Faculty Bibliography
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477
DNA methylation of circulating tumor educated leukocytes as a biomarker of IDH1/2 mutation in diffuse gliomas [Meeting Abstract]
ISI:000434064400020
ISSN: 0022-3069
CID: 3156212
DNA methylation-based classification of central nervous system tumours
Accurate pathological diagnosis is crucial for optimal management of patients with cancer. For the approximately 100 known tumour types of the central nervous system, standardization of the diagnostic process has been shown to be particularly challenging-with substantial inter-observer variability in the histopathological diagnosis of many tumour types. Here we present a comprehensive approach for the DNA methylation-based classification of central nervous system tumours across all entities and age groups, and demonstrate its application in a routine diagnostic setting. We show that the availability of this method may have a substantial impact on diagnostic precision compared to standard methods, resulting in a change of diagnosis in up to 12% of prospective cases. For broader accessibility, we have designed a free online classifier tool, the use of which does not require any additional onsite data processing. Our results provide a blueprint for the generation of machine-learning-based tumour classifiers across other cancer entities, with the potential to fundamentally transform tumour pathology.
PMCID:6093218
PMID: 29539639
ISSN: 1476-4687
CID: 2992882
Programmed death ligand 1 expression and tumor infiltrating lymphocytes in neurofibromatosis type 1 and 2 associated tumors
Immune checkpoint inhibitors targeting programmed cell death 1 (PD-1) or its ligand (PD-L1) have been shown to be effective in treating patients with a variety of cancers. Biomarker studies have found positive associations between clinical response rates and PD-L1 expression on tumor cells, as well as the presence of tumor infiltrating lymphocytes (TILs). It is currently unknown whether tumors associated with neurofibromatosis types 1 and 2 (NF1 and NF2) express PD-L1. We performed immunohistochemistry for PD-L1 (clones SP142 and E1L3N), CD3, CD20, CD8, and CD68 in NF1-related tumors (ten dermal and six plexiform neurofibromas) and NF2-related tumors (ten meningiomas and ten schwannomas) using archival formalin-fixed paraffin-embedded tissues. Expression of PD-L1 was considered positive in cases with > 5% membranous staining of tumor cells, in accordance with previously published biomarker studies. PD-L1 expression in tumor cells (using the SP142 and E1L3N clones, respectively) was assessed as positive in plexiform neurofibromas (6/6 and 5/6) dermal neurofibromas (8/10 and 6/10), schwannomas (7/10 and 10/10), and meningiomas (4/10 and 2/10). Sparse to moderate presence of CD68, CD3, or CD8 positive TILs was found in 36 (100%) of tumor specimens. Our findings indicate that adaptive resistance to cell-mediated immunity may play a major role in the tumor immune microenvironment of NF1 and NF2-associated tumors. Expression of PD-L1 on tumor cells and the presence of TILs suggest that these tumors might be responsive to immunotherapy with immune checkpoint inhibitors, which should be explored in clinical trials for NF patients.
PMCID:5930071
PMID: 29427150
ISSN: 1573-7373
CID: 2969022
A recurrent kinase domain mutation in PRKCA defines chordoid glioma of the third ventricle
Chordoid glioma is a rare brain tumor thought to arise from specialized glial cells of the lamina terminalis along the anterior wall of the third ventricle. Despite being histologically low-grade, chordoid gliomas are often associated with poor outcome, as their stereotypic location in the third ventricle makes resection challenging and efficacious adjuvant therapies have not been developed. Here we performed genomic profiling on 13 chordoid gliomas and identified a recurrent D463H missense mutation in PRKCA in all tumors, which localizes in the kinase domain of the encoded protein kinase C alpha (PKCα). Expression of mutant PRKCA in immortalized human astrocytes led to increased phospho-ERK and anchorage-independent growth that could be blocked by MEK inhibition. These studies define PRKCA as a recurrently mutated oncogene in human cancer and identify a potential therapeutic vulnerability in this uncommon brain tumor.
PMCID:5824822
PMID: 29476136
ISSN: 2041-1723
CID: 2963962
Hacking macrophage-associated immunosuppression for regulating glioblastoma angiogenesis
Glioblastoma (GBM) is the most lethal primary adult brain tumor and its pathology is hallmarked by distorted neovascularization, diffuse tumor-associated macrophage infiltration, and potent immunosuppression. Reconstituting organotypic tumor angiogenesis models with biomimetic cell heterogeneity and interactions, pro-/anti-inflammatory milieu and extracellular matrix (ECM) mechanics is critical for preclinical anti-angiogenic therapeutic screening. However, current in vitro systems do not accurately mirror in vivo human brain tumor microenvironment. Here, we engineered a three-dimensional (3D), microfluidic angiogenesis model with controllable and biomimetic immunosuppressive conditions, immune-vascular and cell-matrix interactions. We demonstrate in vitro, GL261 and CT-2A GBM-like tumors steer macrophage polarization towards a M2-like phenotype for fostering an immunosuppressive and proangiogenic niche, which is consistent with human brain tumors. We distinguished that GBM and M2-like immunosuppressive macrophages promote angiogenesis, while M1-like pro-inflammatory macrophages suppress angiogenesis, which we coin "inflammation-driven angiogenesis." We observed soluble immunosuppressive cytokines, predominantly TGF-β1, and surface integrin (αvβ3) endothelial-macrophage interactions are required in inflammation-driven angiogenesis. We demonstrated tuning cell-adhesion receptors using an integrin (αvβ3)-specific collagen hydrogel regulated inflammation-driven angiogenesis through Src-PI3K-YAP signaling, highlighting the importance of altered cell-ECM interactions in inflammation. To validate the preclinical applications of our 3D organoid model and mechanistic findings of inflammation-driven angiogenesis, we screened a novel dual integrin (αvβ3) and cytokine receptor (TGFβ-R1) blockade that suppresses GBM tumor neovascularization by simultaneously targeting macrophage-associated immunosuppression, endothelial-macrophage interactions, and altered ECM. Hence, we provide an interactive and controllable GBM tumor microenvironment and highlight the importance of macrophage-associated immunosuppression in GBM angiogenesis, paving a new direction of screening novel anti-angiogenic therapies.
PMID: 29421553
ISSN: 1878-5905
CID: 2948312
Pre-treatment lymphopenia and indication of tumor-induced systemic immunosuppression in medulloblastoma
The presence of tumor-induced systemic immune suppression, including lymphopenia, has been recognized in adult patients with glioblastoma for several decades, and pre-treatment neutrophil-to-lymphocyte count ratio (NLCR) is associated with inferior clinical outcome in patients with glioblastoma. Whether tumor-induced systemic immune suppression is also present in children with malignant brain tumors is not known. We performed a retrospective analysis of pretreatment neutrophil and lymphocyte counts in pediatric patients with medulloblastoma (MB) compared to a control group of children with posterior fossa pilocytic astrocytoma (PA). Compared to the control group, we observed statistically significantly lower absolute lymphocyte counts (ALCs) and higher NLCRs in the medulloblastoma group. Our findings suggest the presence of tumor-induced systemic immune suppression in MB patients already present at the time of diagnosis, with potential implications for the development of immune therapies in this population.
PMCID:5807109
PMID: 29143922
ISSN: 1573-7373
CID: 2947242
Whole Genome DNA Methylation Analysis of Human Glioblastoma Using Illumina BeadArrays
In this chapter, we describe the use of Illumina® Infinium® HD Assay in conjunction with Illumina's EPIC Methylation 8-sample array platform to obtain glioblastoma molecular profiles. The procedure spans four days, and can be performed by a single laboratory technician. Starting with as little as 250 ng of DNA input, this method allows the flexibility to begin with DNA derived from either formalin-fixed, paraffin-embedded (FFPE) or fresh tissue and is compatible with an Illumina iScan or HiScan system.
PMID: 29392688
ISSN: 1940-6029
CID: 2933492
A case of molecularly profiled extraneural medulloblastoma metastases in a child
BACKGROUND:Extraneural metastases are relatively rare manifestations of medulloblastoma. CASE PRESENTATION/METHODS:We present the case of a young boy with group three MYCN-amplified medulloblastoma. He received multimodal chemotherapy consisting of gross total resection followed by postoperative craniospinal radiation and adjuvant chemotherapy. The patient developed extraneural metastases 4Â months after the end of therapy. Literature review identifies the poor prognosis of MYCN-amplified medulloblastomas as well as extraneural metastases; we review the current limitations and future directions of medulloblastoma treatment options. CONCLUSION/CONCLUSIONS:To the best of our knowledge, this is the first molecularly characterized report of extraneural metastases of medulloblastoma in a child.
PMCID:5772742
PMID: 29343221
ISSN: 1471-2350
CID: 2915472
Rapid Intraoperative Diagnosis of Pediatric Brain Tumors Using Stimulated Raman Histology
Accurate histopathologic diagnosis is essential for providing optimal surgical management of pediatric brain tumors. Current methods for intraoperative histology are time- and labor-intensive and often introduce artifacts that limit interpretation. Stimulated Raman histology (SRH) is a novel label-free imaging technique that provides intraoperative histologic images of fresh, unprocessed surgical specimens. Here we evaluate the capacity of SRH for use in the intraoperative diagnosis of pediatric type brain tumors. SRH revealed key diagnostic features in fresh tissue specimens collected from 33 prospectively enrolled pediatric type brain tumor patients, preserving tumor cytology and histoarchitecture in all specimens. We simulated an intraoperative consultation for 25 patients with specimens imaged using both SRH and standard hematoxylin and eosin histology. SRH-based diagnoses achieved near-perfect diagnostic concordance (Cohen's kappa, kappa > 0.90) and an accuracy of 92-96%. We then developed a quantitative histologic method using SRH images based on rapid image feature extraction. Nuclear density, tumor-associated macrophage infiltration, and nuclear morphology parameters from 3337 SRH fields of view were used to develop and validate a decision-tree machine-learning model. Using SRH image features, our model correctly classified 25 fresh pediatric type surgical specimens into normal versus lesional tissue and low-grade versus high-grade tumors with 100% accuracy. Our results provide insight into how SRH can deliver rapid diagnostic histologic data that could inform the surgical management of pediatric brain tumors.
PMCID:5844703
PMID: 29093006
ISSN: 1538-7445
CID: 2765832
Altered methylation of olfactory receptor pathways in osteosarcoma [Meeting Abstract]
Background: Osteosarcoma is one of the most common bone malignancies in the pediatric population, although it affects a wide age range. While pathognomonic genomic alterations have been identified in other pediatric bone and soft tissue tumors such as Ewing sarcoma and synovial sarcoma, no such alterations are seen in osteosarcoma. Epigenetic modifications such as global or specific changes in DNA methylation are gaining recognition as a primary mechanism of oncogenesis in pediatric and adult cancers. Identifying unique epigenetic modifications in tumors lacking known fusions could contribute to both diagnosis and selection of potential therapeutic targets. Methods: Using the Illumina Infinium Human Methylation450 BeadChip Array (450K array) platform, we performed genome-wide DNA methylation analysis on 15 osteosarcomas with tissue meeting criteria for methylation analysis, including formalin-fixed paraffin-embedded, frozen, and fresh tissue obtained from NYU and Memorial Sloan Kettering Cancer Center (mean age = 26 years; range 6-80 years). Comparison was made to 10 Ewing sarcomas and 11 synovial sarcomas in the same pilot cohort. Diagnosis was based on histologic criteria and, where available, absence of a known non-osteosarcoma genomic fusion. Unsupervised hierarchical clustering analysis was performed to classify tumor type and to assess for differentially methylated target regions. Results: Osteosarcomas formed a unique subtype on unsupervised hierarchical clustering analysis of DNA methylation. Of the 15 tumors profiled, molecular testing confirming the absence of a known fusion was previously done on 5, and fusion status did not impact clustering. Pathway analysis through MSig
EMBASE:622343650
ISSN: 1615-5742
CID: 3152482
