGFRvIII+ GBM cells to undergo apoptotic cell death relative to wild-type EGFR. Constitutively active STAT5A or STAT5B mitigates saracatinib sensitivity in EGFRvIII+ cells. In vivo, saracatinib treatment decreased survival in mice bearing EGFR WT tumors compared to the control, yet in EGFRvIII+ tumors, treatment with saracatinib in combination with TMZ preferentially improves survival.

Abstract Glioblastoma (GBM) tumors contain a subpopulation of glioma stem cells (GSC) which can escape therapeutic effects through self-renewal and invasion. Epidermal growth factor receptor (EGFR) mutations are the most common alteration in GBM (50%). One example includes extracellular domain missense mutations like G598V, A289V, and R108K (10-15%). These extracellular domain missense mutations increase ligand binding affinity, inducing a highly active receptor. Earlier reports have shown these EGFR missense mutations exhibit therapeutic resistance; however, the molecular mechanism of these missense mutations in GBM remains unknown. In this study, we show high oligodendrocyte transcription factor 2 (OLIG2) expression in GSCs with EGFR-G598V and EGFR-A289V missense mutations. OLIG2 is universally expressed in glioma and essential for reprogramming GBM cells into stem-like tumor cells. Here, we report GSCs with these point mutations display increased self-renewal, growth, invasion, and therapeutic resistance. In addition, EGFR-G598V and EGFR-A289V trigger distinct downstream signaling pathways in GSCs to regulate OLIG2 function. These missense mutation(s) also represent different pathway-based GBM subclassifications, where A289V induces a Neuronal subtype and G598V induces a Glycolytic/Plurimetabolic subtype. We hypothesize that GBM tumors harboring EGFR missense mutations (G598V, A289V) influence stem cell properties via multiple pathways to evade therapeutic effects and inhibiting these different signaling pathways will decrease therapeutic resistance in GBM. Understanding the mechanism of these EGFR mutations may lead to improved therapeutic strategies for GBM patients. Citation Format: Sidney Weaver, Aunay Miller, Mylan Blomquist, James McNamara, Keely Orndorff, Chris Sereduk, Jean Kloss, Joseph Loftus, Shwetal Mehta, Nhan L. Tran. EGFR missense mutation(s) induce OLIG2 expression to regulate glioma stem cells maintenance and therapeutic resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5444.

Abstract Glioblastoma (GBM) is the most common and lethal primary brain tumor in adults, despite current treatment options. One of the major contributing factors to this dismal outcome is a subset of cells called glioma stem cells (GSCs) that are highly tumorigenic, invasive, and resistant to conventional treatments. Thus, studies that focus on the properties of GSC biology are needed to develop novel therapies to improve overall survival. Here we report a novel role of STAT5 in GSC stemness and survival. In GBM tumors, STAT5 has been shown to be active in the infiltrative, residual population of cells remaining post-surgery. Knockdown of STAT5 results in the decrease in GSC stemness and therapeutic resistance. Interestingly, we find that expression of OLIG2, a key cell fate factor important for the tumorigenic potential of GSCs, affects STAT5 activation with a positive correlation between OLIG2 and STAT5 mRNA expression in GBM tumors. Furthermore, we find that in GSCs expressing EGFRvIII, STAT5 interacts with OLIG2 and pharmacological inhibition of STAT5 activation or knockdown of STAT5 expression results in decrease of OLIG2-mediated GSC invasion. Together, these data suggest a novel transcriptional complex, STAT5-OLIG2, in the potential role for GSC survival, maintenance, and invasion. Citation Format: Aunay Miller, Costanza Lo Cascio, Mylan Blomquist, James B. McNamara, Keely Orndorff, Matthew Dufault, Christopher Sereduk, Joseph Loftus, Shwetal Mehta, Nhan L. Tran. A novel transcriptional complex of OLIG2-STAT5 mediates glioma stem cell self renewal and invasion [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 256.

Abstract Glioblastoma (GBM) is the most common and lethal primary brain tumor in adults, despite current treatment options. One of the major contributing factors to this dismal outcome is a subset of cells called glioma stem cells (GSCs) that are highly tumorigenic, invasive, and resistant to conventional treatments. Thus, studies that focus on the properties of GSC biology are needed to develop novel therapies to improve overall survival. Here we report a novel role of STAT5 in GSC stemness and survival. In GBM tumors, STAT5 has been shown to be active in the infiltrative, residual population of cells remaining post-surgery. Knockdown of STAT5 results in the decrease in GSC stemness and therapeutic resistance. Interestingly, we find that expression of OLIG2, a key cell fate factor important for the tumorigenic potential of GSCs, affects STAT5 activation with a positive correlation between OLIG2 and STAT5 mRNA expression in GBM tumors. Furthermore, we find that in GSCs expressing EGFRvIII, STAT5 interacts with OLIG2 and pharmacological inhibition of STAT5 activation or knockdown of STAT5 expression results in decrease of OLIG2-mediated GSC invasion. Together, these data suggest a novel transcriptional complex, STAT5-OLIG2, in the potential role for GSC survival, maintenance, and invasion.

Abstract High-grade glioma continues to have dismal survival owing in part to its intra- and inter-patient heterogeneity. Standard clinical protocol collects tumor samples with the aim of providing or confirming a diagnosis and determining the status of a few key genes (e.g. IDH1, MGMT). However, this protocol is unable to capture the diversity within tumor regions, immune expression or normal cell abundances that play key roles in the development of the disease. To overcome this, during surgery we collect image-localized multi-regional biopsies to characterize this disease heterogeneity. Data collection is ongoing, and we currently have 202 samples from 58 patients with available bulk RNA-Seq. With a single-cell reference dataset from Columbia University, we used CIBERSORTx, a deconvolution method, to predict relative abundances of 7 normal, 6 glioma, and 5 immune cell subpopulations for each sample. We used Cox proportional hazard models with first-order statistics (mean, minimum, maximum) of abundances within patients to determine whether these are prognostic, then used TCGA RNA-Seq data to validate these findings. We found that one glioma proneural subtype was significantly beneficial for patient survival relative to other glioma subtypes across all statistics (and showed significance in TCGA). Proliferative and mesenchymal glioma subtypes also showed significance for one or two of the calculated statistics. Oligodendrocyte progenitor cell abundances were consistently significantly beneficial for patient survival in our cohort, while an increased abundance of abnormal (reactive) astrocytes is associated with poor prognosis. We also ran these analyses within invasive margin and core tumor regions to determine location-specific population abundances associated with patient survival. In conclusion, understanding the in vivo diversity of cellular subpopulations within high grade glioma is important for treatment stratification and patient benefit.