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.

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.

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.

Adult Intracranial Myxoid Mesenchymal Tumor with EWSR1-ATF1 Gene Fusion.

BACKGROUND: Intracranial myxoid mesenchymal tumors (IMMTs) carrying an EWSR1-CREB gene family fusion are extremely rare and have only been identified in 10 previous reports. All but one has been found in children or young adults. Although there appear to be similarities to a myxoid variant of angiomatoid fibrous histiocytoma (AFH), clear histologic differences exist that appear to distinguish IMMTs as a distinct and novel entity. Previous reports have lacked detailed long-term follow-up and recommendations regarding treatment approach. CASE DESCRIPTION: This case describes a 48-year-old woman who presented with a left intraventricular mass that was identified on histology as an IMMT with an EWSR1-ATF1 gene fusion. After initial resection, the tumor demonstrated local recurrence. Repeat resection was performed followed by immediate demonstration of local and distant tumor recurrence. Histologic analysis of the tumor demonstrated a myxoid mesenchymal tumor distinct from AFH. Fractionated stereotactic radiation therapy was administered after the second resection, and tumor control was achieved at 1 year. CONCLUSIONS: Intracranial myxoid mesenchymal tumor is a novel and rare entity that has been previously identified in only 10 cases. This case is particularly remarkable because it is only the second IMMT case to occur in a middle-aged adult and shares striking similarities in clinical presentation to the previously reported case. Given the aggressive recurrence seen with the presented case, we recommend the treatment plan to be surgical resection followed by adjuvant radiation therapy.

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, TGFß, and oxidative stress responses in the melanoma cells. ELISA assays confirmed that TGFß 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.

Autosomal dominant sensory ataxia: a neuroaxonal dystrophy.

Autosomal dominant sensory ataxia (ADSA), a rare hereditary ataxia, is characterized by progressive dysfunction of central sensory pathways. Its pathological features have not been previously documented. We report a case of a 61-year-old man with ADSA who died of congestive heart failure. Autopsy specimens of brain, thoracolumbar spinal cord, peripheral nerve and skeletal muscle were examined. There was no abnormality on gross examination. Microscopically, there were occasional swollen axons within the cerebral cortex and deep nuclei, particularly the subthalamic nucleus, with no neuronal loss, gliosis or microglial activation. There were many axonal spheroids within the medulla, particularly in the dorsal column nuclei. Axonal spheroids were also seen in the dorsal columns and ventral horns in the thoracolumbar spinal cord, but there was no Wallerian degeneration or demyelination. Amyloid precursor protein (APP) immunostaining of some of the spheroids suggested continuing dysfunction of axoplasmic flow in some regions. There was mild inflammation of peripheral nerve roots but no spheroid, and patchy chronic inflammation of skeletal muscle. In summary, the major pathological process in ADSA is a neuroaxonal dystrophy most prominent in the dorsal columns and dorsal column nuclei, consistent with the clinical pattern of central sensory pathway degeneration.

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.

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. CONCLUSIONS: 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 CONCLUSIONS: 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.