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Papers by David Raleigh

Research paper thumbnail of Targeted gene expression profiling predicts meningioma outcomes and radiotherapy responses

Background Surgery is the mainstay of treatment for meningioma, the most common primary intracran... more 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 ...

Research paper thumbnail of Increased mRNA expression of CDKN2A is a transcriptomic marker of clinically aggressive meningiomas

BackgroundHomozygous loss of CDKN2A/B is a genetic alteration found in many cancer types includin... more BackgroundHomozygous loss of CDKN2A/B is a genetic alteration found in many cancer types including meningiomas, where it is associated with poor clinical outcome. It is now also a diagnostic criterion for grade 3 meningiomas in the 2021 WHO classification for central nervous system tumors. However, as in other cancers, the relationship between copy number loss of CDKN2A/B and expression of its gene product is unclear and may be either commensurate or paradoxical in nature. Therefore, we aimed to investigate the association of CDKN2A mRNA expression with clinical prognosis, WHO grade, and other molecular biomarkers in meningiomas such as DNA methylation, molecular group, and proteomics.MethodsWe used multidimensional molecular data of 490 meningioma samples from 4 independent cohorts to examine the relationship between mRNA expression of CDKN2A and copy number status, its correlation to clinical outcome, the transcriptomic pathways altered in differential CDKN2A expression, and its r...

Research paper thumbnail of GENE-04. Comprehensive Genomic Characterization of Aggressive Meningiomas Identifies Molecular Signatures That Predict Clinical Outcomes

Neuro-Oncology

NEURO-ONCOLOGY • NOVEMBER 2017 formation, blocked migration and invasion. Since Magmas is a ROS r... more NEURO-ONCOLOGY • NOVEMBER 2017 formation, blocked migration and invasion. Since Magmas is a ROS regulator, BT#9 treatment resulted in a decrease in respiratory function of glioma cells. DISCUSSION: This is the first study about the role of Magmas in glioma. Our findings suggest that Magmas plays a key role in glioma cell survival and targeting Magmas by Magmas inhibitor has the potential to become an therapeutic strategy in gliomas.

Research paper thumbnail of Superenhancer activation of KLHDC8A drives glioma ciliation and hedgehog signaling

Journal of Clinical Investigation

Research paper thumbnail of PATH-34. Solitary Fibrous Tumor: Natural History and Prognosis in Accordance with the Who 2021 Classification of CNS Tumors

Neuro-Oncology

Meningeal solitary fibrous tumor (SFT) is a rare tumor with high propensity to recur and metastas... more Meningeal solitary fibrous tumor (SFT) is a rare tumor with high propensity to recur and metastasize, even late in the course of disease. The WHO 2021 classification of CNS tumors divides SFT in 3 grades, based on mitotic index and necrosis. We re-examined our cohort of 126 patients (57 F, 69 M; mean age 53.0 years) with SFT, confirmed by STAT6 nuclear positivity and/or NAB2::STAT6 fusion, with extended follow-up (median 7.6 years; range 4 days-26.6 years). Tumors included 76 grade 1, 36 grade 2 and 14 grade 3 according to 2021 WHO criteria, evaluated at primary resection (n=90), recurrence (n=35), or metastasis (n=1). Fifty-six patients had one or more post-surgical events, the earliest event being local recurrence (n=41) or metastasis (n=15). Forty patients died (29 of disease; 9 of other causes; 2 unknown). Overall survival (OS), and progression-free survival (PFS, recurrence and/or metastasis) from time of primary resection (n=90) were not significantly associated with grade; ho...

Research paper thumbnail of RBIO-04. Stereotactic Radiosurgery Reprograms Macrophage, Microglia, and CD8+ T Cell Populations in the Glioblastoma Immune Microenvironment

Neuro-Oncology

INTRODUCTION Fractionated radiotherapy is a first-line treatment for glioblastoma, but daily ioni... more INTRODUCTION Fractionated radiotherapy is a first-line treatment for glioblastoma, but daily ionizing radiation prevents durable immune infiltration of the tumor microenvironment. Hypofractionated radiotherapy is used to treat glioblastomas at recurrence, but the impact of hypofractionated radiotherapy on the glioblastoma immune microenvironment is incompletely understood. Here we define immune microenvironment changes across multiple immunocompetent intracranial mouse models of glioblastoma after treatment with ionizing radiation mimicking stereotactic radiosurgery (SRS) in humans. METHODS Syngeneic GL261 (3x105 cells/mouse) or SB28 glioblastoma cells (3x104 cells/mouse) were implanted into the frontal lobe of immunocompetent C57BL/6J mice (18 mice/arm x 4 arms). Intracranial bioluminescence was used to assess glioblastoma growth. After tumor engraftment, glioblastomas were treated with conformal SRS (18Gy/1Fx) or sham. Glioblastomas were collected for histologic, single-cell, or m...

Research paper thumbnail of BIOM-31. Temporospatial Protein Profiling of Human Glioblastomas Reveals Molecular Mechanisms and Biomarkers Underlying Responses to Immune Checkpoint Inhibition

Neuro-Oncology

Glioblastoma responses to immune checkpoint inhibition (ICI) are rare, and the molecular mechanis... more Glioblastoma responses to immune checkpoint inhibition (ICI) are rare, and the molecular mechanisms underlying ICI responses are incompletely understood. Thus, serial glioblastoma samples are valuable resources for identifying biomarkers or therapeutic targets to increase the efficacy of ICI in patients with glioblastoma. We obtained paired glioblastoma samples from 7 patients who underwent sequential surgery, ICI, and eventual salvage surgery for recurrence. Patients were distinguished as ICI responders (n=3) or non-responders (n=4) based on (1) MRI evidence of tumor stability/reduction over 6+ months after ICI, or (2) pathologic evidence of predominant treatment effect at the time of salvage surgery after ICI. FFPE sections from each tumor (n=14) were stained using H&E or IHC/IF for macrophages/microglia (CD68) or T cells (CD3) and analyzed using light or fluorescence microscopy. Six regions-of-interest (ROIs) comprising viable tumor were selected neuropathologist from each sample...

Research paper thumbnail of CSIG-28. The Hedgehog Gene Expression Program Regulates Lipid Feedback Mechanisms Underlying Hedgehog-Associated Medulloblastoma

Neuro-Oncology

Misactivation of the Hedgehog pathway can cause cancers such as medulloblastomas, the most common... more Misactivation of the Hedgehog pathway can cause cancers such as medulloblastomas, the most common malignant brain tumors in children. Hedgehog signals are transmitted through primary cilia, where Hedgehog ligands bind to Patched1 and activate Smoothened through interactions with cilia-associated sterol lipids. The gene expression programs driving cellular responses to ciliary Hedgehog signals are incompletely understood. Thus, to define Hedgehog target genes and elucidate mechanisms underlying Hedgehog-associated medulloblastomas, we performed RNA sequencing of cells after treatment with Hedgehog ligands (Shh, Dhh, Ihh), cilia-associated lipids (7b,27-dihydroxycholesterol, 24(S),25-epoxycholesterol), or synthetic lipids or small molecules that activate Smoothened (20(S)-hydroxycholesterol, SAG). Nonspecific gene expression changes were identified by performing RNA sequencing (1) after treatment of CRISPR mediated Smo-/- cells with the same Hedgehog pathway agonists, (2) after treatm...

Research paper thumbnail of PATH-37. Spatial Gene Expression Programs and Protein Signaling Mechanisms Drive Meningioma Evolution and Therapeutic Vulnerability

Neuro-Oncology

Intratumor heterogeneity drives cancer evolution and resistance to therapy, but unbiased approach... more 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, p...

Research paper thumbnail of PATH-35. Hypermitotic Meningiomas Harbor Dna Methylation Subgroups with Distinct Biological and Clinical Features

Neuro-Oncology

Meningiomas are the most common primary intracranial tumors, and treatments for meningiomas are l... more Meningiomas are the most common primary intracranial tumors, and treatments for meningiomas are limited to surgery and radiotherapy. Clinically tractable biomarkers for meningiomas are under development, and multiple retrospective studies have reported genetic, epigenetic, or gene expression grouping schemes shedding light on meningioma biology, outcomes, or druggable dependencies. Here we report biologically distinct subgroups within the Hypermitotic meningioma DNA methylation group, validating an architecture that unifies contrasting theories of meningioma biology. To do so, we re-analyzed meningioma DNA methylation profiles from a discovery cohort (n=200) and an independent, consecutive validation cohort (n=365). Median follow-up was 5.6 years for 388/142/35 WHO grade 1/2/3 meningiomas. Copy number variants (CNVs) were calculated for all meningiomas, and RNA sequencing was performed on the discovery cohort. Unsupervised hierarchical clustering of β methylation values was performe...

Research paper thumbnail of CSIG-37. Merlin S13 Dephosphorylation Drives Meningioma WNT Signalling and Cell Proliferation

Neuro-Oncology

How Merlin-intact meningiomas arise in the absence of NF2/Merlin inactivation is incompletely und... more 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 w...

Research paper thumbnail of PATH-07. Multiplatform Molecular Analyses Refine Classification and Prognostication of Gliomas Arising in Patients with Neurofibromatosis Type 1

Neuro-Oncology

BACKGROUND Gliomas arising in patients with neurofibromatosis type 1 (NF1) are heterogeneous, occ... more 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 difference...

Research paper thumbnail of Hypermitotic meningiomas harbor DNA methylation subgroups with distinct biological and clinical features

Neuro-Oncology

Background Meningiomas, the most common primary intracranial tumors, can be separated into 3 DNA ... more Background Meningiomas, the most common primary intracranial tumors, can be separated into 3 DNA methylation groups with distinct biological drivers, clinical outcomes, and therapeutic vulnerabilities. Alternative meningioma grouping schemes using copy number variants, gene expression profiles, somatic short variants, or integrated molecular models have been proposed. These data suggest meningioma DNA methylation groups may harbor subgroups unifying contrasting theories of meningioma biology. Methods A total of 565 meningioma DNA methylation profiles from patients with comprehensive clinical follow-up at independent discovery (n = 200) or validation (n = 365) institutions were reanalyzed and classified into Merlin-intact, Immune-enriched, or Hypermitotic DNA methylation groups. RNA sequencing from the discovery (n = 200) or validation (n = 302) cohort were analyzed in the context of DNA methylation groups to identify subgroups. Biological features and clinical outcomes were analyzed...

Research paper thumbnail of A case (report) for mechanistic validation of meningioma molecular therapies

Research paper thumbnail of Intratumor and informatic heterogeneity influence meningioma molecular classification

Acta Neuropathologica

CDKN2A inactivation or TERT promoter mutation are new criteria for World Health Organization (WHO... more CDKN2A inactivation or TERT promoter mutation are new criteria for World Health Organization (WHO) grade 3 meningiomas [9]. These infrequent alterations can occur in cases that do not otherwise qualify for WHO grade 3 based on histologic criteria [5, 16, 20, 25]. Indeed, most recurring short somatic variants in meningiomas are found in tumors with favorable outcomes [27, 28], but DNA methylation profiling [3, 14, 15, 21, 26], RNA sequencing [17, 26], enhancer analysis [19], copy number variants (CNVs) [4, 10], or integrated molecular strategies [13] can identify broad groups of meningiomas with aggressive biology. Meningioma DNA methylation grouping controlled for artifacts from CNVs further reveals biological drivers and therapeutic vulnerabilities across Merlin-intact, Immune-enriched, or Hyper-mitotic meningioma DNA methylation groups [3]. In sum, these studies suggest molecular classification may improve meningioma stratification or identify draggable dependencies.

Research paper thumbnail of RONC-18 Radiosurgery for Primary and Metastatic CNS Malignancies in the Pediatric Population

Neuro-Oncology

PURPOSE: The purpose of this study is to describe outcomes after pediatric radiosurgery for malig... more PURPOSE: The purpose of this study is to describe outcomes after pediatric radiosurgery for malignant CNS lesions. METHODS: Retrospective chart review was performed for 31 pediatric patients treated at a single institution with Gamma Knife stereotactic radiosurgery (SRS) for primary or metastatic CNS malignancies between 2000-2020. RESULTS: 25 patients were treated with SRS for focal recurrences of primary CNS malignancies, 1 patient was treated in the adjuvant setting after initial resection, and 5 patients were treated for brain metastases. Primary CNS histologies included ependymoma (n=14), glioma (n=4), medulloblastoma (n=2), and meningioma (n=2). 65% were WHO grade 3 or 4. 71% of patients had received a prior course of involved-field external beam radiation to the brain to a median dose of 59.4 Gy in 33 fractions. Median age at SRS was 14 years (range 4-21). Radiosurgery was predominantly performed in a single fraction to a median dose of 17 Gy to a total of 42 targets among 29...

Research paper thumbnail of Meningioma DNA methylation groups identify biological drivers and therapeutic vulnerabilities

Nature Genetics

Meningiomas arising from the meningothelial central nervous system lining are the most common pri... more Meningiomas arising from the meningothelial central nervous system lining are the most common primary intracranial tumors, and a significant cause of neurologic morbidity and mortality 1. There are no effective medical therapies for meningioma patients 2,3 , and new treatments have been encumbered by limited understanding of meningioma biology. DNA methylation profiling provides robust classification of central nervous system tumors 4 , and can elucidate targets for molecular therapy 5. Here we use DNA methylation profiling on 565 meningiomas integrated with genetic, transcriptomic, biochemical, and single-cell approaches to show meningiomas are comprised of 3 epigenetic groups with distinct clinical outcomes and biological features informing new treatments for meningioma patients. Merlin-intact meningiomas (group A, 34%) have the best outcomes and are distinguished by a novel apoptotic tumor suppressor function of NF2/Merlin. Immune-enriched meningiomas (group B, 38%) have intermediate outcomes and are distinguished by immune cell infiltration, HLA expression, and lymphatic vessels. Hypermitotic meningiomas (group C, 28%) have the worst outcomes and are distinguished by convergent genetic mechanisms misactivating the cell cycle. Consistently, we find cell cycle inhibitors block meningioma growth in cell culture, organoids, xenografts, and patients. Our results establish a framework for understanding meningioma biology, and provide preclinical rationale for new therapies to treat meningioma patients.

Research paper thumbnail of Histopathologic findings in malignant peripheral nerve sheath tumor predict response to radiotherapy and overall survival

Neuro-Oncology Advances

Background Malignant peripheral nerve sheath tumor (MPNST) is an aggressive and poorly understood... more Background Malignant peripheral nerve sheath tumor (MPNST) is an aggressive and poorly understood malignant neoplasm. Even in the setting of multimodal therapy, the clinical course of MPNST is frequently marked by metastatic conversion and poor overall prognosis, with optimal treatment paradigms for this rare tumor unknown. Methods We reviewed the medical records and histopathology of 54 consecutive patients who were treated at University of California San Francisco between 1990 and 2018. Results Our cohort consisted of 24 male and 30 female patients (median age 38 years). Fédération Nationale des Centres de Lutte Contre Le Cancer (FNCLCC) sarcoma grading criteria segregated patients into groups with differences in overall survival (OS) (P = .02). Increasing Ki-67 labeling index was associated with poor OS (hazard ratio [HR] 1.36 per 10%, P = .0002). Unsupervised hierarchical clustering-based immunohistochemical staining patterns identified 2 subgroups of tumors with differences in ...

Research paper thumbnail of Stereotactic Radiosurgery for Meningioma

Stereotactic Radiosurgery and Stereotactic Body Radiation Therapy, 2019

Research paper thumbnail of EMBR-03. Pineoblastoma: A Pooled Outcome Study of North American and Australian Therapeutic Data

Neuro-Oncology, 2021

Background Pineoblastoma (PB) is a rare embryonal brain tumour most often diagnosed in young chil... more Background Pineoblastoma (PB) is a rare embryonal brain tumour most often diagnosed in young children. To date, no clinical trials have been conducted specific to pediatric PB. Collaborative studies performed over the past 30 years have included PB in studies accruing for other embryonal tumours, primarily medulloblastoma (MB), but also including the entity formerly known as CNS-PNET and atypical teratoid rhabdoid tumors. Each of these studies have included only a small number of children with PB, making clinical features difficult to interpret and determinants of outcome difficult to ascertain. Patients and Methods Published centrally reviewed series with sufficient treatment and outcome data from North American and Australian cases were pooled. To investigate associations between variables, Fisher’s exact and Wilcoxon-Mann-Whitney tests, and Spearman correlations were used as appropriate. Kaplan-Meier plots, log-rank tests, and Cox proportional hazards models were used in survival...

Research paper thumbnail of Targeted gene expression profiling predicts meningioma outcomes and radiotherapy responses

Background Surgery is the mainstay of treatment for meningioma, the most common primary intracran... more 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 ...

Research paper thumbnail of Increased mRNA expression of CDKN2A is a transcriptomic marker of clinically aggressive meningiomas

BackgroundHomozygous loss of CDKN2A/B is a genetic alteration found in many cancer types includin... more BackgroundHomozygous loss of CDKN2A/B is a genetic alteration found in many cancer types including meningiomas, where it is associated with poor clinical outcome. It is now also a diagnostic criterion for grade 3 meningiomas in the 2021 WHO classification for central nervous system tumors. However, as in other cancers, the relationship between copy number loss of CDKN2A/B and expression of its gene product is unclear and may be either commensurate or paradoxical in nature. Therefore, we aimed to investigate the association of CDKN2A mRNA expression with clinical prognosis, WHO grade, and other molecular biomarkers in meningiomas such as DNA methylation, molecular group, and proteomics.MethodsWe used multidimensional molecular data of 490 meningioma samples from 4 independent cohorts to examine the relationship between mRNA expression of CDKN2A and copy number status, its correlation to clinical outcome, the transcriptomic pathways altered in differential CDKN2A expression, and its r...

Research paper thumbnail of GENE-04. Comprehensive Genomic Characterization of Aggressive Meningiomas Identifies Molecular Signatures That Predict Clinical Outcomes

Neuro-Oncology

NEURO-ONCOLOGY • NOVEMBER 2017 formation, blocked migration and invasion. Since Magmas is a ROS r... more NEURO-ONCOLOGY • NOVEMBER 2017 formation, blocked migration and invasion. Since Magmas is a ROS regulator, BT#9 treatment resulted in a decrease in respiratory function of glioma cells. DISCUSSION: This is the first study about the role of Magmas in glioma. Our findings suggest that Magmas plays a key role in glioma cell survival and targeting Magmas by Magmas inhibitor has the potential to become an therapeutic strategy in gliomas.

Research paper thumbnail of Superenhancer activation of KLHDC8A drives glioma ciliation and hedgehog signaling

Journal of Clinical Investigation

Research paper thumbnail of PATH-34. Solitary Fibrous Tumor: Natural History and Prognosis in Accordance with the Who 2021 Classification of CNS Tumors

Neuro-Oncology

Meningeal solitary fibrous tumor (SFT) is a rare tumor with high propensity to recur and metastas... more Meningeal solitary fibrous tumor (SFT) is a rare tumor with high propensity to recur and metastasize, even late in the course of disease. The WHO 2021 classification of CNS tumors divides SFT in 3 grades, based on mitotic index and necrosis. We re-examined our cohort of 126 patients (57 F, 69 M; mean age 53.0 years) with SFT, confirmed by STAT6 nuclear positivity and/or NAB2::STAT6 fusion, with extended follow-up (median 7.6 years; range 4 days-26.6 years). Tumors included 76 grade 1, 36 grade 2 and 14 grade 3 according to 2021 WHO criteria, evaluated at primary resection (n=90), recurrence (n=35), or metastasis (n=1). Fifty-six patients had one or more post-surgical events, the earliest event being local recurrence (n=41) or metastasis (n=15). Forty patients died (29 of disease; 9 of other causes; 2 unknown). Overall survival (OS), and progression-free survival (PFS, recurrence and/or metastasis) from time of primary resection (n=90) were not significantly associated with grade; ho...

Research paper thumbnail of RBIO-04. Stereotactic Radiosurgery Reprograms Macrophage, Microglia, and CD8+ T Cell Populations in the Glioblastoma Immune Microenvironment

Neuro-Oncology

INTRODUCTION Fractionated radiotherapy is a first-line treatment for glioblastoma, but daily ioni... more INTRODUCTION Fractionated radiotherapy is a first-line treatment for glioblastoma, but daily ionizing radiation prevents durable immune infiltration of the tumor microenvironment. Hypofractionated radiotherapy is used to treat glioblastomas at recurrence, but the impact of hypofractionated radiotherapy on the glioblastoma immune microenvironment is incompletely understood. Here we define immune microenvironment changes across multiple immunocompetent intracranial mouse models of glioblastoma after treatment with ionizing radiation mimicking stereotactic radiosurgery (SRS) in humans. METHODS Syngeneic GL261 (3x105 cells/mouse) or SB28 glioblastoma cells (3x104 cells/mouse) were implanted into the frontal lobe of immunocompetent C57BL/6J mice (18 mice/arm x 4 arms). Intracranial bioluminescence was used to assess glioblastoma growth. After tumor engraftment, glioblastomas were treated with conformal SRS (18Gy/1Fx) or sham. Glioblastomas were collected for histologic, single-cell, or m...

Research paper thumbnail of BIOM-31. Temporospatial Protein Profiling of Human Glioblastomas Reveals Molecular Mechanisms and Biomarkers Underlying Responses to Immune Checkpoint Inhibition

Neuro-Oncology

Glioblastoma responses to immune checkpoint inhibition (ICI) are rare, and the molecular mechanis... more Glioblastoma responses to immune checkpoint inhibition (ICI) are rare, and the molecular mechanisms underlying ICI responses are incompletely understood. Thus, serial glioblastoma samples are valuable resources for identifying biomarkers or therapeutic targets to increase the efficacy of ICI in patients with glioblastoma. We obtained paired glioblastoma samples from 7 patients who underwent sequential surgery, ICI, and eventual salvage surgery for recurrence. Patients were distinguished as ICI responders (n=3) or non-responders (n=4) based on (1) MRI evidence of tumor stability/reduction over 6+ months after ICI, or (2) pathologic evidence of predominant treatment effect at the time of salvage surgery after ICI. FFPE sections from each tumor (n=14) were stained using H&E or IHC/IF for macrophages/microglia (CD68) or T cells (CD3) and analyzed using light or fluorescence microscopy. Six regions-of-interest (ROIs) comprising viable tumor were selected neuropathologist from each sample...

Research paper thumbnail of CSIG-28. The Hedgehog Gene Expression Program Regulates Lipid Feedback Mechanisms Underlying Hedgehog-Associated Medulloblastoma

Neuro-Oncology

Misactivation of the Hedgehog pathway can cause cancers such as medulloblastomas, the most common... more Misactivation of the Hedgehog pathway can cause cancers such as medulloblastomas, the most common malignant brain tumors in children. Hedgehog signals are transmitted through primary cilia, where Hedgehog ligands bind to Patched1 and activate Smoothened through interactions with cilia-associated sterol lipids. The gene expression programs driving cellular responses to ciliary Hedgehog signals are incompletely understood. Thus, to define Hedgehog target genes and elucidate mechanisms underlying Hedgehog-associated medulloblastomas, we performed RNA sequencing of cells after treatment with Hedgehog ligands (Shh, Dhh, Ihh), cilia-associated lipids (7b,27-dihydroxycholesterol, 24(S),25-epoxycholesterol), or synthetic lipids or small molecules that activate Smoothened (20(S)-hydroxycholesterol, SAG). Nonspecific gene expression changes were identified by performing RNA sequencing (1) after treatment of CRISPR mediated Smo-/- cells with the same Hedgehog pathway agonists, (2) after treatm...

Research paper thumbnail of PATH-37. Spatial Gene Expression Programs and Protein Signaling Mechanisms Drive Meningioma Evolution and Therapeutic Vulnerability

Neuro-Oncology

Intratumor heterogeneity drives cancer evolution and resistance to therapy, but unbiased approach... more 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, p...

Research paper thumbnail of PATH-35. Hypermitotic Meningiomas Harbor Dna Methylation Subgroups with Distinct Biological and Clinical Features

Neuro-Oncology

Meningiomas are the most common primary intracranial tumors, and treatments for meningiomas are l... more Meningiomas are the most common primary intracranial tumors, and treatments for meningiomas are limited to surgery and radiotherapy. Clinically tractable biomarkers for meningiomas are under development, and multiple retrospective studies have reported genetic, epigenetic, or gene expression grouping schemes shedding light on meningioma biology, outcomes, or druggable dependencies. Here we report biologically distinct subgroups within the Hypermitotic meningioma DNA methylation group, validating an architecture that unifies contrasting theories of meningioma biology. To do so, we re-analyzed meningioma DNA methylation profiles from a discovery cohort (n=200) and an independent, consecutive validation cohort (n=365). Median follow-up was 5.6 years for 388/142/35 WHO grade 1/2/3 meningiomas. Copy number variants (CNVs) were calculated for all meningiomas, and RNA sequencing was performed on the discovery cohort. Unsupervised hierarchical clustering of β methylation values was performe...

Research paper thumbnail of CSIG-37. Merlin S13 Dephosphorylation Drives Meningioma WNT Signalling and Cell Proliferation

Neuro-Oncology

How Merlin-intact meningiomas arise in the absence of NF2/Merlin inactivation is incompletely und... more 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 w...

Research paper thumbnail of PATH-07. Multiplatform Molecular Analyses Refine Classification and Prognostication of Gliomas Arising in Patients with Neurofibromatosis Type 1

Neuro-Oncology

BACKGROUND Gliomas arising in patients with neurofibromatosis type 1 (NF1) are heterogeneous, occ... more 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 difference...

Research paper thumbnail of Hypermitotic meningiomas harbor DNA methylation subgroups with distinct biological and clinical features

Neuro-Oncology

Background Meningiomas, the most common primary intracranial tumors, can be separated into 3 DNA ... more Background Meningiomas, the most common primary intracranial tumors, can be separated into 3 DNA methylation groups with distinct biological drivers, clinical outcomes, and therapeutic vulnerabilities. Alternative meningioma grouping schemes using copy number variants, gene expression profiles, somatic short variants, or integrated molecular models have been proposed. These data suggest meningioma DNA methylation groups may harbor subgroups unifying contrasting theories of meningioma biology. Methods A total of 565 meningioma DNA methylation profiles from patients with comprehensive clinical follow-up at independent discovery (n = 200) or validation (n = 365) institutions were reanalyzed and classified into Merlin-intact, Immune-enriched, or Hypermitotic DNA methylation groups. RNA sequencing from the discovery (n = 200) or validation (n = 302) cohort were analyzed in the context of DNA methylation groups to identify subgroups. Biological features and clinical outcomes were analyzed...

Research paper thumbnail of A case (report) for mechanistic validation of meningioma molecular therapies

Research paper thumbnail of Intratumor and informatic heterogeneity influence meningioma molecular classification

Acta Neuropathologica

CDKN2A inactivation or TERT promoter mutation are new criteria for World Health Organization (WHO... more CDKN2A inactivation or TERT promoter mutation are new criteria for World Health Organization (WHO) grade 3 meningiomas [9]. These infrequent alterations can occur in cases that do not otherwise qualify for WHO grade 3 based on histologic criteria [5, 16, 20, 25]. Indeed, most recurring short somatic variants in meningiomas are found in tumors with favorable outcomes [27, 28], but DNA methylation profiling [3, 14, 15, 21, 26], RNA sequencing [17, 26], enhancer analysis [19], copy number variants (CNVs) [4, 10], or integrated molecular strategies [13] can identify broad groups of meningiomas with aggressive biology. Meningioma DNA methylation grouping controlled for artifacts from CNVs further reveals biological drivers and therapeutic vulnerabilities across Merlin-intact, Immune-enriched, or Hyper-mitotic meningioma DNA methylation groups [3]. In sum, these studies suggest molecular classification may improve meningioma stratification or identify draggable dependencies.

Research paper thumbnail of RONC-18 Radiosurgery for Primary and Metastatic CNS Malignancies in the Pediatric Population

Neuro-Oncology

PURPOSE: The purpose of this study is to describe outcomes after pediatric radiosurgery for malig... more PURPOSE: The purpose of this study is to describe outcomes after pediatric radiosurgery for malignant CNS lesions. METHODS: Retrospective chart review was performed for 31 pediatric patients treated at a single institution with Gamma Knife stereotactic radiosurgery (SRS) for primary or metastatic CNS malignancies between 2000-2020. RESULTS: 25 patients were treated with SRS for focal recurrences of primary CNS malignancies, 1 patient was treated in the adjuvant setting after initial resection, and 5 patients were treated for brain metastases. Primary CNS histologies included ependymoma (n=14), glioma (n=4), medulloblastoma (n=2), and meningioma (n=2). 65% were WHO grade 3 or 4. 71% of patients had received a prior course of involved-field external beam radiation to the brain to a median dose of 59.4 Gy in 33 fractions. Median age at SRS was 14 years (range 4-21). Radiosurgery was predominantly performed in a single fraction to a median dose of 17 Gy to a total of 42 targets among 29...

Research paper thumbnail of Meningioma DNA methylation groups identify biological drivers and therapeutic vulnerabilities

Nature Genetics

Meningiomas arising from the meningothelial central nervous system lining are the most common pri... more Meningiomas arising from the meningothelial central nervous system lining are the most common primary intracranial tumors, and a significant cause of neurologic morbidity and mortality 1. There are no effective medical therapies for meningioma patients 2,3 , and new treatments have been encumbered by limited understanding of meningioma biology. DNA methylation profiling provides robust classification of central nervous system tumors 4 , and can elucidate targets for molecular therapy 5. Here we use DNA methylation profiling on 565 meningiomas integrated with genetic, transcriptomic, biochemical, and single-cell approaches to show meningiomas are comprised of 3 epigenetic groups with distinct clinical outcomes and biological features informing new treatments for meningioma patients. Merlin-intact meningiomas (group A, 34%) have the best outcomes and are distinguished by a novel apoptotic tumor suppressor function of NF2/Merlin. Immune-enriched meningiomas (group B, 38%) have intermediate outcomes and are distinguished by immune cell infiltration, HLA expression, and lymphatic vessels. Hypermitotic meningiomas (group C, 28%) have the worst outcomes and are distinguished by convergent genetic mechanisms misactivating the cell cycle. Consistently, we find cell cycle inhibitors block meningioma growth in cell culture, organoids, xenografts, and patients. Our results establish a framework for understanding meningioma biology, and provide preclinical rationale for new therapies to treat meningioma patients.

Research paper thumbnail of Histopathologic findings in malignant peripheral nerve sheath tumor predict response to radiotherapy and overall survival

Neuro-Oncology Advances

Background Malignant peripheral nerve sheath tumor (MPNST) is an aggressive and poorly understood... more Background Malignant peripheral nerve sheath tumor (MPNST) is an aggressive and poorly understood malignant neoplasm. Even in the setting of multimodal therapy, the clinical course of MPNST is frequently marked by metastatic conversion and poor overall prognosis, with optimal treatment paradigms for this rare tumor unknown. Methods We reviewed the medical records and histopathology of 54 consecutive patients who were treated at University of California San Francisco between 1990 and 2018. Results Our cohort consisted of 24 male and 30 female patients (median age 38 years). Fédération Nationale des Centres de Lutte Contre Le Cancer (FNCLCC) sarcoma grading criteria segregated patients into groups with differences in overall survival (OS) (P = .02). Increasing Ki-67 labeling index was associated with poor OS (hazard ratio [HR] 1.36 per 10%, P = .0002). Unsupervised hierarchical clustering-based immunohistochemical staining patterns identified 2 subgroups of tumors with differences in ...

Research paper thumbnail of Stereotactic Radiosurgery for Meningioma

Stereotactic Radiosurgery and Stereotactic Body Radiation Therapy, 2019

Research paper thumbnail of EMBR-03. Pineoblastoma: A Pooled Outcome Study of North American and Australian Therapeutic Data

Neuro-Oncology, 2021

Background Pineoblastoma (PB) is a rare embryonal brain tumour most often diagnosed in young chil... more Background Pineoblastoma (PB) is a rare embryonal brain tumour most often diagnosed in young children. To date, no clinical trials have been conducted specific to pediatric PB. Collaborative studies performed over the past 30 years have included PB in studies accruing for other embryonal tumours, primarily medulloblastoma (MB), but also including the entity formerly known as CNS-PNET and atypical teratoid rhabdoid tumors. Each of these studies have included only a small number of children with PB, making clinical features difficult to interpret and determinants of outcome difficult to ascertain. Patients and Methods Published centrally reviewed series with sufficient treatment and outcome data from North American and Australian cases were pooled. To investigate associations between variables, Fisher’s exact and Wilcoxon-Mann-Whitney tests, and Spearman correlations were used as appropriate. Kaplan-Meier plots, log-rank tests, and Cox proportional hazards models were used in survival...