A first-in-human phase 0 clinical study of RNA interference-based spherical nucleic acids in patients with recurrent glioblastoma

Glioblastoma (GBM) is one of the most difficult cancers to effectively treat, in part because of the lack of precision therapies and limited therapeutic access to intracranial tumor sites due to the presence of the blood-brain and blood-tumor barriers. We have developed a precision medicine approach for GBM treatment that involves the use of brain-penetrant RNA interference-based spherical nucleic acids (SNAs), which consist of gold nanoparticle cores covalently conjugated with radially oriented and densely packed small interfering RNA (siRNA) oligonucleotides. On the basis of previous preclinical evaluation, we conducted toxicology and toxicokinetic studies in nonhuman primates and a single-arm, open-label phase 0 first-in-human trial (NCT03020017) to determine safety, pharmacokinetics, intratumoral accumulation and gene-suppressive activity of systemically administered SNAs carrying siRNA specific for the GBM oncogene Bcl2Like12 (Bcl2L12). Patients with recurrent GBM were treated with intravenous administration of siBcl2L12-SNAs (drug moniker: NU-0129), at a dose corresponding to 1/50th of the no-observed-adverse-event level, followed by tumor resection. Safety assessment revealed no grade 4 or 5 treatment-related toxicities. Inductively coupled plasma mass spectrometry, x-ray fluorescence microscopy, and silver staining of resected GBM tissue demonstrated that intravenously administered SNAs reached patient tumors, with gold enrichment observed in the tumor-associated endothelium, macrophages, and tumor cells. NU-0129 uptake into glioma cells correlated with a reduction in tumor-associated Bcl2L12 protein expression, as indicated by comparison of matched primary tumor and NU-0129-treated recurrent tumor. Our results establish SNA nanoconjugates as a potential brain-penetrant precision medicine approach for the systemic treatment of GBM.

Methods for in vitro modeling of glioma invasion: Choosing tools to meet the need

Widespread tumor cell invasion is a fundamental property of diffuse gliomas and is ultimately responsible for their poor prognosis. A greater understanding of basic mechanisms underlying glioma invasion is needed to provide insights into therapies that could potentially counteract them. While none of the currently available in vitro models can fully recapitulate the complex interactions of glioma cells within the brain tumor microenvironment, if chosen and developed appropriately, these models can provide controlled experimental settings to study molecular and cellular phenomena that are challenging or impossible to model in vivo. Therefore, selecting the most appropriate in vitro model, together with its inherent advantages and limitations, for specific hypotheses and experimental questions achieves primary significance. In this review, we describe and discuss commonly used methods for modeling and studying glioma invasion in vitro, including platforms, matrices, cell culture, and visualization techniques, so that choices for experimental approach are informed and optimal.

Abstract 1153: Hypoxic microenvironments promote stemness and enhance the directed migration of glioma stem cells

Glioblastoma (GBM) is a highly malignant primary brain tumor and has a poor prognosis and is resistant to the most advanced therapies. The development of highly hypoxic centrally located necrotic regions is strongly associated with accelerated GBM progression, yet mechanistic explanations are not complete. Hypoxic regions within GBM are highly enriched for glioma stem cells (GSC), which are critical for tumor initiation, recurrence and therapeutic resistance due to their self-renewing capabilites. While most GBM cells migrate outward, away from hypoxia, GSCs accumulate there, forming a hypercellular border called pseudopalisades that promote their survival. Mechanisms that mediate GSC accumulation within pseudopalisades are unknown. We hypothesize that GSCs are enriched in the pseudopalisades due to the homing of a subpopulation towards the supportive hypoxic microenvironment. This in turn activates critical hypoxia-induced drivers to promote stemness, survival and migratory behavior encouraging the recruitment of more GSCs. Using two genetically distinct patient-derived GBM cell lines, we found that exposure to hypoxia in vitro led to enrichment of GSCs among a heterogeneous population of GSCs and non-GSCs. We found that hypoxia enhanced the expression of stem cell, pro-survival and pro-migratory factors in GSCs, such as the pro-migratory chemokine SDF-1α, and its cognate receptor CXCR4. Importantly, we found hypoxia also induced upregulation of OLIG2, one of four core transcription factors necessary and sufficient to induce stemness, in GSCs and non-GSCs exposed to hypoxia. We determined that OLIG2 was necessary for the expression of stem cell markers, and that its knockdown reduced cellular migration in hypoxia vs normoxia in GSCs. This suggests a critical role for OLIG2 in both hypoxia-induced stemness and homing behavior. We also generated a unique model of localized hypoxia in one brain hemisphere through vaso-cclusion and observed the homing of xenografted GBM cells towards hypoxia, regulated by OLIG2 in vivo. These data shed light on how hypoxic tumor microenvironments facilitate mechanisms vital to GBM progression and therapeutic resistance.

Citation Format: Nitya V. Sharma, Monica Chau, Subhas Mukherjee, James Ross, Brandon Miller, Changming Zhang, Jun Kong, Carol Tucker-Burden, Emily Kaissi, John W. Reitnauer, Bilge Dundar, Cheryl L. Olson, Gregory Bix, Daniel J. Brat. Hypoxic microenvironments promote stemness and enhance the directed migration of glioma stem cells [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 1153.

Abstract 2269: Transcription factor relationships associated with androgen-deprivation therapy response and metastatic progression in prostate cancer

Patients with recurrent, aggressive prostate cancer typically undergo androgen-deprivation therapy (ADT), but the benefits are often short-lived, and responses are variable. Failure to respond to ADT invariably leads to metastatic disease, and ultimately death. To investigate differential responses to ADT, we performed whole-transcriptome analysis of 20 patient-matched pre-ADT biopsies and post-ADT prostatectomy specimens, and observed that all patients lost transcriptional signatures indicative of the androgen receptor (AR)-dependent subtype, after treatment. We also identified two subgroups of patients with either a strong or weak transcriptional response to ADT. The strong responders maintained the more aggressive subtype signal, while the weak responders lost expression of these genes and more resembled an AR-suppressed, basal subtype. We generated a strong responder transcriptional network using the PANDA program and integrated expression data from our cohort, protein-protein interaction, and DNA binding motif data. We also leveraged the expression data from a large public dataset of over 800 metastatic and primary samples to construct a metastatic lesion transcriptional network. We identified 20 common transcription factor coordinated groups (TFCGs) associated with both the strong responders and metastatic lesions, including GLI3/GLI2, SOX4/FOXA2/GATA4, ERF/ETV5/ETV3/ELF4, and a TFCG containing JUN, JUNB, JUND, FOS, FOSB, and FOSL1. Many TFCGs in the metastatic network were subsets of larger groups in the strong responders network, implicating these transcription factor associations as potentially critical for both the differential ADT response and metastatic disease progression.

Citation Format: Nitya V. Sharma, Kathryn L. Pellegrini, Veronique Ouellet, Felipe O. Giuste, Selvi Ramalingam, Kenneth Watanabe, Eloise Adam-Granger, Lucresse Fossouo, Sungyong You, Michael R. Freeman, Paula Vertino, Karen Conneely, Adeboye O. Osunkoya, Dominique Trudel, Anne-Marie Mes-Masson, John A. Petros, Fred Saad, Carlos S. Moreno. Transcription factor relationships associated with androgen-deprivation therapy response and metastatic progression in prostate cancer [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 2269.

Effects of genistein supplementation on genome‑wide DNA methylation and gene expression in patients with localized prostate cancer

Epidemiological studies have shown that dietary compounds have significant effects on prostate carcinogenesis. Among dietary agents, genistein, the major isoflavone in soybean, is of particular interest because high consumption of soy products has been associated with a low incidence of prostate cancer, suggesting a preventive role of genistein in prostate cancer. In spite of numerous studies to understand the effects of genistein on prostate cancer, the mechanisms of action have not been fully elucidated. We investigated the differences in methylation and gene expression levels of prostate specimens from a clinical trial of genistein supplementation prior to prostatectomy using Illumina HumanMethylation450 and Illumina HumanHT-12 v4 Expression BeadChip Microarrays. The present study was a randomized, placebo-controlled, double-blind clinical trial on Norwegian patients who received 30 mg genistein or placebo capsules daily for 3–6 weeks before prostatectomy. Gene expression changes were validated by quantitative PCR (qPCR). Whole genome methylation and expression profiling identified differentially methylated sites and expressed genes between placebo and genistein groups. Differentially regulated genes were involved in developmental processes, stem cell markers, proliferation and transcriptional regulation. Enrichment analysis suggested overall reduction in MYC activity and increased PTEN activity in genistein-treated patients. These findings highlight the effects of genistein on global changes in gene expression in prostate cancer and its effects on molecular pathways involved in prostate tumorigenesis.

Abstract A46: Effects of genistein supplementation on genome-wide DNA methylation and gene expression in patients with localized prostate cancer

Prostate cancer is the most commonly diagnosed malignancy and the second leading cause of cancer death among men in the United States, with an estimated 220,800 new cases and 27,540 deaths in 2015. Epidemiological studies have shown that dietary compounds have significant effects on prostate carcinogenesis. Among dietary agents, genistein, the major isoflavone in soybean, is of particular interest because high consumption of soy products has been associated with a low incidence of prostate cancer, suggesting a preventive role of genistein in prostate cancer. In spite of numerous studies to understand the effects of genistein on prostate cancer, the mechanisms of action have not been fully elucidated. Here, we investigated the differences in methylation and gene expression levels of prostate specimens from a clinical trial of genistein supplementation prior to prostatectomy (Lazarevic B, et al. Nutr Cancer 2011). This study was a randomized, placebo-controlled, double-blind clinical trial on forty-seven Norwegian patients who received 30 mg genistein or placebo capsules daily for 3-6 weeks before prostatectomy. Whole genome methylation and expression profiling identified significantly differentially methylated sites and expressed sites between placebo and genistein groups. Differentially regulated genes were involved in developmental processes, stem cell markers, proliferation, and transcriptional regulation. These findings highlight the effects of genistein on global changes in DNA methylation and gene expression in prostate cancer, and provide additional insight into the multiple molecular pathways involved in prostate tumorigenesis.

Citation Format: Birdal Bilir, Jeongseok Edward Lee, Nitya V. Sharma, Bato Lazarevic, Aud Svindland, Omer Kucuk, Carlos S. Moreno. Effects of genistein supplementation on genome-wide DNA methylation and gene expression in patients with localized prostate cancer. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr A46.

Abstract A21: The role of SOX4 in epithelial to mesenchymal transition in prostate cancer

Prostate cancer remains the most commonly diagnosed cancer in U.S. males, and ranks second in mortality with over 28,000 deaths per year. Prostate cancer mortality is typically due to metastases, necessitating the understanding of how metastatic disease develops. One major step for cancer cells to metastasize and acquire migratory and invasive capabilities is the epithelial to mesenchymal transition (EMT). EMT encompasses vast molecular changes in gene expression, mediated by aberrant developmental signaling pathway activation, leading to the loss of cell-cell junctions and planar and apical-basal polarity, increased motility, and resistance to apoptosis and anoikis (cell death due to the detachment from the extracellular matrix). The sex determining region Y-box 4 (SOX4) gene is a developmental transcription factor that is over expressed in prostate cancer and plays a critical role in many developmental pathways inappropriately activated during EMT, such as the transforming growth factor (TGF-beta) and epidermal growth factor receptor (EGFR) signaling pathways. Our data suggest that concomitant treatment of TGF-beta and EGF induces SOX4, and initiates the EMT program in prostate epithelial cell lines. We also demonstrate that SOX4 over expression is sufficient to induce EMT in prostate epithelial cell lines. Currently, the molecular mechanisms that govern how SOX4 initiates EMT via transcriptional activation of target genes are poorly understood. We identified candidate SOX4 targets using the Algorithm for the Reconstruction of Accurate Cellular Networks (ARACNE) on 9755 Pan Cancer samples from The Cancer Genome Atlas (TCGA). Gene ontology analysis of the top 1000 candidate SOX4 targets revealed genes that were enriched for epigenetic processes such as chromatin modification and DNA methylation. One putative target gene, PCAF, is a subunit of a large histone acetyltransferase (HAT) complex. Interestingly, our preliminary data also suggest that SOX4 interacts not only with PCAF, but also with TRRAP, another subunit of the PCAF HAT complex. These data suggest that SOX4 may induce and recruit the PCAF/TRRAP HAT complex in order to transcriptionally activate downstream targets to initiate the EMT program.

Citation Format: Nitya V. Sharma, Soma Sannigrahi, YuHeng Lai, Carlos Moreno. The role of SOX4 in epithelial to mesenchymal transition in prostate cancer. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr A21.

Neisseria Base: a comparative genomics database for Neisseria meningitidis

Neisseria meningitidis is an important pathogen, causing life-threatening diseases including meningitis, septicemia and in some cases pneumonia. Genomic studies hold great promise for N. meningitidis research, but substantial database resources are needed to deal with the wealth of information that comes with completely sequenced and annotated genomes. To address this need, we developed Neisseria Base (NBase), a comparative genomics database and genome browser that houses and displays publicly available N. meningitidis genomes. In addition to existing N. meningitidis genome sequences, we sequenced and annotated 19 new genomes using 454 pyrosequencing and the CG-Pipeline genome analysis tool. In total, NBase hosts 27 complete N. meningitidis genome sequences along with their associated annotations. The NBase platform is designed to be scalable, via the underlying database schema and modular code architecture, such that it can readily incorporate new genomes and their associated annotations. The front page of NBase provides user access to these genomes through searching, browsing and downloading. NBase search utility includes BLAST-based sequence similarity searches along with a variety of semantic search options. All genomes can be browsed using a modified version of the GBrowse platform, and a plethora of information on each gene can be viewed using a customized details page. NBase also has a whole-genome comparison tool that yields single-nucleotide polymorphism differences between two user-defined groups of genomes. Using the virulent ST-11 lineage as an example, we demonstrate how this comparative genomics utility can be used to identify novel genomic markers for molecular profiling of N. meningitidis.

Database URL:http://nbase.biology.gatech.edu