CRISPR-Based Epigenome Editing and Genome Wide Screening Define Mediators of Chemotherapy Response in Glioblastoma

PURPOSE/OBJECTIVE(S)

Alkylating chemotherapies exhibit survival benefit for patients with glioblastoma (GBM), the most common malignant primary brain tumor. CRISPRoff is a programmable epigenetic memory writer that stably and heritably silences any gene through DNA methylation. Epigenetic silencing of MGMT via promoter methylation is predictive of response to alkylating agents as well as prognostic for progression free and overall survival. Here we performed epigenome editing using CRISPRoff to stably silence MGMT through induced promoter methylation, as a therapeutically tractable approach for potentiating GBM to temozolomide (TMZ) or lomustine (CCNU). We then used genome-wide engineered CRISPR/Cas9 systems to broadly define sensitizers of GBM cells to alkylating agents, as a platform to discover novel sensitizing targets.

MATERIALS/METHODS

Targeted epigenome editing was performed through electroporation of modified mRNAs encoding CRISPRoff machinery comprising deactivated Cas9 fused to a DNA methyltransferase complex, combined with sgRNAs, into MGMT unmethylated GBM cell lines (LN18, T98G) and then treated with either vehicle, TMZ, or CCNU. Parallel experiments were performed through electroporation of sgRNA/Cas9 ribonucleoproteins. Gene silencing was assessed using bisulfite targeted sequencing, RT-qPCR, and western blot. Drug sensitization was determined using luminescent cell viability assays. Genome-wide CRISPR interference (CRISPRi) screens were performed in triplicate cultures.

RESULTS

Epigenomic silencing of the MGMT promoter through CRISPRoff-induced methylation reduced MGMT transcript levels by 96.7% and generated up to 88-fold sensitization to TMZ mediated cell death in GBM cells, with IC50 superior to GBM cells with baseline methylated MGMT. In addition, CRISPRoff of MGMT induced 20-fold sensitization to CCNU. CRISPRoff methylation of MGMT was equivalent to CRISPR/Cas9 homozygous deletion of the MGMT gene for drug sensitization and was superior to polyclonal Cas9 mediated deletion of MGMT by a factor of 10. To define additional mediators of chemotherapy response in GBM, CRISPRi screens revealed 185 and 266 genetic sensitizers to TMZ treatment in LN18 and T98G cells, respectively, in addition to validating MGMT. One hundred eighty and 238 sensitizers to CCNU were identified in LN18 and T98G cells, respectively. TMZ sensitizing genes conserved across cell lines were enriched for the ATR (i.e., BCRA2), DNA repair (i.e., REV1), and cell cycle pathways (i.e., PSMD13), while CCNU sensitizing genes were enriched for the Fanconi anemia pathway (i.e., FANCI, FANCD2). In contrast, gene hits that resulted in resistance to alkylating agents were enriched for the mismatch repair pathway (i.e., MSH2, PMS2).

CONCLUSION

We integrate targeted epigenome editing with unbiased genome-wide approaches to build a novel discovery and therapeutic platform in glioblastoma, a framework that is well suited for targeting diseases with known or suspected epigenetic vulnerabilities.

Malignant Peripheral Nerve Sheath Tumors Activate Distinct Immunosuppressive Pathways Following Radiotherapy and are Associated with Immune Depletion In Vivo

PURPOSE/OBJECTIVE(S)

Patients with neurofibromatosis type I, caused by NF1 loss, develop benign plexiform neurofibromas (pNF) in their peripheral nervous system (PNS). Malignant transformation of pNFs into malignant peripheral nerve sheath tumors (MPNSTs) occurs following CDKN2A/B and SUZ12 loss, a process associated with radiotherapy (RT). However, the molecular mechanisms underlying RT responses by different PNS cell types remain unclear. We hypothesized normal peripheral nerve cells, pNFs, and MPNSTs harbor distinct RT responses.

MATERIALS/METHODS

Patient derived NF1 WT immortalized peripheral nerve cells (iPNs), NF1 mutant pNF cells, and NF1/CDKN2AB/SUZ12 mutant MPNST cells were used to study RT responses in vitro. CRISPRi was used to assess the functional effects of candidate gene repression. In vitro viability was measured by cell counts. Transcriptomic signatures were measured by bulk RNA-sequencing and integrated with single-cell RNA sequencing (scRNA-seq) data from patient-derived pNF and MPNST resection specimens.

RESULTS

Radiation dose response curves revealed pNF cells (IC50 0.61 Gy) were more radiosensitive than MPNST cells (4.15 Gy). WT iPNs, NF1 deficient iPNs, and pNFs cells displayed no difference in cell viability (p = 0.67; t-test) following initiation of 2 Gy x 5 fractions, while MPNST cells were significantly more viable (p = 0.02; t-test). Principal component analysis of bulk RNA-sequencing data at 5 or 14 days following 2 Gy x 5 fractions revealed cell line of origin accounted for the greatest inter-sample variation (64.9% variance), with additional components separating samples based on radiation presence and timing. Using the most variable genes in PCA space to identify markers of RT response, iPNs and pNFs upregulated pro-apoptotic pathways (BAD, DAPK3) at 5 days post-radiation while MPNST cells alone upregulated pro-survival growth factor signaling). At 14 days post radiation, MPNST cells uniquely upregulated TGFβ signaling and interferon response circuits. Incorporation of scRNA-seq data revealed enrichment of growth factor signaling and TGFβ signatures in MPNSTs compared to pNF. Moreover, MPNST harbored significantly fewer immune cells than pNFs (p = 0.008, t-test), suggesting cell-autonomous signaling and crosstalk with the microenvironment are both critical to MPNST radioresistance.

CONCLUSION

Our data indicate additional genetic hits beyond NF1 loss may be required for RT-associated malignant transformation of pNFs and radioresistance in MPNSTs. Analysis of transcriptomic responses to RT suggests that upregulated growth factor signaling and TGFβ-associated immunosuppression are distinct features of MPNST. Future work will focus on CRISPRi screens to unbiasedly nominate functional modifiers of RT response in NF1/CDKN2AB deficient tumors, which may be broadly useful in cancer.

Identifying Gene-Treatment Interactions and Targetable Radiation Vulnerabilities in Glioblastoma through Coupling of In Vivo CRISPR Perturbation and Single Cell Transcriptomics

PURPOSE/OBJECTIVE(S)

Glioblastoma (GBM) is an incurable brain tumor comprised of dynamic malignant cell states and microenvironment components that underlie treatment resistance. Here we use genome-wide CRISPR/Cas9 functional genomics to define biological drivers and therapeutic vulnerabilities across human and mouse GBM models. To interrogate these mechanisms in the context of the tumor microenvironment and in vivo physiology, we established in vivo Perturb-seq intracranially, a technique coupling functional genomics with single cell transcriptomics, where each cell is an individual experiment.

MATERIALS/METHODS

Orthotopic intracranial tumor models were established using human (GBM6, GBM43) or mouse (GL261, SB28) GBM cells stably expressing CRISPR interference (CRISPRi) machinery. Perturb-seq target selection for phenotyping of gene-treatment interactions was performed using genome-wide CRISPRi screens ± radiotherapy in cell cultures. Dual sgRNA lentivirus libraries were transduced either ex vivo prior to intracranial GBM cell transplantation or in vivo using intratumor convection enhanced delivery (CED). Transcriptional phenotyping was performed using single-cell RNA-seq with CRISPR direct capture following focal brain radiotherapy (2 Gy x 5) or mock treatment. GBM cell states were validated using single-nucleus RNA-seq data from 86 primary-recurrent patient-matched GBMs. Mechanistic and functional validation was performed using small molecule inhibitors, immunohistochemistry, clonogenic assays, and in vivo survival experiments.

RESULTS

In vivo Perturb-seq ± radiotherapy of 48 genes underlying GBM radiotherapy responses, which were enriched for DNA damage response and metabolic pathways, was performed in > 425,000 single cells. Radiotherapy induced 16 distinct GBM cell states, and genetic perturbations reprogrammed these cell states in a treatment-dependent fashion. Quantitative modeling of gene/radiotherapy interactions using high dimensional manifolds revealed in vivo-specific genetic dependencies. We revealed a critical role for Prkdc, the catalytic subunit of DNA-dependent protein kinase (DNA-PK), as a radiotherapy sensitizer through regulation of cell intrinsic growth and oxidative stress pathways, and cell extrinsic interferon and signaling pathways that altered cell-cell interactions in vivo. These pathways were also disrupted in single-nucleus RNA-seq analysis of post-radiotherapy human GBM tumors. Inhibition of Prkdc using a Food and Drug Administration approved small molecule sensitized GBM cells to radiotherapy and extended survival in mice harboring human intracranial xenografts.

CONCLUSION

We establish in vivo Perturb-seq in orthotopic GBM models as a platform for simultaneous functional genomic discovery and characterization of therapeutic targets, revealing an underappreciated role for Prkdc in GBM tumors in vivo that is targetable using small molecules. These tools are adaptable for a wide range of disease models and treatment modalities.

Spatial genomic, biochemical, and cellular mechanisms drive meningioma heterogeneity and evolution

Intratumor heterogeneity underlies cancer evolution and treatment resistance1-5, but targetable mechanisms driving intratumor heterogeneity are poorly understood. Meningiomas are the most common primary intracranial tumors and are resistant to all current medical therapies6,7. High-grade meningiomas cause significant neurological morbidity and mortality and are distinguished from low-grade meningiomas by increased intratumor heterogeneity arising from clonal evolution and divergence8. Here we integrate spatial transcriptomic and spatial protein profiling approaches across high-grade meningiomas to identify genomic, biochemical, and cellular mechanisms linking intratumor heterogeneity to the molecular, temporal, and spatial evolution of cancer. We show divergent intratumor gene and protein expression programs distinguish high-grade meningiomas that are otherwise grouped together by current clinical classification systems. Analyses of matched pairs of primary and recurrent meningiomas reveal spatial expansion of sub-clonal copy number variants underlies treatment resistance. Multiplexed sequential immunofluorescence (seqIF) and spatial deconvolution of meningioma single-cell RNA sequencing show decreased immune infiltration, decreased MAPK signaling, increased PI3K-AKT signaling, and increased cell proliferation drive meningioma recurrence. To translate these findings to clinical practice, we use epigenetic editing and lineage tracing approaches in meningioma organoid models to identify new molecular therapy combinations that target intratumor heterogeneity and block tumor growth. Our results establish a foundation for personalized medical therapy to treat patients with high-grade meningiomas and provide a framework for understanding therapeutic vulnerabilities driving intratumor heterogeneity and tumor evolution.

Targeted gene expression profiling predicts meningioma outcomes and radiotherapy responses

Background

Surgery is the mainstay of treatment for meningioma, the most common primary intracranial tumor, but improvements in meningioma risk stratification are needed and current indications for postoperative radiotherapy are controversial. Recent studies have proposed prognostic meningioma classification systems using DNA methylation profiling, copy number variants, DNA sequencing, RNA sequencing, histology, or integrated models based on multiple combined features. Targeted gene expression profiling has generated robust biomarkers integrating multiple molecular features for other cancers, but is understudied for meningiomas.

Methods

Targeted gene expression profiling was performed on 173 meningiomas and an optimized gene expression biomarker (34 genes) and risk score (0 to 1) was developed to predict clinical outcomes. Clinical and analytical validation was performed on independent meningiomas from 12 institutions across 3 continents (N = 1856), including 103 meningiomas from a prospective clinical trial. Gene expression biomarker performance was compared to 9 other classification systems.

Results

The gene expression biomarker improved discrimination of postoperative meningioma outcomes compared to all other classification systems tested in the independent clinical validation cohort for local recurrence (5-year area under the curve [AUC] 0.81) and overall survival (5-year AUC 0.80). The increase in area under the curve compared to the current standard of care, World Health Organization 2021 grade, was 0.11 for local recurrence (95% confidence interval [CI] 0.07-0.17, P < 0.001). The gene expression biomarker identified meningiomas benefiting from postoperative radiotherapy (hazard ratio 0.54, 95% CI 0.37-0.78, P = 0.0001) and re-classified up to 52.0% meningiomas compared to conventional clinical criteria, suggesting postoperative management could be refined for 29.8% of patients.

Conclusions

A targeted gene expression biomarker improves discrimination of meningioma outcomes compared to recent classification systems and predicts postoperative radiotherapy responses.

MerlinS13 phosphorylation controls meningioma Wnt signaling and magnetic resonance imaging features

Meningiomas are the most common primary intracranial tumors and are associated with inactivation of the tumor suppressor NF2/Merlin, but one-third of meningiomas retain Merlin expression and typically have favorable clinical outcomes. Biochemical mechanisms underlying Merlin-intact meningioma growth are incompletely understood, and non-invasive biomarkers that predict meningioma outcomes and could be used to guide treatment de-escalation or imaging surveillance of Merlin-intact meningiomas are lacking. Here we integrate single-cell RNA sequencing, proximity-labeling proteomic mass spectrometry, mechanistic and functional approaches, and magnetic resonance imaging (MRI) across meningioma cells, xenografts, and human patients to define biochemical mechanisms and an imaging biomarker that distinguish Merlin-intact meningiomas with favorable clinical outcomes from meningiomas with unfavorable clinical outcomes. We find Merlin drives meningioma Wnt signaling and tumor growth through a feed-forward mechanism that requires Merlin dephosphorylation on serine 13 (S13) to attenuate inhibitory interactions with β-catenin and activate the Wnt pathway. Meningioma MRI analyses of xenografts and human patients show Merlin-intact meningiomas with S13 phosphorylation and favorable clinical outcomes are associated with high apparent diffusion coefficient (ADC) on diffusion-weighted imaging. In sum, our results shed light on Merlin posttranslational modifications that regulate meningioma Wnt signaling and tumor growth in tumors without NF2/Merlin inactivation. To translate these findings to clinical practice, we establish a non-invasive imaging biomarker that could be used to guide treatment de-escalation or imaging surveillance for patients with favorable meningiomas.

BIOM-02. MUTATIONAL ANALYSIS AND SINGLE CELL SEQUENCING OF MELANOMA BRAIN METASTASES REVEALS BRAF STATUS CORRELATES WITH CLINICAL OUTCOME AND DIFFERENTIAL IMMUNE POPULATIONS

Understanding the molecular landscape and microenvironment of melanoma brain metastases is critical to devise improved treatments. Here, we perform bulk and single cell genomic analysis of melanoma brain metastases to identify molecular correlates of clinical outcome. 84 consecutive patients who underwent surgical resection at a single institution with a histo-pathologically confirmed diagnosis of melanoma brain metastasis were retrospectively identified. In 60 patients (71%) with sufficient brain metastasis tissue for targeted next generation sequencing, DNA mutations were assessed with a CLIA certified sequencing assay. Single nuclear RNA sequencing using the 10x platform was performed on n=6 samples from treatment naïve patients. Overall survival (OS) and CNS progression free survival (CNS PFS) from time of brain metastasis diagnosis were estimated using the Kaplan-Meier method. The median patient age was 62 years old (range: 25-78 years), and the median clinical follow up was 17 months. A total of 33 patients (39%) had BRAFV600E melanoma brain metastases. Multivariate analysis incorporating age, performance status, and extracranial disease revealed BRAF status was an independent prognostic factor for OS (p&lt; 0.05). In patients undergoing targeted next generation sequencing, the most common pathogenic variant was TERT promoter mutation (n=44; 73%). With regard to TCGA molecular melanoma subgroups, NRAS mutant (n=22; 37%) brain metastases were most common followed by BRAF mutant (n=20; 33%), NF1 mutant (n=11; 18%), and triple wildtype (n=7; 12%). Evaluation of clinical outcomes in the context of next generation sequencing results revealed no differences by TERT status but demonstrated worse overall survival in the BRAF mutant molecular group (p&lt; 0.01, log-rank test). Single nuclear sequencing of 36,115 nuclei across 6 samples revealed BRAF wildtype tumors exhibit greater infiltrating immune cell populations including microglia and T cell subtypes. Future work will require integration of these findings with different systemic therapy regimens and across larger, prospective, multi-institutional cohorts.

NIMG-15. INTEGRATED RADIOGRAPHIC AND PATHOLOGICAL ANALYSIS OF MALIGNANT PERIPHERAL NERVE SHEATH TUMORS (MPNSTS) REVEALS IMAGING CORRELATES OF MOLECULAR ALTERATIONS AND CLINICAL OUTCOME

Malignant peripheral nerve sheath tumors (MPNSTs) are the most common cause of death in patients with neurofibromatosis type 1 (NF-1) yet non-invasive diagnosis and risk stratification of NF-1-associated peripheral nerve tumors remains challenging. Moreover, the relationship between radiographic features and pathologic measures such as mitotic index and necrosis, or molecular markers of malignant transformation such as H3K27 trimethylation and Schwann cell marker (S100B, SOX10) expression remain unknown. Here, we integrate positron emission tomography (PET) (n=32 studies from 18 patients) and magnetic resonance imaging (MRI) (n=20 studies from 20 patients) with immunohistochemical analysis and clinical follow-up in a total of 20 patients with pathologically confirmed MPNST diagnosis. The median age was 33 years (range 5-74 years), n = 11 were male (55%) and n=13 (65%) harbored a clinical diagnosis of NF-1. Anatomically, n=6 (30%) tumors arose near the spine, n=5 (25%) arose in the extremities, and n=4 (20%) arose in the sacrum. By PET, the average preoperative SUVmax was 8.53 with a trend toward increased SUVmax in Ki-67 high tumors (SUVmax 10.58 vs. 6.47, p=0.08). No significant differences in SUVmax based on H3K27 trimethylation, SOX10, or S100B expression was noted. The appearance of cystic necrosis by MRI was significantly associated with H3K27 trimethylation loss (Chi-square p=0.04) with a trend toward increased KI-67 labeling (43% vs. 24%, p = 0.07), suggesting cystic necrosis identifies aggressive lesions. No other features were correlated with H3K27 trimethylation status or Ki-67 labeling index. With regard to clinical outcome, dichotomized SUVmax identified patient subgroups with significant differences in overall survival (OS), with high SUVmax tumors demonstrating improved survival (median OS: 250 months vs. 60 months, log-rank test p=0.02). Our data support a relationship between radiographic features, histopathologic characteristics and clinical outcomes. Future work will include longitudinal analysis, validation in larger, multi-institutional cohorts and incorporation of radiomic approaches.

CSIG-37. MERLIN S13 DEPHOSPHORYLATION DRIVES MENINGIOMA WNT SIGNALLING AND CELL PROLIFERATION

How Merlin-intact meningiomas arise in the absence of NF2/Merlin inactivation is incompletely understood. Here, we integrate single-cell RNA sequencing of 86,000 cells from meningioma xenografts with APEX2 proteomic proximity-labelling mass spectrometry and functional biochemical approaches to discover Merlin Serine 13 (S13) dephosphorylation drives meningioma Wnt signalling and cell proliferation. Cell biology, molecular biology, and biochemical techniques were used to validate Merlin functions in meningioma cells or xenografts using wildtype Merlin constructs or Merlin constructs encoding S13A, phosphomimetic S13D, or cancer-associated missense substitutions (L46R, A211D). Single-cell RNA sequencing of meningioma xenografts showed Merlin rescue activated the Wnt pathway in Merlin-deficient meningiomas. Proteomic proximity-labelling mass spectrometry revealed b-catenin, PKC, and PP1A interactions with wildtype Merlin, but not with Merlin L46R or A211D. b-catenin does not interact with other FERM family members, and Merlin contains a unique N-terminal domain (NTD) with a PKC phosphorylation motif overlapping with a PP1A dephosphorylation motif at S13. Thus, we hypothesized the Merlin S13, PKC, and PP1A may be important for Wnt signalling in Merlin-intact meningiomas. In support of this hypothesis, over-expression of wildtype Merlin or Merlin S13A but not Merlin DNTD, S13D, L46R, A211D, or other FERM family members drove meningioma Wnt signalling and sustained meningioma cell proliferation in vivo. Moreover, b-catenin was detected in proximity to Merlin S13D but not Merlin S13A in meningioma cells. Meningioma cell fractionation and immunofluorescence showed Merlin S13D over-expression stabilized b-catenin at the plasma membrane and inhibited Wnt signalling. Phospho-proteomic mass spectrometry and custom phospho-specific antibodies integrated with shRNA or siRNA gene suppression demonstrated PKC phosphorylated Merlin S13, but meningioma Wnt pathway activation induced PP1A to dephosphorylate Merlin S13 and drive cell proliferation. In summary, Merlin S13 dephosphorylation drives meningioma Wnt signalling and cell proliferation. These data reveal a novel tumor-promoting function of NF2/Merlin in Merlin-intact meningiomas.

PATH-07. MULTIPLATFORM MOLECULAR ANALYSES REFINE CLASSIFICATION AND PROGNOSTICATION OF GLIOMAS ARISING IN PATIENTS WITH NEUROFIBROMATOSIS TYPE 1

BACKGROUND

Gliomas arising in patients with neurofibromatosis type 1 (NF1) are heterogeneous, occurring from childhood through adulthood, can be histologically low-grade (LG) or high-grade (HG), and follow an indolent or aggressive clinical course. Comprehensive profiling of genetic alterations beyond NF1 and epigenetic classification of these tumors remain limited.

METHODS

Next-generation sequencing and DNA methylation profiling was performed on gliomas from 47 NF1 patients and correlated with clinicopathologic features, treatment, and outcomes.

RESULTS

30 tumors demonstrated biallelic inactivation of NF1 without additional oncogenic alterations (“molecular LG subgroup”, median age 14 yrs). The remaining 17 tumors harbored additional oncogenic alterations beyond NF1 (“molecular HG subgroup”, median age 28), most frequently CDKN2A homozygous deletion (n=13), ATRX mutation (n=8), PIK3CA or PIK3R1 mutation (n=4), and TP53 mutation (n=3). Survival analysis showed significant differences in time to progression (137 vs 11 mos, p&lt; 0.0001) and median survival time (undefined vs 37 mos, p &gt; 0.0001) for molecular LG versus HG subgroups. DNA methylation profiles of the molecular LG subgroup resolved into a new epigenetic cluster closest to but divergent from the three existing reference classes of sporadic pilocytic astrocytoma. DNA methylation profiles of the molecular HG subgroup demonstrated most tumors epigenetically align with either HGAP or various subclasses of IDH-wildtype GBM.

CONCLUSION

NF1-associated gliomas stratify into two molecular subgroups. The “molecular LG subgroup” occurs primarily during childhood, harbors biallelic NF1 inactivation only, follows a more indolent clinical course, and has a unique epigenetic signature for which we propose the terminology “pilocytic astrocytoma, arising in the setting of NF1”. The “molecular HG subgroup” occurs primarily during adulthood, harbors additional oncogenic alterations including CDKN2A homozygous deletion and ATRX mutation, follows a more aggressive clinical course, and is epigenetically diverse. These findings highlight recurrently altered pathways in NF1-associated gliomas and help inform targeted therapeutic strategies for this patient population.

EPCO-01. EPIGENETIC REPROGRAMMING SHAPES THE MOLECULAR AND CELLULAR LANDSCAPE OF SCHWANNOMA

DNA methylation profiling provides robust classification of nervous system tumors, but mechanisms driving epigenetic identity of individual tumor types are incompletely understood. Integrating DNA methylation profiling (n=76), RNA sequencing (n=24), single-cell RNA-sequencing (n=9), and mass cytometry (n=9), we discovered vestibular schwannomas are comprised of two epigenetic groups distinguished by neural crest development pathways or repair and regeneration pathways driving immune infiltration. Analyses of preoperative magnetic resonance imaging studies (n=66) or paired primary and recurrent schwannomas (n=13) suggested radiotherapy was sufficient but not necessary for epigenetic reprogramming of neural crest enriched schwannomas into immune enriched schwannomas. In support of this hypothesis, DNA methylation profiling, RNA sequencing, single-cell RNA sequencing, proteomic mass spectrometry, and lymphocyte migration assays demonstrated radiotherapy epigenetically reprogramed viable schwannoma cells to secrete immunomodulatory signals and recruit lymphocytes in vitro. Genome-wide CRISPRi screens identified histone acetyltransferases or DNA methyltransferases driving schwannoma radiotherapy responses, including the epigenetic regulators KDM5C or KDM1A. CRISPRi and lymphocyte migration assays ± radiotherapy confirmed KDM5C drives schwannoma immune infiltration whereas KDM1A inhibits schwannoma immune infiltration. To define genomic mechanisms underlying epigenetic group identity, we performed pooled CRISPRi screening coupled with single-cell RNA sequencing (Perturb-seq) of 44 schwannoma markers. In parallel, we developed single nuclei profiling of chromatin accessibility through paired ATAC sequencing and RNA sequencing coupled with pooled CRISPRi screening (snARC-seq) of 54 epigenetic regulators identified by our genome-wide CRISPRi screen. Functional genomic approaches revealed the tyrosine phosphatase PTPRG as a regulator of survival, and KDM5C and KDM1A as regulators of inflammation. In summary, we report two epigenetic groups of schwannomas and mechanisms underlying epigenetic group identity using a new functional genomic technique allowing for simultaneous interrogation of single-cell epigenetic and gene expression changes in the context of genetic and therapeutic perturbations. These data elucidate a novel epigenetic mechanism of action of radiotherapy.

BIOM-54. ANALYTICAL VALIDATION OF A TARGETED GENE EXPRESSION BIOMARKER PREDICTING MENINGIOMA OUTCOMES AND RADIOTHERAPY RESPONSES

BACKGROUND

Improvements in meningioma risk stratification are needed to guide postoperative management. We previously developed and externally validated a targeted gene expression biomarker predicting meningioma outcomes and radiotherapy response using fresh frozen meningiomas. Here, we present the analytical validity, test-retest and cross-platform reproducibility, intra-tumor heterogeneity, and formalin fixed paraffin embedded (FFPE) concordance for this biomarker.

METHODS

Matched FFPE and fresh frozen samples from 50 meningiomas underwent RNA extraction for concordance testing using a custom Nanostring gene expression panel comprised of 34 meningioma genes and 7 housekeeping genes. Matched Nanostring gene expression profiling and RNA-sequencing was available from 173 fresh frozen meningiomas. Nanostring batch, machine, and technician variability was tested on 10 FFPE meningiomas using 2 independent batches of biomarker reagents that were processed at 2 independent laboratories. To study intra-tumor heterogeneity, 68 spatially distinct meningioma biopsies obtained under stereotactic guidance from 13 tumors were analyzed using the Nanostring gene expression biomarker.

RESULTS

Matched FFPE and fresh frozen meningioma samples (N=50) demonstrated high gene expression concordance (Pearson R=0.89, F-test P&lt; 2.2e-16) and risk score concordance (R=0.78, F-test P&lt; 1.8e-11, residual standard error 0.12). The biomarker achieved high performance on FFPE samples (local freedom from recurrence [LFFR] c-index 0.75±SEM 0.05, 5y LFFR AUC 0.84, 95% interval 0.67-0.96). Test-retest concordance on FFPE samples (N=10) across independent reagent batches, machines, and technicians was high (gene expression concordance: R=0.97; risk score concordance R=0.94). Transcript counts were concordant across Nanostring and RNA sequencing approaches (N=173 frozen samples, R=0.90). Stereotactic intra-operative sampling (N=68 samples from 13 patients) revealed low levels of intra-tumor heterogeneity (median inter-quartile risk score within tumor: 0.10±0.01).

CONCLUSIONS

We demonstrate analytical reproducibility and robustness of a gene expression biomarker predicting meningioma outcomes and radiotherapy responses in FFPE and frozen samples across multiple conditions and platforms.

DDDR-06. NEUROFIBROMATOSIS TUMOR SUPPRESSORS COOPERATIVELY DRIVE TUMOR DE-DIFFERENTIATION AND MEK INHIBITOR RESISTANCE IN PERIPHERAL NERVOUS SYSTEM TUMORS

Schwann cell derived tumors comprising schwannomas, neurofibromas, and malignant peripheral nerve sheath tumors (MPNSTs) are the most common cancers of the peripheral nervous system and often arise in patients with neurofibromatosis type-1 (NF-1) or type-2 (NF-2). NF-1 is caused by loss of NF1, a negative regulator of Ras signaling, and NF-2 is caused by loss of NF2, a pleiotropic tumor suppressor with numerous functions including inhibition of PAK signaling. However, whether functional interactions exist between the NF1 and NF2 tumor suppressors remain unclear. More broadly, there are currently no effective molecular therapies for patients with Schwann cell tumors beyond the MEK inhibitor selumetinib to treat neurofibromas in patients with NF-1. Here, we integrate DNA methylation profiling, whole exome sequencing, bulk and single-cell RNA sequencing, biochemistry, and pharmacology across human samples, cell lines, and mouse xenografts to identify cellular de-differentiation as a driver of malignant transformation and selumetinib resistance. Single nuclear RNA-sequencing of human neurofibromas (n = 3) or MPNSTs (n = 3) revealed a total of 13 cell types with increased proliferating, de-differentiated tumor cell populations in MPNST samples. Single cell RNA-sequencing of MPNST mouse xenografts revealed persistence of de-differentiated cell populations in selumetinib treated samples compared to vehicle control, suggesting cellular de-differentiation underlies treatment resistance. A genome-wide CRISPRi screen for mediators of selumetinib response in NF1 deficient neurofibroma cells revealed NF2 loss drives selumetinib resistance. Consistently, NF2 suppression in NF1 deficient neurofibroma cells caused Schwann cell de-differentiation and activation of PAK, a serine threonine kinase. Translationally, a small molecule PAK inhibitor in combination with selumetinib formed an effective therapy in mouse MPNST xenografts. In sum, we elucidate a paradigm of de-differentiation driving malignant transformation and treatment resistance in Schwann cell tumors, uncovering a functional link between the NF1 and NF2 tumor suppressors that sheds light on a novel therapeutic vulnerability.

PATH-37. SPATIAL GENE EXPRESSION PROGRAMS AND PROTEIN SIGNALING MECHANISMS DRIVE MENINGIOMA EVOLUTION AND THERAPEUTIC VULNERABILITY

Intratumor heterogeneity drives cancer evolution and resistance to therapy, but unbiased approaches to elucidate mechanisms driving intratumor heterogeneity have been lacking. Here, we integrate spatial gene expression programs and protein signaling mechanisms across 16 meningioma samples to define how intratumor heterogeneity drives molecular classification, temporal evolution, or spatial evolution of the most common primary intracranial tumor. Spatial transcriptomic analysis was performed on 38,718 regions and spatial profiling of 72 proteins comprising proliferation, stress, microenvironment, immune, or signaling modules was performed on 82 regions. DNA methylation, copy number variant, targeted gene expression profiling, targeted DNA sequencing, histologic, or immunohistochemical analyses (Ki67, H3K27me3, p16) were performed on all meningiomas to study intratumor heterogeneity in the context of pre-existing classification schemes. Primary meningioma cells, CRISPR interference, pharmacology, and 3D co-culture models were used for mechanistic and functional validation. Spatial analyses revealed significant intratumor or intertumor heterogeneity irrespective of meningioma histologic subtype or grade, DNA methylation group (Merlin-intact, Immune-enriched, Hypermitotic), copy number variant (1p loss, 1q gain, 6p gain, 9p loss, 14q loss, 22q loss), gene expression risk score, or driver mutation (NF2, CDKN2A/B, TERT promoter, BAP1, SMARCB1, ARID1A). Spatial analyses on paired histologically or molecularly distinct regions from individual meningiomas (n=4), or on paired primary and recurrent meningioma samples (n=9), revealed conserved proliferation, immune, or signaling mechanisms underlying meningioma evolution. Mechanistic and functional studies validated therapeutic vulnerabilities across spatial clusters to combinations of FDA-approved small molecules inhibiting the cell cycle (abemaciclib), epigenetic regulators (vorinostat), the DNA damage response (nariparib), MAPK signaling (erlotinib, selumetinib), or PI3K-AKT signaling (copanlisib). In summary, these data define spatial gene expression programs and protein signaling mechanisms driving meningioma evolution and therapeutic vulnerability, shedding light on past clinical failures and elucidating novel combinations of concurrent or sequential molecular therapies to treat meningiomas that are resistant to standard interventions.

A targeted gene expression biomarker and association with meningioma outcomes and radiotherapy

2007

Background: Improvements in risk stratification of meningioma are needed to guide post-operative management and application of adjuvant therapy. Although profiling of DNA methylation, copy number variants (CNVs), RNA sequencing, and exome sequencing have better elucidated meningioma biology, these approaches have not revealed clinically tractable biomarkers for radiotherapy responses. In this study, we develop and validate a targeted gene expression biomarker to predict meningioma outcomes and benefit from radiotherapy. Methods: Targeted gene expression profiling was performed on a development set of 173 meningiomas (median follow-up 8.1 years) and a validation set of 331 consecutive meningiomas (median follow-up 6.1 years) treated at independent institutions (70% WHO grade 1, 24% WHO grade 2, 6% WHO grade 3). All patients underwent surgery (n = 504) with or without postoperative radiotherapy (n = 73 with radiation). Regularized Cox regression within the development set resulted in a continuous gene expression risk score for local freedom from recurrence (LFFR). The model (34 genes and 7 housekeeping genes) and thresholds for low, intermediate, and high-risk scores were locked and applied to the validation set. Results: The gene expression risk score outperformed WHO grade (validation 5-year LFFR delta-AUC 0.15, 95% CI 0.076-0.229, p = 0.001) and DNA methylation grouping (delta-AUC 0.075, 95% CI 0.006-0.130, p = 0.01) for LFFR, disease-specific survival, and OS, achieving a negative predictive value for recurrence at 5-years of 93.2%. The biomarker reclassified 35.8% of WHO grade 1 tumors as intermediate or high risk (5-year LFFR/OS 62%/79%), and 18.3% of WHO grade 2-3 tumors as low risk (5-year LFFR/OS 78%/100%). The biomarker was independently prognostic after accounting for WHO grade, extent of resection, primary versus recurrent presentation, CNV status, DNA methylation group, and Ki67 labeling index, and was predictive for LFFR after postoperative radiotherapy, with a hazard ratio of 0.41 for intermediate to high risk propensity-matched meningiomas (95% CI 0.2-0.9, p = 0.0002) versus 0.79 for low risk meningiomas (95% CI 0.1-8.8, p = 0.5182). Conclusions: Targeted gene expression profiling of 504 meningiomas resulted in a biomarker which improved discrimination of meningioma local recurrence, disease-specific survival, and overall survival, and also predicted benefit from radiotherapy.

Genomic analysis and clinical correlations of non-small cell lung cancer (NSCLC) brain metastasis (BM)

2008

Background: Approximately 30% of patients with NSCLC present with BM, and up to 50% of patients ultimately develop BM. While modern NSCLC-directed agents yield excellent systemic response, most patients require focal treatment. Prior reports of BM genomics have been limited by low numbers, missing clinical data, and lack of matched specimens. Here, we report the largest cohort to date of molecularly profiled NSCLC BM samples with clinical correlates. Methods: Clinical data and outcomes for 244 patients with NSCLC and resected BM were identified, and BM samples were assessed with one of four versions (341, 410, 468, 505) of MSK-IMPACT, a custom FDA-approved next generation sequencing-based tumor sequencing assay. 51 (20.9%) patients had matched primary site tissue, and 44 (18%) patients had matched tissue from another metastatic site or CSF. Genomic alterations were filtered for driver variants using OncoKB. Results: Median age was 66 years (range 31-91), and median follow-up was 2.3 years (IQR 1.3-4.3). Adenocarcinoma was the most common histology (183, 78%). Half presented with a single BM, and 121 (51%) patients were treatment naive. Most (197, 83%) received adjuvant stereotactic radiosurgery (SRS) to the resection site and 28% received SRS to additional BM. After resection, 130 (55.1%) had CNS progression, often regional (54, 42%). SRS to new BMs (32%) was the most common salvage treatment. Median overall survival from BM diagnosis was 2.5 years (95%CI 2.1-3.2). Median CNS-progression-free survival was 1.2 years (95%CI 0.9-1.4). The most frequently altered genes in BM samples were TP53 (72%), CDKN2A (34%), KRAS (31%), KEAP1 (26%), and EGFR (21%). CDKN2A was more frequently altered in BM samples when compared to NSCLC primary samples (34% vs 14%, p = 0.003, q = 0.034). With regard to overrepresented gene sets, cell cycle pathway alterations were enriched in BM (56% vs 31%, p = 0.002, q = 0.022). BM samples had a significantly higher fraction of genome altered relative to the primary samples (p < 0.0001, q < 0.0001). After grouping patients based on type of CNS progression, we found that EGFR alterations were enriched in patients with leptomeningeal failures when compared to both patients without progression (42% vs 18%, p = 0.03, q = 0.93) and to patients with either local or regional progression (42% vs 19%, p = 0.03, q = 0.9). Conclusions: In the largest-ever assembled cohort of genomically-profiled NSCLC BM, we found significant enrichment for CDKN2A and cell cycle pathway alterations in BM compared to extracranial disease, as well as a higher fraction of genome altered, in BMs compared to matched primary tumor controls. We also observed EGFR alteration enrichment in patients who develop LMD, suggesting specific biologic underpinnings driving patterns of CNS failure. Further investigation into the role of systemic therapy and time course will elucidate potential mechanisms for CNS failure in patients with NSCLC.

CSIG-01. EPIGENETIC REPROGRAMMING DRIVES MALIGNANT PERIPHERAL NERVE SHEATH TUMOR (MPNST) DE-DIFFERENTIATION AND TREATMENT RESISTANCE

Schwann cell derived tumors comprising schwannomas, neurofibromas, and malignant peripheral nerve sheath tumors are the most common malignancies of the peripheral nervous system. While schwannomas and neurofibromas are benign, MPNSTs are malignant, metastasize, and respond poorly to treatment. Neurofibromas and MPNSTs are associated with loss of NF1, a tumor suppressor that inhibits Ras/MEK signaling, and MPNSTs alone are distinguished by loss of the Polycomb Repressive Complex 2 (PRC2), an epigenetic regulator of methylation. To understand the genomic mechanisms of Schwann cell tumorigenesis and treatment resistance, we performed DNA methylation profiling, RNA-sequencing, and whole exome sequencing of primary Schwann cell tumor resection specimens (n=119 total: n=66 schwannoma, n=13 neurofibroma, n=40 MPNSTs). Hierarchical clustering identified three epigenetic Schwann cell tumor groups with transcriptional differences in PRC2 target genes associated with Schwann cell differentiation. Integrating biochemical and genomic approaches in primary human tumor cell lines from NF1 intact peripheral nerve, NF1 mutant neurofibromas, and MPNSTs, we found MPNST and neurofibroma cell lines with CRISPR knockout SUZ12 or EZH1/2 neurofibroma cell lines demonstrated repression of Schwann cell differentiation genes and induction of Ras signaling target genes. Further, MPNST cells deficient in PRC2 and NF1 exhibited increased basal active Ras-GTP levels, and therapeutically, PRC2 deficient MPNST cell lines were more resistant to the MEK inhibitor selumetinib and radiotherapy when compared to NF1-deficient neurofibroma cells. Single cell RNA sequencing analysis suggested distinct mechanisms of selumetinib resistance in PRC2 intact neurofibroma cells compared to PRC2-deficient MPNST cells. Taken together, our data demonstrate the importance of epigenetic dysregulation in malignant Schwann cell transformation and suggest differentiation status underlies a novel mechanism of MEK inhibitor resistance.

BIOM-40. TARGETED GENE EXPRESSION PROFILING PREDICTS MENINGIOMA OUTCOMES AND RADIOTHERAPY RESPONSES

BACKGROUND

Surgery is the mainstay of meningioma treatment, but improvements in meningioma risk stratification are needed and indications for postoperative radiotherapy are controversial. DNA methylation profiling, copy number variants (CNVs), exome sequencing, and RNA sequencing have improved understanding of meningioma biology, but have not superseded histologic grading, or revealed biomarkers for radiotherapy responses. To address these unmet needs, we optimized and validated a targeted gene expression biomarker predicting meningioma outcomes and responses to radiotherapy.

METHODS

Targeted gene expression profiling was performed on a discovery cohort of 173 meningiomas (median follow-up 8.1 years) and a validation cohort of 331 meningiomas (median follow-up 6.1 years) treated with surgery (n=504) and postoperative radiotherapy (n=73) at independent, international institutions (70% WHO grade 1, 24% WHO grade 2, 6% WHO grade 3). Optimized targeted gene expression models predicting clinical outcomes (34 genes) or radiotherapy responses (12 genes) were developed from the discovery cohort, and compared to histologic and molecular classification systems by performing DNA methylation profiling, CNV analysis, exome sequencing, and RNA sequencing on the same meningiomas.

RESULTS

Targeted gene expression profiling achieved a concordance-index of 0.75 ± 0.03 (SEM) for local freedom from recurrence (LFFR) and 0.72 ± 0.03 for overall survival (OS) in the validation cohort, outperforming WHO grade (5-year LFFR delta-AUC 0.15, 95% CI 0.076-0.229, p=0.001) and DNA methylation grouping (delta-AUC 0.075, 95% CI 0.006-0.130, p=0.01) for LFFR, disease-specific survival, and OS. The biomarker was independently prognostic after accounting for WHO grade, extent of resection, primary versus recurrent presentation, CNV status, DNA methylation group, and Ki67 labeling index, and identified meningiomas benefiting from radiotherapy (interaction p-value=0.0008), suggesting postoperative radiotherapy could be refined in 30.2% of cases.

CONCLUSIONS

Targeted gene expression profiling of 504 meningiomas improves discrimination of meningioma local recurrence, disease-specific survival, and overall survival, and predicts radiotherapy responses.

PATH-36. INTRATUMOR HETEROGENEITY AND BIOINFORMATIC DIFFERENCES INFLUENCE MENINGIOMA MOLECULAR CLASSIFICATION

Molecular alterations such as CDKN2A inactivation and TERT promoter mutation are new criteria for grade 3 meningiomas in the 5th edition of the WHO Classification of Tumors of the Central Nervous System. However, consensus approaches to identify copy number variants (CNVs) and short somatic variants in meningiomas are lacking. Here, we performed integrated DNA methylation profiling, RNA-sequencing, and targeted DNA mutational profiling on 10 stereotactically-collected, regionally-distinct samples from 4 meningiomas. Targeted DNA sequencing revealed numerous private short somatic variants from multiple sites within individual meningiomas, including a TERT promoter mutation in only 1 of 2 samples from the same tumor. DNA methylation profiling revealed differences in biologic groups and immune cell enrichment between regionally-distinct samples within individual meningiomas. CNV status was evaluated using DNA methylation profiling and RNA sequencing on 14 stereotactically-collected, regionally-distinct samples from 2 meningiomas. Phylogenetic architectures from DNA methylation profiling and targeted DNA sequencing were highly concordant and shared 99.12% of CNVs while RNA sequencing identified only 39% of the CNVs called from DNA based approaches. Finally, CNV analysis based on single-cell RNA sequencing revealed partially overlapping CNVs across meningioma cells within an individual tumor, suggesting subclonal populations may influence CNV-based meningioma molecular classification and underlie limitations in defining CNVs from bulk RNA-sequencing. In sum, these data highlight the relative strengths and weaknesses of various approaches for molecular analysis of meningiomas complicated by intratumor heterogeneity due to non-tumor cells and subclonal populations of meningioma cells. Future efforts to incorporate molecular analysis into the diagnostic paradigm for meningiomas may require orthogonal validation across multiple platforms or image-guided meningioma sampling to select the most aggressive regions for molecular profiling.

Digital droplet PCR accurately quantifies SARS-CoV-2 viral load from crude lysate without nucleic acid purification

The COVID-19 pandemic caused by the SARS-CoV-2 virus motivates diverse diagnostic approaches due to the novel causative pathogen, incompletely understood clinical sequelae, and limited availability of testing resources. Given the variability in viral load across and within patients, absolute viral load quantification directly from crude lysate is important for diagnosis and surveillance. Here, we investigate the use of digital droplet PCR (ddPCR) for SARS-CoV-2 viral load measurement directly from crude lysate without nucleic acid purification. We demonstrate ddPCR accurately quantifies SARS-CoV-2 standards from purified RNA and multiple sample matrices, including commonly utilized universal transport medium (UTM). In addition, we find ddPCR functions robustly at low input viral copy numbers on nasopharyngeal swab specimens stored in UTM without upfront RNA extraction. We also show ddPCR, but not qPCR, from crude lysate shows high concordance with viral load measurements from purified RNA. Our data suggest ddPCR offers advantages to qPCR for SARS-CoV-2 detection with higher sensitivity and robustness when using crude lysate rather than purified RNA as input. More broadly, digital droplet assays provide a potential method for nucleic acid measurement and infectious disease diagnosis with limited sample processing, underscoring the utility of such techniques in laboratory medicine.

MNGI-04. PATTERNS OF FAILURE AND FACTORS INFLUENCING LOCAL RECURRENCE OF MENINGIOMA TREATED WITH POSTOPERATIVE RADIATION THERAPY

BACKGROUND

Factors associated with meningioma recurrence after postoperative radiotherapy are poorly understood, and the optimal postoperative radiotherapy target delineation for meningioma is unknown. The objective of this study was to identify factors influencing meningioma recurrence after postoperative radiotherapy to inform patient selection and treatment design.

METHODS

Medical records were retrospectively reviewed for patients who underwent meningioma resection at a single institution between 1991 and 2015. Patients with sufficient tumor tissue for histologic classification and who received postoperative radiation therapy with external beam radiotherapy (EBRT), stereotactic radiosurgery (SRS) or brachytherapy, were included. Local freedom from recurrence (LFFR) was analyzed according to tumor and treatment characteristics using the Kaplan Meier method.

RESULTS

We identified 86 patients with 96 meningiomas who met inclusion criteria. Nineteen meningiomas (20%) were WHO grade I, 56 (58%) were grade II and 21 (22%) were grade III. Forty-one meningiomas (43%) were recurrent, and 55 (57%) were de novo. The postoperative radiotherapy modality was EBRT for 58 patients (60%), SRS for 20 (21%) patients and brachytherapy for 18 (19%) patients. With a median follow up of 4.3 years (IQR 2.1–8.8 years), there were 48 (50%) local failures that occurred a median of 17 months after immediate prior resection (IQR 9–33 months). WHO grade II/III and recurrent meningiomas had worse LFFR (p< 0.001). The 5-year LFFR was 53% after EBRT (95% CI 41–69%), 53% after SRS (95% CI 34–84%) and 15% after brachytherapy (95% CI 3–74%), although meningiomas that were treated with brachytherapy were significantly more likely to have received prior EBRT or SRS (86% versus 29%, p< 0.001).

CONCLUSIONS

These data provide a foundation for understanding patterns of meningioma recurrence after postoperative radiotherapy. Ongoing analyses aim to quantify the relationships between postoperative radiotherapy dose, target delineation and local control of meningioma.

GENE-37. VESTIBULAR SCHWANNOMA IS COMPRISED OF NEURAL CREST AND IMMUNE SUBGROUPS

BACKGROUND

Vestibular schwannomas (VS) are tumors arising from cranial nerve Schwann cells and show variable outcomes after treatment, including oscillation in size for many years after radiosurgery. To understand the unique biology of VS, we performed multiplatform molecular profiling to develop a single cell atlas of VS and reveal that VS exists on a molecular axis defined by neural crest and immune genes.

METHODS

Sixty-six sporadic VS with available tissue for molecular profiling from 59 consecutive patients at a single institution were included. 850K DNA methylation arrays and RNA sequencing were used to profile both primary (76%) and recurrent (24%) tumors. Single nuclei RNA sequencing of 7 tumors and single cell RNA sequencing of 3 tumors and cell lines were used to define the cellular composition of VS and heterogeneous changes in molecular programs following irradiation. Molecular subtyping was performed by hierarchical clustering of differentially-methylated DNA probes and validated using transcriptomic data. Mechanistic experiments were performed using cultured human schwann cells and human vestibular schwannoma cells, confocal microscopy, CRISPR interference, proteomic mass spectrometry and lymphocyte migration assays.

RESULTS

Multiplatform genomic profiling and machine learning revealed that VS is comprised of two distinct molecular subtypes characterized by heterogeneous cell populations. Neural crest enriched VS express primary cilia and are associated with misactivation of the Hedgehog pathway. Consistently, we find that the Hedgehog pathway antagonist vismodegib blocks the growth of human Schwann cells. Irradiation epigenetically reprograms tumors and cell lines to reduce ciliary length, attenuate Hedgehog signaling, activate senescence pathways, and express cytokines and apolipoproteins that recruit lymphocytes and macrophages to immune enriched VS.

CONCLUSIONS

Our data reveal novel molecular subtypes of VS and establish a framework for understanding how irradiation modifies the epigenome and tumor microenvironment.

TMOD-27. A NEURAL CREST CELL SUBPOPULATION UNDERLIES INTRATUMOR HETEROGENEITY IN MENINGIOMA

BACKGROUND

Meningiomas are the most common primary intracranial tumor, and high grade meningiomas are resistant to most cancer therapies. Intratumor heterogeneity is a recognized source of resistance to treatment in numerous malignancies. Thus, we hypothesized that investigating molecular heterogeneity in meningiomas would elucidate biologic drivers and shed light on tumor evolution and mechanisms of resistance.

METHODS

We collected 86 spatially distinct samples at the time of resection from 13 meningiomas. Seven meningiomas were WHO grade I (46 samples), three were grade II (22 samples), and three were grade III (18 samples). Seven meningiomas were sampled at the time of salvage surgery (48 samples), and 6 were sampled at the time of initial diagnosis (38 samples). We performed multiplatform molecular profiling of these samples to identify drivers of intratumor heterogeneity, and validated our results using meningioma cells co-cultured with human cerebral organoids and RNA sequencing of paired primary and recurrent meningiomas.

RESULTS

Using bulk RNA sequencing, DNA methylation profiling and phylogenetic analysis of spatially distinct samples, we discovered significant transcriptomic, epigenomic and genomic heterogeneity in meningioma. In particular, we identified chromosomal structural alterations and differences in immune and neuronal signaling that underlie clonal evolution in high grade tumors. Using MRI-stratified bulk RNA sequencing, single nuclear RNA sequencing, RNA sequencing of paired primary and recurrent meningiomas, and live cell microscopy and single cell RNA sequencing of meningioma cells in co-culture with human cerebral organoids, we revealed a rare meningioma cell subpopulation with strong transcriptional concordance to the neural crest, a multipotent embryonic tissue that forms the meninges in development.

CONCLUSIONS

These data suggest that misactivation of a developmental cell population underlies intratumor heterogeneity in meningioma and that expression of neural crest and immediate early genes are an important step in meningeal oncogenesis.

Inhibition of matrix metalloproteinase-2 improves endothelial function and prevents hypertension in insulin-resistant rats

BACKGROUND AND PURPOSE

Insulin resistance is often found to be associated with high blood pressure. We propose that in insulin-resistant hypertension, endothelial dysfunction is the consequence of increased activity of vascular MMP-2. As MMP-2 proteolytically cleaves a number of extracellular matrix proteins, we hypothesized that MMP-2 impairs endothelial function by proteolytic degradation of endothelial NOS (eNOS) or its cofactor, heat shock protein 90 (HSP90).

EXPERIMENTAL APPROACH

We tested our hypothesis in bovine coronary artery endothelial cells and fructose-fed hypertensive rats (FHR), a model of acquired systolic hypertension and insulin resistance.

KEY RESULTS

Treatment of FHRs with the MMP inhibitor doxycycline, preserved endothelial function as well as prevented the development of hypertension, suggesting that MMPs impair endothelial function. Furthermore, incubating endothelial cells in vitro with a recombinant MMP-2 decreased NO production in a dose-dependent manner. Using substrate cleavage assays and immunofluorescence microscopy studies, we found that MMP-2 not only cleaves and degrades HSP90, an eNOS cofactor but also co-localizes with both eNOS and HSP90 in endothelial cells, suggesting that MMPs functionally interact with the eNOS system. Treatment of FHRs with doxycycline attenuated the decrease in eNOS and HSP90 expression but did not improve insulin sensitivity.

CONCLUSIONS AND IMPLICATIONS

Our data suggest that increased activity of MMP-2 in FHRs impairs endothelial function and promotes hypertension. Inhibition of MMP-2 could be a potential therapeutic strategy for the management of hypertension.

Effects of insulin resistance and testosterone on the participation of cyclooxygenase isoforms in vascular reactivity

Testosterone plays an important role in mediating hypertension and altered vascular reactivity associated with insulin resistance. In addition to other pathways, testosterone-dependent changes in aortic cyclooxygenase (COX-2) mRNA levels affect blood pressure following insulin resistance. However their effects on vascular tone are unclear. We studied the changes in contraction response to phenylephrine (PE) in the aorta and superior mesenteric artery (SMA) from intact and gonadectomized fructose-fed rats. Constriction response to PE was studied in tissues incubated with the COX-1 and COX-2-selective antagonists, SC-560 and NS-398, respectively, and indomethacin, in addition to assessing its role in endothelium-dependent relaxation. Finally changes in COX-2 protein expression and plasma thromboxane A2 (TXA2), a downstream vasoconstrictor metabolite of COX-2, were measured. In fructose-fed rats, castration prevented the increase in blood pressure but not insulin resistance. The involvement of COX-2 in mediating the alpha-adrenergic vasoconstriction was higher in intact rat aorta compared to COX-1, which was prevented by castration. However, in the SMA, COX-2 participation was dependent on testosterone alone. Fructose-induced attenuation of endothelial relaxation was restored by indomethacin, which suggests a pro-vasoconstrictor role for COX. Both diet and testosterone did not alter vascular COX-2 expression thus suggesting the involvement of downstream testosterone-dependent pathways. This is supported by increased plasma TXA2 in the castrated rats compared to intact rats. Isoform-specific actions of COX are tissue-selective in states of insulin resistance and involve potential testosterone-dependent downstream targets. Further studies are needed to investigate the role of androgens and insulin resistance in vascular arachidonic acid metabolism.

Renal expression of arachidonic acid metabolizing enzymes and RhoA/Rho kinases in fructose insulin resistant hypertensive rats

Fructose feeding has been shown to induce insulin resistance and hypertension. Renal protein expression for the cytochrome P (CYP) 450 arachidonic acid metabolizing enzymes has been shown to be altered in other models of diet-induced hypertension. Of special interest is CYP4A, which produces the potent vasoconstrictor, 20-hydroxyeicosatetraenoic acid and CYP2C, which catalyzes the formation of the potent dilators epoxyeicosatrienoic acids as well as soluble epoxide hydrolase (sEH) which metabolizes the latter to dihydroxyeicosatrienoic acids. The RhoA/Rho kinase (ROCK) signaling pathway is downstream of arachidonic acid and is reported to mediate metabolic-cardio-renal dysfunctions in some experimental models of insulin resistance and diabetes. The aim of the present study was to determine the expression of CYP4A, CYP2C23, CYP2C11, sEH, RhoA, ROCK-1, ROCK-2, and phospho-Lin-11/Isl-1/Mec-3 kinase (LIMK) in kidneys of fructose-fed (F) rats. Male Wistar rats were fed a high fructose diet for 8 weeks. Body weight, systolic blood pressure, insulin sensitivity, and renal expression of the aforementioned proteins were assessed. No change was observed in the body weight of F rats; however, euglycemia and hyperinsulinemia implicating impaired glucose tolerance and significant elevation in systolic blood pressure were observed. Renal expression of CYP4A and CYP2C23 was significantly increased while that of CYP2C11 and sEH was not changed in F rats. Equal expression for RhoA in both control and F rats and an enhanced level of ROCK-1 and ROCK-2 constitutively activate 130 kDa cleavage fragments as well as phospho-LIMK. These data suggest that the kidneys could be actively participating in the pathogenesis of insulin resistance-induced hypertension through the arachidonic acid CYP 450-RhoA/Rho kinase pathway(s).

Endothelin-1 blockade prevents COX2 induction and TXA2 production in the fructose hypertensive rat

Feeding rats with a high fructose diet results in insulin resistance and hypertension. Fructose-hypertensive rats (FHR) have increased vascular levels of endothelin-1 (ET-1) and thromboxane (TXA2). We have previously shown that chronic treatment with either the dual endothelin receptor blocker, bosentan, or the thromboxane synthase inhibitor, dazmegrel, prevented fructose-induced increases in blood pressure, suggesting that both ET-1 and TXA2 play important roles in the development of hyperinsulinemia/insulin resistance-associated hypertension. In this study, we investigated the potential interrelationship between ET-1 and TXA2 in the development of fructose-induced hypertension in vivo. Male Wistar rats were fed on a high fructose diet for 9 weeks. Either bosentan or dazmegrel treatment (daily by oral gavage) was initiated 3 weeks after the start of fructose feeding for a total duration of 6 weeks. At the end of drug treatment, blood and aorta were collected from each animal. Plasma thromboxane B2 (TXB2), a stable TXA2 metabolite, increased significantly in FHR and was reduced to control level by both chronic bosentan and dazmegrel treatment. Protein expression of cyclooxygenase 2 (COX2) was elevated significantly in FHR aortas and treatment with bosentan and dazmegrel corrected these changes. These results indicate that the actions of ET-1 in the aorta of FHR may be mediated through COX2-derived TXA2. Bosentan may prevent the development of hypertension in fructose-fed rats through inhibition of COX2 induction and subsequently the reduction in plasma TXA2.