Meade, Paola Suarez

Abstract Glioblastoma (GBM) is the most common and aggressive primary brain tumor in adults with a poor prognosis of 15 months despite aggressive therapies. GBM malignancy is often driven by a high degree of inter- and intra-tumoral heterogeneity that is dynamic through time and regulated by interactions between tumor cells and their neural microenvironment. For instance, GBM tumors located near the lateral ventricles (LV) of the brain grow more aggressively and result in significantly worse patient survival, compared to tumors that grow far from the LV. This suggests that interactions between GBM and cells in the LV microenvironment may regulate tumor malignancy. Understanding the mechanisms underlying GBM malignancy near the LV is essential to determine if regulation of tumor biology is driven by the presence of healthy neural cells, and to ultimately develop therapeutic approaches that target GBM-LV interactions. Here, we tested the hypothesis that region-specific cellular identities and activation of unique transcriptional programs regulate GBM malignancy near the LV. Paired primary biopsies were collected from 14 GBM patients. Image-guided biopsies proximal and distal to the brain’s LV (LV-proximal GBM and LV-distal GBM, respectively) were processed for bulk RNA sequencing, single-nucleus RNA sequencing, and in situ spatial transcriptomic (Xenium) analyses. We found significant inter-patient and intra-tumoral transcriptional heterogeneity in GBM samples collected proximal and distal to the LV. After accounting for tumoral and patient heterogeneity, we found that proximal GBM tumors exhibit an increased immune-related gene signature, compared with tumors distal to the LV. Single-nucleus RNA sequencing and in situ spatial transcriptomic analyses showed no significant differences in the proportion of cellular states or identities between proximal and distal GBM samples. However, within each cellular identity, significant differences in gene expression were identified between proximal and distal GBM, suggesting that distinct cell-specific transcriptional pathways characterize regional differences in GBM biology. Our results suggest that GBM tumors near the LV have increased interactions with immune cells that lead to the enrichment of immune-related transcriptional pathways, compared to tumors growing far from the LV. This work will inform the development of therapies that target GBM-immune cell interactions to decrease tumor malignancy and improve individual patient outcomes. Citation Format: Maria F. Gonzalez-Aponte, Jhan C. Salazar, Aura Figueroa-Gonzalez, Emily S. Norton, Paola Suarez-Meade, Hugo Guerrero-Cazares. Integrating RNA sequencing and spatial transcriptomic analyses reveals drivers of glioblastoma malignancy near the brains’ lateral ventricles [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Brain Cancer; 2026 Mar 23-25; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2026;86(6_Suppl):Abstract nr B035.

Abstract NF2-related schwannomatosis is a genetic condition characterized by mutation in the NF2 gene resulting in tumor formation throughout the nervous system. The most common tumors in these patients include bilateral vestibular schwannomas and multiple meningiomas which, despite their benign classification, lead to significant neurologic deficits including hearing loss, ataxia, hydrocephalus, and brainstem compression. Loss of NF2, which encodes the protein Merlin, is also the most common mutation in spontaneous meningiomas and schwannomas. Current treatment consists of resection followed by radiation for more aggressive tumors. Unfortunately, these treatments are not curative and are associated with significant risk due to tumor location, involvement of neurovasculature, cognitive impairment, and radiation-induced tumor induction. Therefore, identifying additional therapeutics for these patients is critical. Molecular profiling across large cohorts of sporadic meningiomas have identified molecular signatures associated with NF2 mutation, indicating upregulation of Wnt5a/b and the alternative Wnt5a/b-YAP/TAZ signaling pathway. In NF2 knock-out human arachnoid and Schwann cells, we find a significant upregulation of YAP in NF2-null lines compared to controls. Additionally, when stimulated with Wnt5a/b, controls upregulate both beta catenin (canonical Wnt) and YAP (alternative Wnt). However, in NF2-null lines only YAP is increased, indicating a preference for the alternative pathway in the absence of canonical Wnt signaling. In primary NF2-mutant meningioma lines, targeting this pathway via blocking Wnt secretion with the inhibitor LGK974 or YAP signaling with verteporfin, which is FDA approved, results in decreased cell viability and proliferation in vitro. These results indicate activation of the Wnt5a/b-YAP/TAZ alternative signaling pathway in NF2-mutant meningeal and Schwann cells, and a potential therapeutic effect of blocking this pathway in NF2-mutant meningiomas with a previously-FDA approved inhibitor. Additional research is needed on the receptors and molecular mediators playing a role in this pathway and how these drugs may have therapeutic benefits in vivo

Abstract Extracellular matrix (ECM) stiffening correlates with tumor invasion in various cancer types, including glioblastoma (GBM). Increased matrix stiffness promotes a migratory phenotype through dysregulation of cell-ECM bidirectional communication. Exposure to stiffer environments is sensed by cells, which then adapt in ways that promote invasive behavior. These adaptive changes are imprinted onto the cells and persist even after they are placed in new, softer microenvironments via a process known as “mechanical memory.” Mechanical memory is believed to be driven by mechanosensitive transcription factor activity and epigenetic remodeling. Glioblastoma recurrence is linked to the ability of cells to disperse and infiltrate the surrounding healthy tissue. Extracellular matrix stiffness in GBM is heterogeneous; it starts with a softer tumor core and becomes progressively stiffer toward the tumor’s edges, potentially promoting sustained tumor invasion through mechanical memory. This review discusses the role of ECM stiffness in cancer cell behavior and the implications of ECM stiffening in GBM. We then describe the findings associated with mechanical memory and relay underlying mechanisms currently understood to drive the preservation of mechanically primed phenotypes. Finally, we discuss how matrix stiffness can drive migratory phenotypes in GBM cells and the potential role that progressive ECM dysregulation at the tumor periphery can link the formation of invasive tumor niches to the aggressive, resistant, and mesenchymal-like phenotypes present in GBM recurrent tumors.

e13121 Background: Metastatic breast cancer remains a major clinical challenge, characterized by poor prognosis and limited therapeutic options. The incidence of metastatic female breast cancer increased from 5.8 to 7.9 per 100,000 females from 2001 to 2021. The Hippo pathway effector YAP1 plays a critical role in driving tumor growth and metastasis in many cancers including breast but little is known about the gene-specific changes that occur when breast cancers have metastasized. This study aimed to investigate the extent of genomic alterations, including copy number alterations (CNAs) and mutations, in YAP1 and its downstream genes in metastatic breast cancer compared to nonmetastatic breast cancer. Methods: Genomic data for the YAP1 gene and its downstream target genes (CTGF, Cyr61, MCL-1, TOP2A, FOSL2, and ANKRD1) were obtained from cBioPortal. This included mutation data and CNA data, considering both amplifications and deletions as CNA events. The chi-square test was performed using GraphPad Prism 10 to compare the frequencies of mutations and CNAs between metastatic and non-metastatic breast cancer cases. Results: A total of 2390 samples of metastatic breast cancer and 9289 samples of non-metastatic breast cancer were analyzed for mutations. Among them, a significantly higher percentage of mutations in the YAP1 (P ≤ 0.0001), ANKRD1 (P ≤ 0.0001), MCL-1 (P ≤ 0.0001), and TOP2A (P ≤ 0.0001) genes was observed in metastatic breast cancer compared to non-metastatic breast cancer. Evaluating CNAs in 2197 cases in the metastatic breast cancer group compared to 9289 cases in the non-metastatic breast cancer group demonstrated a significantly higher frequency of CNAs in the YAP1 ( P ≤ 0.0001), Cyr61 (P ≤ 0.0001), CTGF ( P ≤ 0.0001), ANKRD1 ( P ≤ 0.0001), TOP2A (P ≤ 0.0001) and FOSL2 (P ≤ 0.0001) genes among metastatic breast cancer. Conclusions: This study revealed significant genomic alterations in the YAP1 gene and its downstream genes in metastatic breast cancer. These findings highlight the importance of the YAP1 pathway in breast cancer metastasis and suggest that targeting this pathway may have therapeutic potential for primary and metastatic breast cancer. Frequency of mutations and copy number alterations (CNAs) in metastatic vs. non-metastatic breast cancer. Gene Metastatic Breast Cancer Mutation Frequency (%) Non-Metastatic Breast Cancer Mutation Frequency (%) P-value Metastatic Breast Cancer CNA Frequency (%) Non-Metastatic Breast Cancer CNA Frequency (%) P-value YAP1 0.75 0.17 <0.0001 5.1 1.18 <0.0001 CTGF 0.13 0.18 0.781 5.42 0.65 <0.0001 Cyr61 0.17 0.16 0.999 3.9 0.65 <0.0001 MCL-1 0.63 0.11 <0.0001 10.74 11.93 0.121 ANKRD1 1.17 0.09 <0.0001 1.96 0.25 <0.0001 TOP2A 0.96 0.18 <0.0001 8.06 3.6 <0.0001 FOSL2 0.17 0.1 0.317 3.64 0.62 <0.0001

Abstract The extracellular matrix (ECM) plays a critical role in cancer progression, with its biophysical properties influencing cancer behavior. ECM stiffness can induce long-lasting adaptations in cancer cells, promoting sustained invasion through a process known as “mechanical memory” (MM). Glioblastoma (GBM) exhibits spatial heterogeneity in stiffness, with stiffer ECM found at the tumor periphery where invasive cells reside and promote recurrence. We hypothesize that increased stiffness at the tumor periphery primes GBM cells for sustained invasion through MM. METHODS Cell lines were established from image-guided human GBM samples from tumor margin and core (n=10 patients, 20 cell lines). Cells from random locations were conditioned in physiologically relevant extracellular matrices for two weeks. Human organotypic assay (n=3), Migration Assays, Atomic Force Microscopy (AFM), Immunocytochemistry, Western Blot, and RNA-sequencing (n=6) were performed. RESULTS GBM cells at higher stiff surfaces displayed increased migration (p&lt;0.01). Magnetic Resonance Elastography (n=9) confirmed GBM heterogeneity, with softer cores (0.2-0.5kPa) transitioning to stiffer margins (&gt;2kPa). Organotypic scaffolds mimicking the tumor margin promoted enhanced migration of GFP-labeled GBM cells. Margin cells and cells conditioned on stiffer matrices demonstrated higher migratory potential compared to their core and soft-conditioned counterparts (p&lt;0.05). These trends persist over time and across multiple passages. ECM stiffness exposure causes nanomechanical, cytoskeletal, and transcriptional adaptations. AFM shows that cells from the margin (n=6) are softer (p&lt;0.01) and more deformable (p&lt;0.01). RNAseq identified upregulation of MM-specific genes in GBM margin cells. The mechanosensitive transcription factor YAP1 emerged as a key driver of MM. Notably, YAP1 is targetable by the FDA-approved drug Verteporfin. YAP1 expression was elevated in margin and stiff-conditioned cells (p&lt;0.05). Stiff-conditioned cells and margin cells displayed increased sensitivity to Verteporfin treatment (p&lt;0.05), with treatment significantly reducing margin migration compared to the core (p&lt;0.001). CONCLUSION Stiffer GBM margins promote the formation of aggressive phenotypes through MM. Targeting YAP1 with Verteporfin, a readily available drug, presents a promising strategy to halt GBM invasion and improve patient outcomes.

Abstract Differences in clonality, genomic and epigenetic alterations are known to occur between primary Glioblastoma (pGBM) and recurrent (rGBM), but this has been insufficient to yield a promising therapeutic approach. Recent studies show that the GBM tumor microenvironment (TME), composed of reactive glial cells, microglial subtypes, neuronal activity, myeloid cells, lymphocytes, etc., plays a crucial role in the invasiveness and evolution of the glioma cells. Nevertheless, how the spatial architecture and interplay among these cells facilitates GBM resurgence is largely unknown. To this point, we developed a pipeline for characterizing the TME changes using single nucleus and spatial transcriptomics (ST). We retrospectively collected matched, fresh-frozen, IDH-wildtype pGBM and rGBM samples (n=14, 7 patients) from the Mayo Clinic Neuroscience Biobank. Single nucleus RNA sequencing was performed using the 10x Chromium platform. Matched FFPE blocks from 8 samples were collected from the Mayo Clinic pathology department for 4 of the 7 patients. A region of interest was identified from the corresponding histopathology slide by a pathologist, avoiding areas of necrosis and hemorrhage. The region was collected from the block using a 5mm biopsy punch. The tissue was re-paraffinized, and a 5µm thick section was used to perform ST with the 10x Visium for FFPE platform. We performed transcriptomic and image texture-based clustering of capture dots along with differential gene expression analysis. Based on gene expression, we identified and characterized conserved regions across samples. We used single nucleus data to infer cell composition. Spatial correlation and autocorrelation statistics were calculated on features, such as gene expression, gene set scores, cell type prediction, and antibody capture. The features’ relative spatial changes were compared between pGBM and rGBM. Our analyses showed high heterogeneity within and across samples, but we found higher molecular and textural heterogeneity in rGBM samples compared to pGBM. We found higher androgen response activity (p &lt; 0.001) presents diffusely (I: 0.09) throughout rGBM tissue but localized to mesenchymal-like regions in pGBM (I: 0.15). KRAS signaling signature was decreased in pGBM (p &lt; 0.01) and increased in rGBM (p &lt; 0.01). This increase was significantly overexpressed in cluster 0 for rGBM (p=0.02), which is an area characterized by neural progenitor signature. No significant difference in KRAS or EGFR magnitude or distribution of expression was present for either GBM type, indicating an independent mechanism for pGBM. We established a pipeline for assessing the spatio-temporal changes of the GBM TME. We found evidence indicating differences in the type of growth signaling, the cells bing targeted, and their distribution across the TME between pGBM and rGBM. Our work suggests how ST can help us better understand the intricate dynamics of GBM. Citation Format: Jean R. Clemenceau, Paola Suarez Meade, Mark E. Jentoft, Alfredo Quiñones-Hinojosa, Tae Hyun Hwang. Spatial transcriptomic landscape of the primary and recurrent glioblastoma tumor microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 144.

Abstract Glioblastoma (GBM) is the most common and aggressive primary brain tumor in adults. Currently, treatment is focused on achieving maximal safe resection, followed by chemo- and radiotherapy. Although surgery remains the most important therapeutic component, complete surgical resection is virtually impossible, as GBM cells readily infiltrate the adjacent brain parenchyma. One fundamental mechanism for GBM cell migration is the ability of these cells to use cell volume regulation as a driving force of cell infiltration and potentially interfering with apoptosis and cell cycle progression. In this work, we targeted the master regulators of cell volume, the kinases STE20/SPS1-Related Proline-Alanine-Rich Protein Kinase (SPAK) and Oxidative stress-responsive kinase-1) (OSR1) by using a novel proprietary small molecule inhibitor. In order to study the effects of inhibiting SPAK and OSR1, we analyzed cell proliferation and migration. First, we determined the IC50 using six different patient-derived GBM cell lines; we found IC50 values ranging from 0.2–2μM. Next, cell proliferation was determined by cell cycle analysis through Edu labeling. We found a significant decrease in S phase and cell cycle arrest in G2M (p= 0.001, n=6). In addition, cell migration was determined using boyden chamber assay. We found a dose-dependent reduction in cell migration (p=0.001, n=3). These results correlated with the phenomenon observed in an orthotopic murine model of GBM, in which the inhibitor showed a decrease in tumor growth (p=0.0026, n=4) and greater survival rates in vivo (p=0.0046, n=8). When used in combination with radiation therapy, this small molecule inhibitor was capable of radio-sensitizing GBM cells decreasing clonogenicity (p=0.01, n=3) were observed in vitro. In summary, by targeting the SPAK/OSR1 kinases with a small molecule inhibitor, GBM cells become less aggressive, mainly by interfering with cell migration and proliferation and becoming more sensitive to radiation.