Novel SOX10 indel mutations drive schwannomas through impaired transactivation of myelination gene programs

BACKGROUND

Schwannomas are common peripheral nerve sheath tumors that can cause severe morbidity given their stereotypic intracranial and paraspinal locations. Similar to many solid tumors, schwannomas and other nerve sheath tumors are primarily thought to arise due to aberrant hyperactivation of the RAS growth factor signaling pathway. Here, we sought to further define the molecular pathogenesis of schwannomas.

METHODS

We performed comprehensive genomic profiling on a cohort of 96 human schwannomas, as well as DNA methylation profiling on a subset. Functional studies including RNA sequencing, chromatin immunoprecipitation-DNA sequencing, electrophoretic mobility shift assay, and luciferase reporter assays were performed in a fetal glial cell model following transduction with wildtype and tumor-derived mutant isoforms of SOX10.

RESULTS

We identified that nearly one-third of sporadic schwannomas lack alterations in known nerve sheath tumor genes and instead harbor novel recurrent in-frame insertion/deletion mutations in SOX10, which encodes a transcription factor responsible for controlling Schwann cell differentiation and myelination. SOX10 indel mutations were highly enriched in schwannomas arising from nonvestibular cranial nerves (eg facial, trigeminal, vagus) and were absent from vestibular nerve schwannomas driven by NF2 mutation. Functional studies revealed these SOX10 indel mutations have retained DNA binding capacity but impaired transactivation of glial differentiation and myelination gene programs.

CONCLUSIONS

We thus speculate that SOX10 indel mutations drive a unique subtype of schwannomas by impeding proper differentiation of immature Schwann cells.

Development of a "Geo-Tagged" tumor sample registry: intra-operative linkage of sample location to imaging

PURPOSE

There is a growing body of literature documenting glioma heterogeneity in terms of radiographic, histologic, molecular, and genetic characteristics. Incomplete spatial specification of intraoperative tumor samples may contribute to variability in the results of pathological and biological investigations. We have developed a system, termed geo-tagging, for routine intraoperative linkage of each tumor sample to its location via neuronavigation.

METHODS

This is a single-institution, IRB approved, prospective database of undergoing clinically indicated surgery. We evaluated relevant factors affecting data collection by this registry, including tumor and surgical factors (e.g. tumor volume, location, grade and surgeon).

RESULTS

Over a 2-year period, 487 patients underwent craniotomy for an intra-axial tumor. Of those, 214 underwent surgery for a newly diagnosed or recurrent glioma. There was significant variation in the average number of samples collected per registered case, with a range of samples from 2.53 to 4.75 per tumor type. Histology and grade impacted on sampling with a range of 2.0 samples per tumor in Grade four, IDH-WT gliomas to 4.5 samples in grade four, IDH-mutant gliomas. The range of cases with sampling per surgeon was 6 to 99 with a mean of 47.6 cases and there was a statistically significant differences between surgeons. Tumor grade did not have a statistically significant impact on number of samples per case. No significant correlation was found between the number of samples collected and enhancing tumor volume, EOR, or volume of tumor resected.

CONCLUSION

We are using the results of this analysis to develop a prospective sample collection protocol.

Single-Cell Characterization of the Immune Microenvironment of Melanoma Brain and Leptomeningeal Metastases

PURPOSE

Melanoma brain metastases (MBM) and leptomeningeal melanoma metastases (LMM) are two different manifestations of melanoma CNS metastasis. Here, we used single-cell RNA sequencing (scRNA-seq) to define the immune landscape of MBM, LMM, and melanoma skin metastases.

EXPERIMENTAL DESIGN

scRNA-seq was undertaken on 43 patient specimens, including 8 skin metastases, 14 MBM, and 19 serial LMM specimens. Detailed cell type curation was performed, the immune landscapes were mapped, and key results were validated by IHC and flow cytometry. Association analyses were undertaken to identify immune cell subsets correlated with overall survival.

RESULTS

The LMM microenvironment was characterized by an immune-suppressed T-cell landscape distinct from that of brain and skin metastases. An LMM patient with long-term survival demonstrated an immune repertoire distinct from that of poor survivors and more similar to normal cerebrospinal fluid (CSF). Upon response to PD-1 therapy, this extreme responder showed increased levels of T cells and dendritic cells in their CSF, whereas poor survivors showed little improvement in their T-cell responses. In MBM patients, therapy led to increased immune infiltrate, with similar T-cell transcriptional diversity noted between skin metastases and MBM. A correlation analysis across the entire immune landscape identified the presence of a rare population of dendritic cells (DC3) that was associated with increased overall survival and positively regulated the immune environment through modulation of activated T cells and MHC expression.

CONCLUSIONS

Our study provides the first atlas of two distinct sites of melanoma CNS metastases and defines the immune cell landscape that underlies the biology of this devastating disease.

Proteomic Analysis of CSF from Patients with Leptomeningeal Melanoma Metastases Identifies Signatures Associated with Disease Progression and Therapeutic Resistance

PURPOSE

The development of leptomeningeal melanoma metastases (LMM) is a rare and devastating complication of the late-stage disease, for which no effective treatments exist. Here, we performed a multi-omics analysis of the cerebrospinal fluid (CSF) from patients with LMM to determine how the leptomeningeal microenvironment shapes the biology and therapeutic responses of melanoma cells.

EXPERIMENTAL DESIGN

A total of 45 serial CSF samples were collected from 16 patients, 8 of these with confirmed LMM. Of those with LMM, 7 had poor survival (<4 months) and one was an extraordinary responder (still alive with survival >35 months). CSF samples were analyzed by mass spectrometry and incubated with melanoma cells that were subjected to RNA sequencing (RNA-seq) analysis. Functional assays were performed to validate the pathways identified.

RESULTS

Mass spectrometry analyses showed the CSF of most patients with LMM to be enriched for pathways involved in innate immunity, protease-mediated damage, and IGF-related signaling. All of these were anticorrelated in the extraordinary responder. RNA-seq analysis showed CSF to induce PI3K/AKT, integrin, B-cell activation, S-phase entry, TNFR2, TGFβ, and oxidative stress responses in the melanoma cells. ELISA assays confirmed that TGFβ expression increased in the CSF of patients progressing with LMM. CSF from poorly responding patients conferred tolerance to BRAF inhibitor therapy in apoptosis assays.

CONCLUSIONS

These analyses identified proteomic/transcriptional signatures in the CSF of patients who succumbed to LMM. We further showed that the CSF from patients with LMM has the potential to modulate BRAF inhibitor responses and may contribute to drug resistance.See related commentary by Glitza Oliva and Tawbi, p. 2083.

Abstract 3876: EphrinB3 and EphrinB4 receptors: potential therapeutic targets in glioblastoma

Introduction: Glioblastoma (GBM) is the most common primary malignant neoplasm of the central nervous system in adults with poor median overall survival despite advances in tumor. CD133 is a known putative cancer stem cell marker, and we aimed to identify markers in CD133+ GBM tumor initiating cell lines (CSCs) with an infiltrative phenotype that could serve as therapeutic targets.

Methods: Expression (mRNA) microarray datasets including 22,278 probes for known cell-surface markers in three CD133+ CSCs and 17 normal brain tissue lines were obtained. We identified genes with uniformly high mRNA expression, filtered for known localization at the cell-surface and for non- or low expression in normal brain. Ephrin B3 receptor (EphB3), ephrin B4 receptor (EphB4) and fibroblast growth factor receptor (FGFR1) were highly expressed. Protein expression was established by mass spectrometry using CD133+ cell line extracts and then assessed in 27 patient GBM (IDH-wildtype) tumor samples by immunohistochemistry. Expression was graded based of the percentage of cells positive and intensity of staining the tumor, interface and uninvolved brain. One-way ANOVA was used to test any group difference among any combination of two genes; Tukey honest significant difference method was used to adjust for p value for pairwise comparison in tumor locations. Spearman correlation analysis was applied to determine potential correlation co-expression EphB3 and EphB4. The Gamma statistic was used to identify correlation of intensity of staining with tumor location, and the Fisher's exact test was utilized to elucidate potential significance.

Results: High expression (&gt; 50% of cells stained) was 7/27 for EphB3, 8/27 for EphB4, and 18/27 for FGFR1. EphB3 and EphB4 are significantly associated with tissue location based on percentage of cells stained in each location (p &lt; 0.05). When compared to the uninvolved brain, EphB3 and EphB4 expression in the tumor and interface tissues were significantly higher (p&lt;0.05). EphB3 expression was significantly correlated with EphB4 expression (p &lt; 0.05) in tumor tissue, though the correlation was weak (r = 0.414) EphB3 and EphB4 intensity were positively associated with tissue location: 0.53 [0.21 - 0.86] and EphB4 0.45 [0.09 - 0.80] respectively. FGFR-1 was not associated with tumor location in terms of both percentage and intensity of staining.

Conclusion: In terms of percentage and intensity of staining at the uninvolved brain, interface and normal tissue, EphB3 and EphB4 were significantly associated with those three tissue locations. EphB3 and EphB4 were highly expressed in tumor and interface tissue relative to the normal tissue. Co-expression of EphB3 and EphB4 in tumor tissue was correlated. Evaluation with clinical parameters may disclose subsets of these tumors with varying infiltrative potential.

Citation Format: Radhika Sreeraman Kumar, Robert J. B. Macaulay, Hannah C. Rutherford, Natalie Barkey, Jiannong Li, Jongphil Kim, John M. Koomen, David L. Morse. EphrinB3 and EphrinB4 receptors: potential therapeutic targets in glioblastoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3876.

Cell-Cycle Gene Expression in Lovastatin-Induced Medulloblastoma Apoptosis

Background:

3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase is a key rate-limiting enzyme in the mevalonate pathway, which generates precursors both for cholesterol biosynthesis and for the production of nonsteroidal mevalonate derivatives that are involved in a number of growth-regulatory processes. We have reported that lovastatin, a competitive inhibitor of HMG-CoA reductase, not only inhibits medulloblastoma proliferation in vitro, but also induces near-complete cell death via apoptosis. The mechanism of this phenomenon is unclear. Possible involvement of changes in expression of certain cell-cycle related genes led us to study some of them in more detail.

Methods:

Medulloblastoma cell lines were exposed in vitro to lovastatin, and the effects of gene expression changes were studied using RT-PCR, antisense oligonucleotide, DNA electrophoresis and Western blotting analysis.

Results:

1) Levels of total Ras gene mRNA and individual Ras gene mRNA are stable in lovastatin treatment in all examined medulloblastoma cell lines. 2) Blocking c-myc gene over-expression does not enhance medulloblastoma cell sensitivity to lovastatin. 3) Following lovastatin treatment, p16 expression exhibits no change, but pronounced increases of p27KIP1 protein are observed in all examined cell lines. Lovastatin induces pronounced increases of p21WAF1 protein only in Daoy and UW228, but not in D283 Med and D341 Med. 4) Following lovastatin treatment, increased p53 protein is detected only in D341 Med, and bax protein is unchanged in all cell lines.

Conclusion:

Lovastatin-induced growth inhibition and apoptosis in medulloblastoma are not dependent on the regulation of Ras and c-myc gene expression, but may be mediated by p27KIP1 gene expression. Lovastatin-induced apoptosis in medulloblastoma is probably p53 independent, but p53 and p21WAF1 gene expression may also mediate anti-proliferative effects of lovastatin on specific medulloblastoma cell lines.

Fourth Ventricular Neurocytoma: Case Report and Review of the Literature

Objectives:

Central neurocytoma is a tumour that typically occurs in young adults in close association with the lateral and third ventricles of the cerebrum.

Methods:

We report the unusual case of a central neurocytoma that developed in the fourth ventricle of a 59-year-old woman and metastasized to the upper cervical canal. Subtotal excision and adjuvant radiotherapy were used to treat the lesion. Microscopic evaluation, discussion of the pathologic differential diagnosis and theories of the histogenesis of the tumour are presented. Results and

Conclusion:

Fourth ventricular neurocytoma is rare and has only been reported twice previously. It appears most likely that this tumour arises from subependymal progenitor cell lines.

Oligodendrogliomas with neurocytic differentiation. A report of 4 cases with diagnostic and histogenetic implications

Oligodendroglioma represents a distinct type of diffuse glioma with a relatively favorable prognosis. Although an O2A-like glial progenitor cell of origin has been suggested, a neuronal-oligodendroglial progenitor cell is also of interest, particularly because variable degrees of neuronal marker expression have been reported in typical oligodendrogliomas. We present 2 female and 2 male patients (ages 34-54) with frontal lobe oligodendrogliomas containing a) morphologically distinct collections of small round cells with hyperchromatic nuclei, b) well-formed Homer Wright-like and perivascular rosettes, and c) demonstrable neuronal differentiation by immunohistochemistry and/or electron microscopy in the rosette-associated regions. Unlike extraventricular neurocytomas, these cases featured an infiltrative growth pattern and a classic oligodendroglioma immunophenotype in non-rosette bearing portions of each tumor. FISH analysis demonstrated chromosome 1p and 19q codeletions in 3 (75%) cases, both in regions with and without rosettes. Recurrences were common, although all patients are currently alive 4 months to 13 yr from initial diagnosis. Based on clinicopathologic and genetic features, we diagnosed these tumors as oligodendrogliomas with neurocytic differentiation. However, it is unclear whether they represent a) gliomas with divergent neuronal differentiation, b) a distinctive form of glioneuronal neoplasm, or c) a reflection of glioneuronal histogenesis in oligodendrogliomas in general. In any case, their occurrence suggests a histogenetic overlap between oligodendroglioma and extraventricular neurocytoma not previously recognized.