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Dorris K, Mettetal A, Dahl N, Hemenway M, Winzent-Oonk S, Prince E, Vijmasi T, McWilliams J, Jordan K, Mirsky D, Hoffman L, Hankinson T. RARE-32. Phase 0 and feasibility single-institution clinical trial of intravenous tocilizumab for adamantinomatous craniopharyngioma. Neuro Oncol 2022. [PMCID: PMC9165090 DOI: 10.1093/neuonc/noac079.057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND: Adamantinomatous craniopharyngioma (ACP) is a devastating skull-base tumor believed to derive from epithelial remnants of the primordial craniopharyngeal duct (Rathke’s pouch), which gives rise to the anterior pituitary gland. ACP lacks medical antitumor therapies. Current standard therapy with surgery and radiation is associated with poor quality of life. Clinical and preclinical data indicate that IL-6 blockade may contribute to ACP tumor control. METHODS: Children aged 2–21 years with newly diagnosed or previously treated ACP with measurable disease are eligible for the Phase 0/feasibility single-institution clinical trial (NCT03970226) of intravenous (IV) tocilizumab at Children’s Hospital Colorado. The phase I stratum involves IV tocilizumab prior to a standard-of-care surgical resection. The feasibility portion of the trial involves IV tocilizumab every two weeks for up to 13 28-day cycles. Tocilizumab is administered at the established weight-based pediatric dosage of 8 mg/kg for patients who weigh ≥30kg or 12 mg/kg for patients who weigh <30kg. RESULTS: To date, three patients have been enrolled on the Phase 0 component of the trial. These patients demonstrated clinically relevant levels of tocilizumab (≥ 4µg/mL) in serum, cyst fluid, and/or tumor tissue, compared to undetectable levels in control samples. Two patients (1 male and 1 female; median age 10.5 years) have enrolled on the feasibility stratum; one patient had best response of minor response but met definition of progressive disease at cycle 11. One patient with extensive disease required dose reduction for myelosuppression. CONCLUSION: Systemic delivery of tocilizumab at the established pediatric dosage is promising for treatment of ACP based on preclinical work and its demonstrated penetration into cystic and solid portions of ACP tumors. The therapy to date has been well tolerated overall. Further study is planned through a CONNECT consortium international Phase II trial.
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Alimova I, Wang D, Pierce A, Lakshmanachetty S, Prince E, Danis E, Serkova N, Madhavan K, Balakrishnan I, Yang M, Lin H, Foreman N, Venkataraman S, Vibhakar R. ATRT-23. SIRT2 cooperates with SMARCB1 to induce a differentiation block in ATRT. Neuro Oncol 2022. [PMCID: PMC9165152 DOI: 10.1093/neuonc/noac079.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Atypical Teratoid Rhabdoid Tumor is a highly aggressive pediatric brain tumor with poor prognosis driven by loss of the chromatin remodeling factor SMARCB1 that is responsible for determining cellular pluripotency and lineage commitment. The mechanisms by which SMARCB1 deletion results in tumorigenesis remain unclear. We investigated the effect of SIRT2 inhibition in ATRT which was identified as a primary dependency in ATRT. SIRT2 inhibition with shRNA or Thiomyristoyl (TM) decreased ATRT cell growth, inhibited clonogenic potential and leaded to the cell cycle arrest. SIRT2 inhibition effectively suppresses pluripotency-associated genomic programs, significantly changed stem cell frequency, decreased tumor-sphere formation of ATRT cells and attenuated tumor cell self-renewal. In vivo SIRT2 inhibition decreased oncogenic markers and increased accumulation neuronal differentiation markers. Furthermore, SIRT2 induced apoptosis, decreased tumor growth and prolonged survival in orthotopic xenograft models. Single-cell RNA transcriptome analysis of xenoftaft tumors reveals elimination of tumor cells expressing stem cell genes and expansion of tumor cells expressing differentiated genes following TM treatment in ATRT. We demonstrated that SIRT2 inhibition is a molecular vulnerability in SMARCB1-deleted ATRT.
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Affiliation(s)
- Irina Alimova
- Department of Pediatrics University of Colorado Denver, Anschutz Medical Campus , Aurora, Colorado , USA
| | - Dong Wang
- Department of Pediatrics University of Colorado Denver, Anschutz Medical Campus , Aurora, Colorado , USA
| | - Angela Pierce
- Department of Pediatrics University of Colorado Denver, Anschutz Medical Campus , Aurora, Colorado , USA
| | | | - Eric Prince
- Department of Biostatistics and Informatics University of Colorado Denver Anschutz Medical Campus , Aurora, Colorado , USA
- Department of Neurosurgery University of Colorado Denver Anschutz Medical Campus , Aurora, Colorado , USA
| | - Etienne Danis
- Department of Pediatrics University of Colorado Denver, Anschutz Medical Campus , Aurora, Colorado , USA
| | - Natalie Serkova
- Department of Radiology University of Colorado Denver, School of Medicine , Aurora, Colorado , USA
| | - Krishna Madhavan
- Department of Pediatrics University of Colorado Denver, Anschutz Medical Campus , Aurora, Colorado , USA
| | - Ilango Balakrishnan
- Department of Pediatrics University of Colorado Denver, Anschutz Medical Campus , Aurora, Colorado , USA
| | - Min Yang
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, NY , USA
| | - Henning Lin
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, NY , USA
| | - Nicholas Foreman
- Department of Pediatrics University of Colorado Denver, Anschutz Medical Campus , Aurora, Colorado , USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado , Aurora, Colorado , USA
| | - Sujatha Venkataraman
- Department of Pediatrics University of Colorado Denver, Anschutz Medical Campus , Aurora, Colorado , USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado , Aurora, Colorado , USA
| | - Rajeev Vibhakar
- Department of Pediatrics University of Colorado Denver, Anschutz Medical Campus , Aurora, Colorado , USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado , Aurora, Colorado , USA
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Jomaa D, Khadka P, Novikov D, Condurat AL, Tsai JW, Dubois F, Zhang S, Zhou K, Gold R, Sousa C, Vogelzang J, Prince E, Lu S, Slivova V, Otto GW, Hereza SC, Ashley D, Cohen-Gadol AA, Thompson E, Beroukhim R, Apps J, Martinez-Barbera JP, Hankinson T, Bandopadhayay P. RARE-22 Characterizing the landscape of structural variants in adamantinomatous craniopharyngioma. Neuro Oncol 2022. [PMCID: PMC9164984 DOI: 10.1093/neuonc/noac079.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
INTRODUCTION: Adamantinomatous craniopharyngiomas (ACPs) are rare brain tumors that primarily occur in children and impact long-term morbidity and mortality. The canonical driver mutation for ACP growth occurs in CTNNB1 and leads to constitutive activation of the Wnt/β-catenin signaling pathway. In this study, we outline the genomic, transcriptomic, and structural variant (SV) landscape in a cohort of 41 ACP samples. METHODS: We performed whole-genome sequencing (WGS) and RNA-sequencing of 41 ACP samples. Matched normal samples were also characterized by WGS. Mutect2 was used to detect single nucleotide variants (SNVs) and indels, and copy number data was generated using the GATK pipeline. SvABA was used to perform SV analysis and to identify significantly recurrent breakpoints and juxtapositions. DESeq2 was used to perform differential gene expression analysis based on clinical and molecular annotation data. RESULTS: 29/41 (70%) of the ACP samples harbored missense mutations in exon 3 of CTNNB1, all of which have previously been reported in ACP tumors. SV analysis identified a median of 11.5 events per tumor. Overall, 9.7% of events were interchromosomal. Of the remainder, the majority (78.6%) were deletions. No SVs occurred within CTNNB1. A positive correlation (r = 0.533) was observed between the frequency of SVs and SNVs within samples. Analysis of significantly recurring breakpoints (SRBs) did not identify recurrent breakpoint events. Differential gene expression analysis comparing samples with and without CTNNB1 variants identified 2,143 differentially expressed genes with q-value < 0.05. CONCLUSION: This study identifies activating mutations in exon 3 of CTNNB1 in a large cohort of ACP samples. We also integrate SV and transcriptomic data to comprehensively investigate ACP tumor genomes and identify putative novel tumorigenic mechanisms that advance our understanding of ACP biology.
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Affiliation(s)
- Danny Jomaa
- Harvard Medical School , Boston, MA , USA
- Dana-Farber Cancer Institute , Boston, MA , USA
| | - Prasidda Khadka
- Harvard Medical School , Boston, MA , USA
- Dana-Farber Cancer Institute , Boston, MA , USA
| | | | | | - Jessica W Tsai
- Dana-Farber Cancer Institute , Boston, MA , USA
- Boston Children's Hospital , Boston, MA , USA
| | | | - Shu Zhang
- Dana-Farber Cancer Institute , Boston, MA , USA
| | - Kevin Zhou
- Dana-Farber Cancer Institute , Boston, MA , USA
| | - Rose Gold
- Dana-Farber Cancer Institute , Boston, MA , USA
| | | | | | - Eric Prince
- Department of Neurosurgery, University of Colorado School of Medicine , Aurora, CO , USA
- Morgan Adams Foundation for Pediatric Brain Tumor Research Program, University of Colorado School of Medicine , Aurora, CO , USA
| | - Sophie Lu
- Milken Institute of Public Health, George Washington University , Washington, DC , USA
| | | | - Georg W Otto
- University College London, London , England , United Kingdom
| | | | - David Ashley
- Department of Neurosurgery, Duke University , Durham, NC , USA
| | | | - Eric Thompson
- Department of Neurosurgery, Duke University , Durham, NC , USA
| | - Rameen Beroukhim
- Dana-Farber Cancer Institute , Boston, MA , USA
- Brigham and Women's Hospital , Boston, MA , USA
| | - John Apps
- University College London, London , England , United Kingdom
- University of Birmingham, Birmingham , England , United Kingdom
| | | | - Todd Hankinson
- Department of Neurosurgery, University of Colorado School of Medicine , Aurora, CO , USA
- Morgan Adams Foundation for Pediatric Brain Tumor Research Program, University of Colorado School of Medicine , Aurora, CO , USA
| | - Pratiti Bandopadhayay
- Dana-Farber Cancer Institute , Boston, MA , USA
- Boston Children's Hospital , Boston, MA , USA
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Veo B, Goodspeed A, Prince E, Venkataraman S, Vibhakar R. MEDB-70. Metabolism mediated radiation resistance in MYC-driven Medulloblastoma. Neuro Oncol 2022. [PMCID: PMC9165022 DOI: 10.1093/neuonc/noac079.444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Medulloblastoma (MB) is the most prevalent malignant brain tumor in children and demonstrates a high level of heterogeneity. Treatment for MB includes chemotherapy and radiation often resulting in long-term morbidity. MYC-driven MB, are high-risk tumors with poor long-term survival and increased susceptibility to develop recurrent tumors. Recurrent MB is far more aggressive with limited treatment options leading to a 5-year survival rate of 12%. To understand what drives MYC-amplified MB relapse we performed single-cell RNA sequencing of irradiated MB xenograft tumors. We identified an overall enhancement of metabolic activity in radiation-resistant cells. We further observe enhanced wild-type IDH1 and IDH2 expression in two clusters, which coincide with hypoxia and Nestin expression, marking a stem-cell like niche. Stem-like cancer cells are notoriously resilient against radiation therapy. Furthermore, wtIDH1 and IDH2 represent a unique target in radiation-resistant MB which has not previously been identified. Wild type IDH1/IDH2 are more recently shown to promote tumor proliferation and mediate metabolic reprogramming through the production of oncometabolites and substrates that functionally alter chromatin structure and gene transcription. We hypothesized that MYC modulation of wtIDH1/IDH2 facilitates metabolic reprogramming and promotes radiation-resistant cell populations. We show the change in the structural integrity of chromatin altered in radiation-resistant MB by metabolic adaptation and the effect of disrupting IDH1/IDH2 activity. We further compare these results to the chromatin profile of patient primary and matched relapsed MB samples at the single-cell level. We demonstrate that targeting IDH1/2 with chemical inhibitors suppresses MB cell growth. Our results disclose insights into the development of radiation resistance and provide a potential therapeutic target for the treatment of relapsed MYC-MB.
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Affiliation(s)
| | | | | | | | - Rajeev Vibhakar
- University of Colorado , Aurora, CO , USA
- Childrens Hospital Colorado , Aurora, CO , USA
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Prince E, Trudeau T, Chatain O, Staulcup S, Martinez-Barbera JP, Goerg C, Hankinson T. RARE-29. Transcriptome characterization of pediatric adamantinomatous craniopharyngioma at the cellular level. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac079.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
BACKGROUND: Adamantinomatous Craniopharyngioma (ACP) is a neurologically devastating brain tumor that affects children and adults. It is histologically heterogeneous with epithelial populations that are characterized by the nuclear accumulation of mutated β-catenin, and activated Wnt signaling. Current models suggest that ACP growth is driven through paracine mechanisms characterized by the senescence-associated secretory phenotype (SASP). However, detailed pathogenic mechanisms remain unknown. Improved definition of the various cellular phenotypes that compose ACP will inform and advance our understanding of this disease. METHODS: Single cell RNA-sequencing (scRNA-seq) and multiplex ELISA were performed on pediatric ACP tissue and cyst fluid, respectively. Reference scRNA-seq data was obtained from PanglaoDB. Preprocessing and standard analyses were conducted using Seurat software. Cellular phenotypes were annotated using the Human Primary Cell atlas. Differential expression and functional enrichment analyses were utilized to identify Wnt-signaling activation and epithelial subpopulations. Paracrine signaling was inferred via CellChatDB. SASP Atlas was utilized to query marker gene lists. Pseudotemporal ordering was performed using monocle3. RESULTS: ACP tissue is heterogenous and contains multiple distinct immune signatures. ACP tissue contains 2 unique epithelial subpopulations, which demonstrate canonical Wnt-signaling and SASP, respectively. Pseudotemporal ordering suggests the initial oncogenic event to be of epidermal character, with subsequent aggressive behavior from a separate epithelial cell population. CONCLUSIONS: Based on gene expression, cell populations that correspond to the histologically identifiable epithelial whorls and palisading epithelium can be identified. These subpopulations display unique functional signatures. Simultaneous and synergistic therapeutic targeting of these separate epithelial populations may lead to improved patient care.
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Affiliation(s)
- Eric Prince
- University of Colorado School of Medicine , Aurora, CO , USA
- Children's Hospital Colorado , Aurora, CO , USA
| | - Tammy Trudeau
- University of Colorado School of Medicine , Aurora, CO , USA
- Children's Hospital Colorado , Aurora, CO , USA
| | - Oscar Chatain
- University of Colorado School of Medicine , Aurora, CO , USA
- Children's Hospital Colorado , Aurora, CO , USA
| | - Susan Staulcup
- University of Colorado School of Medicine , Aurora, CO , USA
- Children's Hospital Colorado , Aurora, CO , USA
| | | | | | - Todd Hankinson
- University of Colorado School of Medicine , Aurora, CO , USA
- Children's Hospital Colorado , Aurora, CO , USA
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Trudeau T, Prince E, Chatain O, Chee K, Jackson E, Limbrick D, Naftel R, Feldstein N, Grant G, Ginn K, Niazi T, Smith A, Kilburn L, Chern J, Drapeau A, Lam S, Johnston J, Dudley R, Staulcup S, Hankinson T. RARE-24. The use of novel in vitro models to study adamantinomatous craniopharyngioma disease biology and drug response. Neuro Oncol 2022. [PMCID: PMC9165211 DOI: 10.1093/neuonc/noac079.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
BACKGROUND: Challenges around the design and investigation of cell culture models of adamantinomatous craniopharyngioma (ACP) have arisen from the cellular heterogeneity of these tumors, with populations that harbor disparate requirements in culture. Novel approaches to in vitro modeling of ACP are needed. METHODS: Intraoperatively collected tumor specimens were mechanically digested and plated under conditions tailored to the cell population of interest. ACP tumor-derived fibroblasts and epithelial cells were isolated using serum-containing and keratinocyte-specific media respectively. ACP-derived epithelial cells were immortalized via SV40 virus transfection and puromycin treatment for stable cell-line generation. Cell line validation included immunofluorescence with markers appropriate for the cell population of interest. RNA sequencing of cell lines was compared to ACP transcriptome reference data. Cell typing was conducted using short tandem repeat sequencing. RESULTS: ACP fibroblasts and ACP epithelial cells maintained spindle-like and cobblestone morphologies respectively, even after 4 passages. Immunofluorescence staining confirmed high levels of Vimentin expression in ACP-derived fibroblasts, and panCK and B-catenin in ACP-derived epithelial cells. Point mutation in exon 3 of the CTNNB1 gene was identified in ACP-derived epithelial cells. CONCLUSION: Initial limits related to cell line development in ACP may be addressed through the isolation and culture-specific ACP cell populations. This experience demonstrates the maintenance of validated markers of the cell populations of interest ex vivo. While preliminary, such cell lines offer promise as tools for the identification and study of potential therapeutic vulnerabilities in ACP.
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Affiliation(s)
- Tammy Trudeau
- University of Colorado, School of Medicine , Aurora, CO , USA
| | - Eric Prince
- University of Colorado, School of Medicine , Aurora, CO , USA
| | - Oscar Chatain
- University of Colorado, School of Medicine , Aurora, CO , USA
| | - Keanu Chee
- University of Colorado, School of Medicine , Aurora, CO , USA
| | - Eric Jackson
- Johns Hopkins Medicine, Neurosurgery Department , Baltimore, MD , USA
| | - David Limbrick
- Washington University School of Medicine in St. Louis, St. Louis , MO , USA
| | - Robert Naftel
- Vanderbilt University Medical Center , Nashville, TN , USA
| | - Neil Feldstein
- Columbia University Irving Medical Center, New York , NY , USA
| | | | - Kevin Ginn
- Children's Mercy Kansas City, Kansas City , MO , USA
| | - Toba Niazi
- Nicklaus Children's Hospital , Miami, FL , USA
| | - Amy Smith
- Orlando Health Arnold Palmer Hospital for Children , Orlando, FL , USA
| | | | - Joshua Chern
- Children's Healthcare of Atlanta , Atlanta, GA , USA
| | | | - Sandi Lam
- Ann & Robert H. Lurie Hospital of Chicago , Chicago, IL , USA
| | | | - Roy Dudley
- Montreal Children's Hospital , Montreal , Canada
| | - Susan Staulcup
- University of Colorado, School of Medicine , Aurora, CO , USA
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Chopra T, Neuberger I, Prince E, White C, Maloney J, Stence N, Mirsky D. Age-related changes in the completeness of the circle of Willis in children. Childs Nerv Syst 2022; 38:1181-1184. [PMID: 35394211 DOI: 10.1007/s00381-022-05505-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/16/2022] [Indexed: 11/03/2022]
Abstract
PURPOSE The circle of Willis is a circulatory anastomosis that supplies blood to the brain. If any of the bridging segments are hypoplastic or absent, the capacity for collateral flow in the setting of large vessel occlusion may be decreased. Outside of the neonatal period, the prevalence of a complete circle of Willis (CoW) in the pediatric population has not been well described. Our objectives include determining the prevalence of a complete CoW in children and identifying if there is an age-related "loss" of arterial segments. METHODS Following IRB approval, angiograms of the CoW performed on a 3-T MR platform from 2016 to 2020 on patients 21 years or younger were retrospectively reviewed. Any patient with underlying arterial pathology that may affect the CoW was excluded. Patient age and gender at the time of imaging were obtained. RESULTS In total, 592 pediatric CoW were assessed. Frequencies of completeness were calculated in two different fashions: scenario 1 where a CoW was characterized as complete even if it contained hypoplastic vessels (88.8%), and scenario 2 where it was characterized as complete after excluding hypoplastic vessels (44.0%). In both scenarios, our data showed that older age was more associated with an incomplete CoW (p < 0.0001). In addition, we found a higher percentage of males with an incomplete CoW compared with females (p < 0.0001). CONCLUSIONS The presence of a complete CoW is greater in our pediatric population than what has been reported in adults. The prevalence of an incomplete circle of Willis also increases significantly with age.
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Affiliation(s)
- Tavishi Chopra
- Creighton University School of Medicine, AZ, Phoenix, USA.
| | | | - Eric Prince
- University of Colorado Anschutz Medical Campus, Aurora, USA
| | | | - John Maloney
- Neuroradiology, Children's Hospital Colorado, Aurora, USA
| | | | - David Mirsky
- Neuroradiology, Children's Hospital Colorado, Aurora, USA
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Prince E, Trudeau T, Chatain O, Chee K, Vijmasi T, Staulcup S, Donson A, Foreman N, Hankinson T. RARE-19. NETWORK AND DEEP LEARNING INFERENCE IN SINGLE CELL RNA SEQUENCING REVEAL DETAILED TRANSCRIPTIONAL SIGNATURES CONGRUENT WITH MOLECULAR UNDERSTANDING OF ADAMANTINOMATOUS CRANIOPHARYNGIOMA. Neuro Oncol 2021. [PMCID: PMC8168248 DOI: 10.1093/neuonc/noab090.180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Adamantinomatous Craniopharyngioma (ACP) is a highly morbid, cellularly heterogeneous pediatric tumor arising in the sellar/suprasellar region of the brain. This cellular heterogeneity makes ACP an ideal candidate for study using single-cell RNA-sequencing (scRNA-seq). We collected a 10,000 cell scRNA-seq dataset on the 10X v3 platform, from 6 unique patients. Using the industry standard Seurat software package, we identified 34 unique cell clusters. By crossing the results of two separate expert curated cellular reference atlases (Azimuth and scHCL), we determined that 33 of these cell types were immune-related (e.g., T cells, monocytes, etc.) or histologically related (e.g., glial cells). The remaining 2,048 cells were inferred to be ACP driver cells. Rigorous statistical testing of third-generation graph topology-based network enrichment methods utilizing the Reactome database supported this conclusion. In order to identify effective antitumor therapies, it is critical to understand the temporal evolution of tumor cell behavior. Computational solutions that describe the potential lifecycle of tumor cells have been derived using scRNA-seq datasets. Using a well-established method, Monocle3, we generated a potential model of temporal evolution of the ACP driver cell population. To identify a specific transcriptional “point-of-no-return” for ACP driver cells, which may help define a rational target for intervention, we created a custom probabilistic Deep Learning framework in the form of a Convolutional Variational Autoencoder (CVAE). By applying this CVAE to our data, we identified 31 anomalous transcripts, each of which was aberrantly active at all times or demonstrated a temporal pattern of anomalous activity. Strikingly, this small list – representing roughly 0.15% of the protein coding genome – aligns closely with extant data describing the molecular behavior of ACP. This work provides a novel transcriptome benchmark for comparison of in vitromodels, a deeper understanding of ACP heterogeneity, as well as a generalizable approach for scRNA-seq analysis.
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Affiliation(s)
- Eric Prince
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Tammy Trudeau
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Oscar Chatain
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Keanu Chee
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Trinka Vijmasi
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Susan Staulcup
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Andrew Donson
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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Griesinger A, Riemondy K, Donson A, Willard N, Prince E, Harris F, Amani V, Grimaldo E, Hankinson T, Grundy R, Jackson A, Foreman N, Ritzmann T. EPEN-07. SINGLE-CELL RNA SEQUENCING IDENTIFIES A UNIQUE MYELOID SUBPOPULATION ASSOCIATED WITH MESENCHYMAL TUMOR SUBPOPULATION IN POOR OUTCOME PEDIATRIC EPENDYMOMA. Neuro Oncol 2021. [PMCID: PMC8168243 DOI: 10.1093/neuonc/noab090.057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
We have previously shown immune gene phenotype variations between posterior fossa ependymoma subgroups. PFA1 tumors chronically secrete IL-6, which induces secretion of myeloid cell IL-8 and pushes the infiltrating myeloid cells to an immune suppressive function. In contrast, PFA2 tumors have a more immune activated phenotype associated with a better prognosis. The objective of this study was to use single-cell(sc) RNAseq to descriptively characterize the infiltrating myeloid cells. We analyzed approximately 8500 cells from 21 PFA patient samples. Using advanced machine learning, we identified eight myeloid cell subpopulations with unique gene expression profiles. Interestingly, only one subpopulation was significantly enriched in PFA1 tumors. This subpopulation, denoted as the hypoxia myeloid subpopulation, was defined by genes associated with angiogenesis, response to hypoxia, wound healing, cell migration, neutrophil activation and response to oxygen levels. These myeloid cells also share similar gene expression profile to a mesenchymal tumor subpopulation (MEC) enriched in PFA1 and associated with poor outcome in EPN patients. This tumor subpopulation was the only population expressing IL-6. Using immunohistochemistry, we found the hypoxia myeloid located in regions of tumor necrosis and perivascular niches. The MEC cells were also more abundant in these regions. In an independent single-cell cytokine release assay, we identified eight subpopulations of functional myeloid cells. One subpopulation significantly secreted IL-8, which represented the hypoxia subpopulation based on IL-8 gene expression in the scRNAseq dataset. This data suggests the tumor necrosis resulting in the development of MEC tumor subpopulation is driving the immune suppressive myeloid phenotype in PFA1 tumors through polarization of myeloid cells to the hypoxia subpopulation. Further studies are needed to determine how these myeloid cells interact with the lymphocyte subpopulations and whether they contribute to the progression of PFA1 EPN.
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Affiliation(s)
- Andrea Griesinger
- CU Anschutz Medical Campus, Aurora, CO, USA
- Children’s Hospital Colorado, Aurora, CO, USA
| | | | - Andrew Donson
- CU Anschutz Medical Campus, Aurora, CO, USA
- Children’s Hospital Colorado, Aurora, CO, USA
| | - Nicholas Willard
- CU Anschutz Medical Campus, Aurora, CO, USA
- Children’s Hospital Colorado, Aurora, CO, USA
| | - Eric Prince
- CU Anschutz Medical Campus, Aurora, CO, USA
- Children’s Hospital Colorado, Aurora, CO, USA
| | - Faith Harris
- CU Anschutz Medical Campus, Aurora, CO, USA
- Children’s Hospital Colorado, Aurora, CO, USA
| | - Vladimir Amani
- CU Anschutz Medical Campus, Aurora, CO, USA
- Children’s Hospital Colorado, Aurora, CO, USA
| | - Enrique Grimaldo
- CU Anschutz Medical Campus, Aurora, CO, USA
- Children’s Hospital Colorado, Aurora, CO, USA
| | - Todd Hankinson
- CU Anschutz Medical Campus, Aurora, CO, USA
- Children’s Hospital Colorado, Aurora, CO, USA
| | | | | | - Nicholas Foreman
- CU Anschutz Medical Campus, Aurora, CO, USA
- Children’s Hospital Colorado, Aurora, CO, USA
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10
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Gillen AE, Riemondy KA, Amani V, Griesinger AM, Gilani A, Venkataraman S, Madhavan K, Prince E, Sanford B, Hankinson TC, Handler MH, Vibhakar R, Jones KL, Mitra S, Hesselberth JR, Foreman NK, Donson AM. Single-Cell RNA Sequencing of Childhood Ependymoma Reveals Neoplastic Cell Subpopulations That Impact Molecular Classification and Etiology. Cell Rep 2021; 32:108023. [PMID: 32783945 DOI: 10.1016/j.celrep.2020.108023] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 06/16/2020] [Accepted: 07/21/2020] [Indexed: 12/11/2022] Open
Abstract
Ependymoma (EPN) is a brain tumor commonly presenting in childhood that remains fatal in most children. Intra-tumoral cellular heterogeneity in bulk-tumor samples significantly confounds our understanding of EPN biology, impeding development of effective therapy. We, therefore, use single-cell RNA sequencing, histology, and deconvolution to catalog cellular heterogeneity of the major childhood EPN subgroups. Analysis of PFA subgroup EPN reveals evidence of an undifferentiated progenitor subpopulation that either differentiates into subpopulations with ependymal cell characteristics or transitions into a mesenchymal subpopulation. Histological analysis reveals that progenitor and mesenchymal subpopulations co-localize in peri-necrotic zones. In conflict with current classification paradigms, relative PFA subpopulation proportions are shown to determine bulk-tumor-assigned subgroups. We provide an interactive online resource that facilitates exploration of the EPN single-cell dataset. This atlas of EPN cellular heterogeneity increases understanding of EPN biology.
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Affiliation(s)
- Austin E Gillen
- RNA Biosciences Initiative, University of Colorado Denver, Aurora, CO 80045, USA
| | - Kent A Riemondy
- RNA Biosciences Initiative, University of Colorado Denver, Aurora, CO 80045, USA
| | - Vladimir Amani
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO 80045, USA; Department of Pediatrics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Andrea M Griesinger
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO 80045, USA; Department of Pediatrics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Ahmed Gilani
- Department of Pathology, University of Colorado Denver, Aurora, CO 80045, USA
| | - Sujatha Venkataraman
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO 80045, USA; Department of Pediatrics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Krishna Madhavan
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO 80045, USA; Department of Pediatrics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Eric Prince
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO 80045, USA; Department of Neurosurgery, University of Colorado Denver, Aurora, CO 80045, USA
| | - Bridget Sanford
- Department of Pediatrics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Todd C Hankinson
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO 80045, USA; Department of Neurosurgery, University of Colorado Denver, Aurora, CO 80045, USA
| | - Michael H Handler
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO 80045, USA; Department of Neurosurgery, University of Colorado Denver, Aurora, CO 80045, USA
| | - Rajeev Vibhakar
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO 80045, USA; Department of Pediatrics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Ken L Jones
- Department of Pediatrics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Siddhartha Mitra
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO 80045, USA; Department of Pediatrics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Jay R Hesselberth
- RNA Biosciences Initiative, University of Colorado Denver, Aurora, CO 80045, USA
| | - Nicholas K Foreman
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO 80045, USA; Department of Pediatrics, University of Colorado Denver, Aurora, CO 80045, USA; Department of Neurosurgery, University of Colorado Denver, Aurora, CO 80045, USA
| | - Andrew M Donson
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO 80045, USA; Department of Pediatrics, University of Colorado Denver, Aurora, CO 80045, USA.
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11
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Hengartner AC, Prince E, Vijmasi T, Hankinson TC. Adamantinomatous craniopharyngioma: moving toward targeted therapies. Neurosurg Focus 2021; 48:E7. [PMID: 31896087 DOI: 10.3171/2019.10.focus19705] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 10/17/2019] [Indexed: 11/06/2022]
Abstract
The evolving characterization of the biological basis of adamantinomatous craniopharyngioma (ACP) has provided insights critical for novel systemically delivered therapies. While current treatment strategies for ACP are associated with low mortality rates, patients experience severely lowered quality of life due to high recurrence rates and chronic sequelae, presenting a need for novel effective treatment regimens. The identification of various dysregulated pathways that play roles in the pathogenesis of ACP has prompted the investigation of novel treatment options. Aberrations in the CTNNB1 gene lead to the dysregulation of the Wnt pathway and the accumulation of nuclear β-catenin, which may play a role in tumor invasiveness. While Wnt pathway/β-catenin inhibition may be a promising treatment for ACP, potential off-target effects have limited its use in current intervention strategies. Promising evidence of the therapeutic potential of cystic proinflammatory mediators and immunosuppressants has been translated into clinical therapies, including interleukin 6 and IDO-1 inhibition. The dysregulation of the pathways of mitogen-activated protein kinase/extracellular signal-regulated kinase (MAPK/ERK), epidermal growth factor receptor (EGFR), and programmed cell death protein 1 and its ligand (PD-1/PD-L1) has led to identification of various therapeutic targets that have shown promise as clinical strategies. The Sonic Hedgehog (SHH) pathway is upregulated in ACP and has been implicated in tumorigenesis and tumor growth; however, inhibition of SHH in murine models decreased survival, limiting its therapeutic application. While further preclinical and clinical data are needed, systemically delivered therapies could delay or replace the need for more aggressive definitive treatments. Ongoing preclinical investigations and clinical trials of these prospective pathways promise to advance treatment approaches aimed to increase patients' quality of life.
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Affiliation(s)
- Astrid C Hengartner
- 1Pediatric Neurosurgery, Children's Hospital Colorado, University of Colorado School of Medicine; and
| | - Eric Prince
- 1Pediatric Neurosurgery, Children's Hospital Colorado, University of Colorado School of Medicine; and
| | - Trinka Vijmasi
- 1Pediatric Neurosurgery, Children's Hospital Colorado, University of Colorado School of Medicine; and
| | - Todd C Hankinson
- 1Pediatric Neurosurgery, Children's Hospital Colorado, University of Colorado School of Medicine; and.,2Morgan Adams Foundation Pediatric Brain Tumor Program, Aurora, Colorado
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12
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Prince E, Vijmasi T, McWilliams J, Hengartner A, Staulcup S, Foreman N, Jordan K, Dorris K, Hoffman L, Hankinson T. RARE-10. ADAMANTINOMATOUS CRANIOPHARYNGIOMA RESIDES OUTSIDE THE BLOOD BRAIN BARRIER. Neuro Oncol 2020. [PMCID: PMC7715731 DOI: 10.1093/neuonc/noaa222.721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Adamantinomatous craniopharyngioma (ACP) is a devastating skull-base tumor believed to derive from epithelial remnants of the primordial craniopharyngeal duct (Rathke’s pouch), which gives rise to the anterior pituitary gland. Genetically engineered mouse models of ACP demonstrate that perturbation of the fetal anterior pituitary can generate tumors analogous to ACP. Clinical and preclinical data indicate that IL-6 blockade may contribute to ACP tumor control, with the most common agent being the humanized monoclonal antibody, tocilizumab. This agent demonstrated poor blood-brain barrier (BBB) penetration in primates. We present findings from two children enrolled on a phase 0 clinical trial (NCT03970226) of a single dose of preoperative intravenous tocilizumab prior to resection of newly diagnosed ACP. METHODS Blood samples were obtained at multiple timepoints. Serum was isolated via ficoll separation. Tumor tissue and cyst fluid were obtained 4–6 hours following the single IV dose of tocilizumab. Tissue was snap-frozen. Tumor was homogenized in RIPA buffer. Free tocilizumab in serum, cyst fluid, and tumor tissue was measured using enzyme-linked immunosorbent assay (ELISA) against a standard curve. RESULTS Both patients in this trial demonstrated clinically relevant levels of tocilizumab (≥ 4µg/mL) in serum, cyst fluid, and tumor tissue, compared to undetectable levels in control samples. CONCLUSION ACP resides outside BBB protection. In addition to demonstrating the feasibility of systemic delivery of tocilizumab, these findings indicate that other large molecules, including those known to have poor BBB penetration, may be systemically delivered as part of an antitumor regimen in the treatment of ACP.
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Affiliation(s)
- Eric Prince
- Children’s Hospital Colorado, Aurora, CO, USA
| | | | | | | | | | | | - Kimberly Jordan
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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13
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Vijmasi T, Prince E, Hengartner A, Staulcup S, Griesinger A, Donson A, Gilani A, Foreman N, Hankinson T. MODL-24. AN ORGANOTYPIC CHUNK CULTURE TECHNIQUE TO STUDY DISEASE MECHANISM AND DEVELOP TARGETED THERAPEUTICS FOR PEDIATRIC ADAMANTINOMATOUS CRANIOPHARYNGIOMA. Neuro Oncol 2020. [PMCID: PMC7715791 DOI: 10.1093/neuonc/noaa222.597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
BACKGROUND
Advances in the treatment of Adamantinomatous Craniopharyngioma (ACP) face challenges with translation to clinical study due to the absence of robust culture models of the disease. We developed a technique for culturing human ACP tissue in an organotypic chunk culture format that retains the tumor microenvironment for a duration sufficient to evaluate potential targeted therapeutics.
METHODS
Intraoperatively collected tumor tissue from pediatric ACP was cut into volumes of approximately 3 mm3 and rested over a semi-permeable insert placed in the wells of a 6-well plate. Specimens were cultured in (1) Control media, media containing (2) Tocilizumab, (3) Trametinib, and (4) combination of Tocilizumab and Trametinib, for 24 and 96 hours. Specimens were harvested for paraffin embedding, protein and gene expression assays. Supernatants were collected to assay secreted components. Paraffin embedded specimens were sectioned and stained for H&E, Pan-CK, Beta-Catenin, cleaved Caspase-3, Ki-67, and Phospho-ERK.
RESULTS
H&E staining revealed characteristic histologic features of ACP with epithelial cells with palisading nuclei, wet keratin and ghost cells. Tumor sections were markedly positive for epithelial cell markers, Pan-CK and Beta-Catenin. Ki-67 and cleaved Caspase-3 were restricted to a small fraction of cells, indicating low index of proliferation and apoptosis under the culture conditions. The response to drug treatments shall be determined using gene expression assays and evaluation of the secreted components.
CONCLUSION
The organotypic chunk culture technique appears to maintain the viability and integrity of ACP tumors for several days and may serve as an appropriate model for pre-clinical studies to develop targeted therapeutics for pediatric ACP.
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Affiliation(s)
- Trinka Vijmasi
- Department of Neurosurgery, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Eric Prince
- Department of Neurosurgery, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Astrid Hengartner
- Department of Neurosurgery, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Susan Staulcup
- Department of Neurosurgery, Children’s Hospital Colorado, Aurora, CO, USA
| | - Andrea Griesinger
- Deparment of Pediatrics, Children’s Hospital Colorado, Aurora, CO, USA
| | - Andrew Donson
- Deparment of Pediatrics, Children’s Hospital Colorado, Aurora, CO, USA
| | - Ahmed Gilani
- Department of Pathology, Children’s Hospital Colorado, Aurora, CO, USA
| | - Nicholas Foreman
- Deparment of Pediatrics, Children’s Hospital Colorado, Aurora, CO, USA
| | - Todd Hankinson
- Department of Neurosurgery, Children’s Hospital Colorado, Aurora, CO, USA
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Vijmasi T, Prince E, Hengartner A, Agwu C, Staulcup S, Pavlova M, Griesinger A, Donson A, Dorris K, Handler M, Hankinson T. RARE-08. CYST FLUID CYTOKINES MAY PROMOTE EPITHELIAL-TO-MESENCHYMAL TRANSITION IN PEDIATRIC ADAMANTINOMATOUS CRANIOPHARYNGIOMA. Neuro Oncol 2020. [PMCID: PMC7715255 DOI: 10.1093/neuonc/noaa222.719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
BACKGROUND
Despite poor clinical outcomes, no targeted therapies have been established for the treatment of Adamantinomatous Craniopharyngioma (ACP). The only known genetic aberration is a mutation in CTNNB1 that results in the nuclear accumulation of beta-catenin. Nuclear beta-catenin is an established inducer of Epithelial-to-Mesenchymal Transition (EMT). ACP cyst fluid is enriched with pro-inflammatory and SASP cytokines, many of which are also directly implicated in EMT. We sought to investigate the role of EMT in ACP pathology.
METHODS
Normal human epithelial cells were cultured and treated with ACP cyst fluid (10%) for 1, 2, 4 and 8 days. Cell morphology was monitored by live cell brightfield microscopy. The expression of EMT associated genes, ZEB1, ZEB2, SNAI-1, SLUG, TWIST, E-Cadherin, Beta-Catenin and Vimentin was determined by RT-qPCR.
RESULTS
ACP cyst fluid treated epithelial cells were markedly transformed into long, spindle-shaped cells. ACP cyst fluid treatment resulted in the progressive up-regulation of ZEB2 over 8 days (RQ=12.0; P<0.01), the progressive up-regulation of SNAI-1 over 4 days (RQ=5.1; P<0.05) and up-regulation of Vimentin (RQ=2.2; p<0.01), identified only on Day 8.
CONCLUSION
ACP cyst fluid can induce EMT-like changes in normal human epithelial cells. In conjunction with the frequency of beta-catenin mutation in ACP, it is possible that EMT plays a crucial role in the pathology of ACP. Understanding ACP pathology in the context of the EMT paradigm may aid the development of new targeted therapeutics.
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Affiliation(s)
- Trinka Vijmasi
- Department of Neurosurgery, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Eric Prince
- Department of Neurosurgery, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Astrid Hengartner
- Department of Neurosurgery, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Chibueze Agwu
- School of Medicine, Washington University Saint Louis, St. Louis, MO, USA
| | - Susan Staulcup
- Department of Neurosurgery, Children’s Hospital Colorado, Aurora, CO, USA
| | - Maryna Pavlova
- Charles C. Gates Center for Regenerative Medicine and Stem Cell Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Andrea Griesinger
- Department of Pediatrics, Children’s Hospital Colorado, Aurora, CO, USA
| | - Andrew Donson
- Department of Pediatrics, Children’s Hospital Colorado, Aurora, CO, USA
| | - Kathleen Dorris
- Department of Pediatrics, Children’s Hospital Colorado, Aurora, CO, USA
| | - Michael Handler
- Department of Neurosurgery, Children’s Hospital Colorado, Aurora, CO, USA
| | - Todd Hankinson
- Department of Neurosurgery, Children’s Hospital Colorado, Aurora, CO, USA
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Prince E, Hankinson T. TBIO-11. DEEP LEARNING-BASED SINGLE-CELL RNA SEQUENCING DIFFERENTIATION IDENTIFIES SIMPLE AND COMPLEX TRANSCRIPTIONAL NETWORKS FOR SUBPOPULATION CLASSIFICATION. Neuro Oncol 2020. [PMCID: PMC7715250 DOI: 10.1093/neuonc/noaa222.838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
BACKGROUND
Genomic assays capable of cellular resolution (i.e. scRNA-seq) are becoming ubiquitous in biomedical research. Machine learning, and the subtype known as Deep Learning, have broad application within scRNA-seq analytics. However, methods to facilitate the classification of cell populations are lacking. We present the novel computational framework HD Spot, which generates interpretable and robust Deep Learning classifiers that enable unbiased interrogation of linear and non-linear genomic signatures.
METHODS
HD Spot is written in python and relies on Google’s TensorFlow2 deep learning framework. Four datasets of immune cells were obtained from the publicly available Seurat repository, generated using the 10X chromium platform. Data preprocessing used standard Seurat methodology. HD Spot generated optimized classifiers via a custom platform. Network interpretability was achieved using Shapley values. Ontology analysis was performed using Metascape.
RESULTS
HD Spot identified meaningful ontologic signatures across all tested datasets. In the binary case of control versus IFN-B stimulated CD4+ T cells, gene ontologies reflected Th0 and Th2 T cell populations, congruent with T cell activation. In the 9-class case of PBMCs, HD Spot identified meaningful gene networks characteristic of the ground-truth populations using raw feature counts alone. When feature counts are processed into expression values, HD Spot demonstrates increased specificity of top genes and respective ontologies between subpopulations.
CONCLUSION
This work introduces a broadly applicable computational tool for the advanced bioinformatician to decipher complex cellular heterogeneity (e.g., tumors) in an unbiased way. Additionally, HD Spot lowers the barrier for novice bioinformaticists to derive actionable insights from their data.
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Affiliation(s)
- Eric Prince
- Children’s Hospital Colorado, Aurora, CO, USA
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16
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Griesinger A, Prince E, Donson A, Riemondy K, Ritzman T, Harris F, Amani V, Handler M, Hankinson T, Grundy R, Jackson A, Foreman N. EPEN-22. SINGLE-CELL RNA SEQUENCING IDENTIFIES UPREGULATION OF IKZF1 IN PFA2 MYELOID SUBPOPULATION DRIVING AN ANTI-TUMOR PHENOTYPE. Neuro Oncol 2020. [PMCID: PMC7715268 DOI: 10.1093/neuonc/noaa222.159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We have previously shown immune gene phenotype variations between posterior fossa ependymoma subgroups. PFA1 tumors chronically secrete IL-6, which pushes the infiltrating myeloid cells to an immune suppressive function. In contrast, PFA2 tumors have a more immune activated phenotype and have a better prognosis. The objective of this study was to use single-cell(sc) RNAseq to descriptively characterize the infiltrating myeloid cells. We analyzed approximately 8500 cells from 21 PFA patient samples and used advanced machine learning techniques to identify distinct myeloid and lymphoid subpopulations. The myeloid compartment was difficult to interrupt as the data shows a continuum of gene expression profiles exist within PFA1 and PFA2. Through lineage tracing, we were able to tease out that PFA2 myeloid cells expressed more genes associated with an anti-viral response (MHC II, TNF-a, interferon-gamma signaling); while PFA1 myeloid cells had genes associated with an immune suppressive phenotype (angiogenesis, wound healing, IL-10). Specifically, we found expression of IKZF1 was upregulated in PFA2 myeloid cells. IKZF1 regulates differentiation of myeloid cells toward M1 or M2 phenotype through upregulation of either IRF5 or IRF4 respectively. IRF5 expression correlated with IKZF1, being predominately expressed in the PFA2 myeloid cell subset. IKZF1 is also involved in T-cell activation. While we have not completed our characterization of the T-cell subpopulation, we did find significantly more T-cell infiltration in PFA2 than PFA1. Moving forward these studies will provide us with valuable information regarding the molecular switches involved in the tumor-immune microenvironment and to better develop immunotherapy for PFA ependymoma.
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Affiliation(s)
- Andrea Griesinger
- The Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, CO, USA
- Department of Pediatrics-Hematology and Oncology, University of Colorado Anschutz, Aurora, CO, USA
| | - Eric Prince
- The Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, CO, USA
- Department of Neurosurgery, University of Colorado Anschutz, Aurora, CO, USA
| | - Andrew Donson
- The Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, CO, USA
- Department of Pediatrics-Hematology and Oncology, University of Colorado Anschutz, Aurora, CO, USA
| | - Kent Riemondy
- RNA Biosciences Initiative, University of Colorado, Aurora, CO, USA
| | - Timothy Ritzman
- Children’s Brain Tumor Research Centre, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Faith Harris
- The Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, CO, USA
- Department of Pediatrics-Hematology and Oncology, University of Colorado Anschutz, Aurora, CO, USA
| | - Vladimir Amani
- The Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, CO, USA
- Department of Pediatrics-Hematology and Oncology, University of Colorado Anschutz, Aurora, CO, USA
| | - Michael Handler
- The Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, CO, USA
- Department of Neurosurgery, University of Colorado Anschutz, Aurora, CO, USA
| | - Todd Hankinson
- The Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, CO, USA
- Department of Neurosurgery, University of Colorado Anschutz, Aurora, CO, USA
| | - Richard Grundy
- Children’s Brain Tumor Research Centre, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Andrew Jackson
- Host-tumour interactions Group, Division of Cancer and Stem cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Nicholas Foreman
- The Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, CO, USA
- Department of Pediatrics-Hematology and Oncology, University of Colorado Anschutz, Aurora, CO, USA
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17
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Mirsky D, Prince E, Staulcup S, Hengartner A, Vijmasi T, Johnston J, Massimi L, Anderson R, Souweidane M, Naftel R, Limbrick D, Grant G, Niazi T, Dudley R, Kilburn L, Jackson E, Jallo G, Ginn K, Smith A, Chern J, Lee A, Drapeau A, Krieger M, Handler M, Hankinson T. RARE-11. QUANTITATIVE MR IMAGING FEATURES ASSOCIATED WITH UNIQUE TRANSCRIPTIONAL CHARACTERISTICS IN PEDIATRIC ADAMANTINOMATOUS CRANIOPHARYNGIOMA: A POTENTIAL GUIDE FOR THERAPY. Neuro Oncol 2020. [PMCID: PMC7715942 DOI: 10.1093/neuonc/noaa222.722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
METHODS Through the Advancing Treatment for Pediatric Craniopharyngioma (ATPC) consortium we accumulated preoperative MRIs and tumor RNA for 50 unique ACP patients. MRIs were assessed quantitatively for 28 different features and analyzed using Multiple Factor Analysis (MFA) and optimal clustering was determined via maximization of Bayesian Information Criterion (BIC). Following bulk RNAseq, differential expression and pathway enrichment were performed using standard methodologies (i.e., DESeq2 and GSEA). RESULTS MRI features were well represented in the first 3 dimensions of MFA (variance explained=67.32%); specifically tumor/cyst size, ventricular size, and cyst fluid diffusivity. Using this three-way axis, we identified 3 patient subgroups. Transcriptional differences between these subgroups indicated one group was enriched for DNA damage response and MYC related pathways, one group enriched for SHH, and one group enriched for WNT/β-catenin and EMT-related pathways. CONCLUSION This preliminary work suggests that there may be unique gene expression variants within ACP, which may be identified preoperatively using easily quantifiable MRI parameters. These radiogenomic signatures could provide prognostic information and/or guidance in the selection of antitumor therapies for children with ACP.
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Affiliation(s)
| | - Eric Prince
- Children’s Hospital Colorado, Aurora, CO, USA
| | | | | | | | - James Johnston
- University of Alabama at Birmingham, Birmingham, AL, USA
| | - Luca Massimi
- Università Cattolica del Sacro Cuore, Rome, Italy
| | | | - Mark Souweidane
- Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Robert Naftel
- Vanderbilt University Medical Center, Nashville, TN, USA
| | - David Limbrick
- Washington University School of Medicine, St. Louis, MO, USA
| | - Gerald Grant
- Lucile Packard Children’s Hospital at Stanford University, Palo Alto, CA, USA
| | - Toba Niazi
- Nicklaus Children’s Hospital, Miami, FL, USA
| | | | | | - Eric Jackson
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - George Jallo
- Johns Hopkins All Children’s Hospital, St. Petersburg, FL, USA
| | - Kevin Ginn
- Children’s Mercy Hospital, Kansas City, MO, USA
| | - Amy Smith
- Arnold Palmer Hospital, Orlando, FL, USA
| | - Joshua Chern
- Emory University School of Medicine, Atlanta, GA, USA
| | - Amy Lee
- Seattle Children’s Hospital, Seattle, WA, USA
| | | | - Mark Krieger
- Children’s Hospital Los Angeles, Los Angeles, CA, USA
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Khadka P, Prince E, Lu S, Santagata S, Ligon K, Manley P, Beroukhim R, Hankinson T, Bandopadhayay P. RARE-07. THE LANDSCAPE OF GENOMIC ALTERATIONS IN ADAMANTINOMATOUS CRANIOPHARYNGIOMAS. Neuro Oncol 2020. [PMCID: PMC7715698 DOI: 10.1093/neuonc/noaa222.718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
INTRODUCTION
Adamantinomatous craniopharyngiomas (ACPs) are characterized by activating mutations in the CTNNB1 gene. Here we perform a comprehensive genomic analysis of 23 ACPs to define the landscape of genomic alterations in this disease.
METHODS
We performed whole-genome sequencing of 24 ACPs and their matched normal tissues. We used Mutect 2.0 to detect mutations and indels in these samples and MutSig2CV to identify significant mutations. Copy numbers were called using the GATK4 pipeline and GISTIC 2.0 was applied to identify significant alterations. Finally, SvABA was applied to identify genome-wide structural variants and rearrangements.
RESULTS
18/24 (75%) of the sequenced ACPs harbored activating mutations in exon 3 of CTNNB1 gene with an average variant allele fraction (VAF) of 0.4±0.1. These mutations have previously been shown to activate the WNT signaling pathway in these tumors. No other significantly recurrent mutations were detected in our samples. The ACPs were quiet with regard to copy number alterations and no recurrent amplifications or deletions were detected. 528 structural variations and rearrangements were detected in total in all 24 samples with an average of 22 variants per sample. Gene-Set Enrichment Analysis (GSEA) of the RNAseq data revealed upregulation of WNT/B-catenin (FDR q-value <0.25) in the CTNNB1 mutant samples compared to CTNNB1 WT samples.
CONCLUSION
Our study identified previously described activating CTNNB1 mutations in the majority of ACPs. In addition, we identified several rearrangements and structural variations in these tumors that could play an important role in the pathogenesis of the disease.
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Affiliation(s)
- Prasidda Khadka
- Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Eric Prince
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Sophie Lu
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sandro Santagata
- Brigham and Women’s Hospital, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Keith Ligon
- Dana-Farber Cancer Institute, Boston, MA, USA
- Brigham and Women’s Hospital, Boston, MA, USA
| | | | - Rameen Beroukhim
- Dana-Farber Cancer Institute, Boston, MA, USA
- Brigham and Women’s Hospital, Boston, MA, USA
| | - Todd Hankinson
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Pratiti Bandopadhayay
- Dana-Farber Cancer Institute, Boston, MA, USA
- Boston Children’s Hospital, Boston, MA, USA
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19
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Hengartner AC, Prince E, Staulcup S, Vijmasi T, Souweidane M, Jackson EM, Johnston JM, Anderson RCE, Naftel RP, Grant G, Niazi TN, Dudley R, Limbrick DD, Ginn K, Smith A, Kilburn L, Jallo G, Wilkening G, Hankinson T. QOL-22. MACHINE-LEARNING INFERENCE MAY PREDICT QUALITY OF LIFE SUBGROUPS OF ADAMANTINOMATOUS CRANIOPHARYNGIOMA. Neuro Oncol 2020. [PMCID: PMC7715913 DOI: 10.1093/neuonc/noaa222.684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Due to disease and/or treatment-related injury, such as hypothalamic, visual, and endocrine damage, quality of life (QoL) scores after childhood-onset Adamantinomatous Craniopharyngioma (ACP) are among the lowest of all pediatric brain tumors. Decision-making regarding management would be aided by more complete understanding of a patients likely QoL trajectory following intervention. METHODS We retrospectively analyzed caregiver and patient-reported QoL-instruments from the first 50 patients (ages 1–17 years at diagnosis) enrolled in the international Advancing Treatment for Pediatric Craniopharyngioma (ATPC) consortium. Surveys included 205 pediatric-relevant questions and were completed at diagnosis, and 1- and 12-months following diagnosis. Using Multiple Correspondence Analysis (MCA), these categorical QoL surveys were interrogated to identify time-dependent patient subgroups. Additionally, custom deep learning classifiers were developed using Google’s TensorFlow framework. RESULTS By representing QoL data in the reduced dimensionality of MCA-space, we identified QoL subgroups that either improved or declined over time. We assessed differential trends in QoL responses to identify variables that were subgroup specific (Kolmogorov-Smirnov p-value < 0.1; n=20). Additionally, our optimized deep learning classifier achieved a mean 5-fold cross-validation area under precision-recall curve score > 0.99 when classifying QoL subgroups at 12 month follow-up, using only baseline data. CONCLUSIONs This work demonstrates the existence of time-dependent QoL-based ACP subgroups that can be inferred at time-of-diagnosis via machine learning analyses of baseline survey responses. The ability to predict an ACP patient’s QoL trajectory affords caregivers valuable information that can be leveraged to maximize that patient’s psychosocial state and therefore improve overall therapy.
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Affiliation(s)
- Astrid C Hengartner
- Children’s Hospital Colorado, Division of Pediatric Neurosurgery, Aurora, CO, USA
- University of Colorado School of Medicine, Department of Neurosurgery, Aurora, CO, USA
| | - Eric Prince
- Children’s Hospital Colorado, Division of Pediatric Neurosurgery, Aurora, CO, USA
- University of Colorado School of Medicine, Department of Neurosurgery, Aurora, CO, USA
| | - Susan Staulcup
- Children’s Hospital Colorado, Division of Pediatric Neurosurgery, Aurora, CO, USA
- University of Colorado School of Medicine, Department of Neurosurgery, Aurora, CO, USA
| | - Trinka Vijmasi
- Children’s Hospital Colorado, Division of Pediatric Neurosurgery, Aurora, CO, USA
- University of Colorado School of Medicine, Department of Neurosurgery, Aurora, CO, USA
| | - Mark Souweidane
- Memorial Sloan Kettering Cancer Center, Department of Neurosurgery, New York, NY, USA
- Weill Cornell Medical College, Department of Neurological Surgery, New York, NY, USA
| | - Eric M Jackson
- Johns Hopkins University School of Medicine, Department of Neurosurgery, Baltimore, MD, USA
| | - James M Johnston
- University of Alabama at Birmingham, Department of Neurosurgery, Division of Pediatric Neurosurgery, Birmingham, AL, USA
| | - Richard C E Anderson
- Columbia University, Morgan Stanley Children’s Hospital of NewYork-Presbyterian, Department of Neurosurgery, New York, NY, USA
| | - Robert P Naftel
- Vanderbilt University Medical Center, Monroe Carell Jr, Children’s Hospital at Vanderbilt, Department of Neurological Surgery, Nashville, TN, USA
| | - Gerald Grant
- Lucile Packard Children’s Hospital at Stanford University, Department of Pediatric Neurosurgery, Palo Alto, CA, USA
| | - Toba N Niazi
- Nicklaus Children’s Hospital, Department of Pediatric Neurosurgery, Miami, FL, USA
| | - Roy Dudley
- McGill University, Department of Neurosurgery, Montreal, QC, Canada
| | - David D Limbrick
- Washington University School of Medicine, Department of Pediatrics, St, Louis, MO, USA
- Washington University School of Medicine, Department of Neurosurgery, St, Louis, MO, USA
| | - Kevin Ginn
- Children’s Mercy Hospital, The Division of Pediatric Hematology and Oncology, the Department of Pediatrics, Kansas City, MO, USA
| | - Amy Smith
- Arnold Palmer Hospital, Department of Pediatric Hematology-Oncology, Orlando, FL, USA
| | - Lindsay Kilburn
- Children’s National Health System, Center for Cancer and Blood Disorders, Washington DC, USA
- Children’s National Health System, Brain Tumor Institute, Washington DC, USA
| | - George Jallo
- Johns Hopkins All Children’s Hospital, Institute of Brain Protection Sciences, St, Petersburg, FL, USA
| | - Greta Wilkening
- Children’s Hospital Colorado, Department of Pediatric Neuropsychology, Aurora, CO, USA
- University of Colorado School of Medicine, Department of Pediatrics-Neurology, Aurora, CO, USA
| | - Todd Hankinson
- Children’s Hospital Colorado, Division of Pediatric Neurosurgery, Aurora, CO, USA
- University of Colorado School of Medicine, Department of Neurosurgery, Aurora, CO, USA
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20
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Whelan R, Hengartner A, Folzenlogen Z, Prince E, Hankinson TC. Adamantinomatous craniopharyngioma in the molecular age and the potential of targeted therapies: a review. Childs Nerv Syst 2020; 36:1635-1642. [PMID: 32440897 DOI: 10.1007/s00381-020-04677-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 05/11/2020] [Indexed: 12/11/2022]
Abstract
Pediatric adamantinomatous craniopharyngiomas (ACPs) are histologically benign brain tumors that often follow an aggressive clinical course. Arising in the sellar/suprasellar region, they grow in close proximity to critical neurological and vascular structures and can result in significant neuroendocrine morbidity. First-line treatment often involves surgical resection with or without radiotherapy and has been associated with significant morbidity and poor quality of life outcomes. As a result, the discovery of alternative effective and safe treatments is clearly desirable. In recent years, laboratory studies have harnessed sophisticated techniques to identify the upregulation of several markers that may represent potential therapeutic targets. These targets include IL-6, PD1/PD-L1, MEK, IDO-1, and others. Agents that target these pathways exist, and there is an opportunity to investigate their potential efficacy in the treatment of ACP. Trials investigating some of these agents as monotherapy and in combination for the treatment of pediatric ACP are underway or in development. If positive, these trials may result in a paradigm shift in treatment that will hopefully result in reduced morbidity and better outcomes for patients.
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Affiliation(s)
- Ros Whelan
- Department of Neurosurgery, University of Colorado Hospital, Aurora, CO, USA.
| | - Astrid Hengartner
- Department of Neurosurgery, University of Colorado Hospital, Aurora, CO, USA.,Division of Pediatric neurosurgery, Children's Hospital Colorado, University of Colorado, Aurora, CO, USA
| | - Zach Folzenlogen
- Department of Neurosurgery, University of Colorado Hospital, Aurora, CO, USA
| | - Eric Prince
- Department of Neurosurgery, University of Colorado Hospital, Aurora, CO, USA.,Division of Pediatric neurosurgery, Children's Hospital Colorado, University of Colorado, Aurora, CO, USA.,Morgan Adams Foundation Pediatric Brain Tumor Program, Aurora, CO, USA
| | - Todd C Hankinson
- Department of Neurosurgery, University of Colorado Hospital, Aurora, CO, USA.,Division of Pediatric neurosurgery, Children's Hospital Colorado, University of Colorado, Aurora, CO, USA.,Morgan Adams Foundation Pediatric Brain Tumor Program, Aurora, CO, USA
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21
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Prince E, Whelan R, Donson A, Staulcup S, Hengartner A, Vijmasi T, Agwu C, Lillehei KO, Foreman NK, Johnston JM, Massimi L, Anderson RCE, Souweidane MM, Naftel RP, Limbrick DD, Grant G, Niazi TN, Dudley R, Kilburn L, Jackson EM, Jallo GI, Ginn K, Smith A, Chern JJ, Lee A, Drapeau A, Krieger MD, Handler MH, Hankinson TC. Transcriptional analyses of adult and pediatric adamantinomatous craniopharyngioma reveals similar expression signatures regarding potential therapeutic targets. Acta Neuropathol Commun 2020; 8:68. [PMID: 32404202 PMCID: PMC7222517 DOI: 10.1186/s40478-020-00939-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/27/2020] [Indexed: 11/23/2022] Open
Abstract
Adamantinomatous craniopharyngioma (ACP) is a biologically benign but clinically aggressive lesion that has a significant impact on quality of life. The incidence of the disease has a bimodal distribution, with peaks occurring in children and older adults. Our group previously published the results of a transcriptome analysis of pediatric ACPs that identified several genes that were consistently overexpressed relative to other pediatric brain tumors and normal tissue. We now present the results of a transcriptome analysis comparing pediatric to adult ACP to identify biological differences between these groups that may provide novel therapeutic insights or support the assertion that potential therapies identified through the study of pediatric ACP may also have a role in adult ACP. Using our compiled transcriptome dataset of 27 pediatric and 9 adult ACPs, obtained through the Advancing Treatment for Pediatric Craniopharyngioma Consortium, we interrogated potential age-related transcriptional differences using several rigorous mathematical analyses. These included: canonical differential expression analysis; divisive, agglomerative, and probabilistic based hierarchical clustering; information theory based characterizations; and the deep learning approach, HD Spot. Our work indicates that there is no therapeutically relevant difference in ACP gene expression based on age. As such, potential therapeutic targets identified in pediatric ACP are also likely to have relvance for adult patients.
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22
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Moreira DC, Venkataraman S, Subramanian A, Desisto J, Balakrishnan I, Prince E, Pierce A, Griesinger A, Green A, Eberhardt CG, Foreman NK, Vibhakar R. Targeting MYC-driven replication stress in medulloblastoma with AZD1775 and gemcitabine. J Neurooncol 2020; 147:531-545. [PMID: 32180106 DOI: 10.1007/s11060-020-03457-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 03/09/2020] [Indexed: 12/22/2022]
Abstract
PURPOSE MYC-driven medulloblastomas are highly aggressive childhood tumors with dismal outcomes and a lack of new treatment paradigms. We identified that targeting replication stress through WEE1 inhibition to suppress the S-phase replication checkpoint, combined with the attenuation of nucleotide synthesis with gemcitabine, is an effective strategy to induce apoptosis in MYC-driven medulloblastoma that could be rapidly translated into early phase clinical trials in children. Attenuation of replication stress is a key component of MYC-driven oncogenesis. Previous studies revealed a vulnerability in MYC medulloblastoma through WEE1 inhibition. Here, we focused on elucidating combinations of agents to synergize with WEE1 inhibition and drive replication stress toward cell death. METHODS We first analyzed WEE1 expression in patient tissues by immunohistochemistry. Next, we used high-throughput drug screens to identify agents that would synergize with WEE1 inhibition. Synergy was confirmed by in vitro live cell imaging, ex vivo slice culture models, and in vivo studies using orthotopic and flank xenograft models. RESULTS WEE1 expression was significantly higher in Group 3 and 4 medulloblastoma patients. The WEE1 inhibitor AZD1775 synergized with inhibitors of nucleotide synthesis, including gemcitabine. AZD1775 with gemcitabine suppressed proliferation and induced apoptosis. Ex vivo modeling demonstrated efficacy in Group 3 medulloblastoma patients, and in vivo modeling confirmed that combining AZD1775 and gemcitabine effectively suppressed tumor growth. CONCLUSION Our results identified a potent new synergistic treatment combination for MYC-driven medulloblastoma that warrants exploration in early phase clinical trials.
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Affiliation(s)
- Daniel C Moreira
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sujatha Venkataraman
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
| | - Apurva Subramanian
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - John Desisto
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Ilango Balakrishnan
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Eric Prince
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Angela Pierce
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Andrea Griesinger
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Adam Green
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
| | - Charles G Eberhardt
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Nicholas K Foreman
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
- Department of Neurosurgery, University of Colorado Denver, Aurora, CO, USA
| | - Rajeev Vibhakar
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA.
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23
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Whelan R, Prince E, Gilani A, Hankinson T. The Inflammatory Milieu of Adamantinomatous Craniopharyngioma and Its Implications for Treatment. J Clin Med 2020; 9:jcm9020519. [PMID: 32075140 PMCID: PMC7074265 DOI: 10.3390/jcm9020519] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 01/28/2020] [Accepted: 02/12/2020] [Indexed: 12/14/2022] Open
Abstract
Pediatric Adamantinomatous Craniopharyngiomas (ACPs) are histologically benign brain tumors that often follow an aggressive clinical course. Their suprasellar location leaves them in close proximity to critical neurological and vascular structures and often results in significant neuroendocrine morbidity. Current treatment paradigms, involving surgical resection and radiotherapy, confer significant morbidity to patients and there is an obvious need to discover effective and safe alternative treatments. Recent years have witnessed significant efforts to fully detail the genomic, transcriptomic and proteomic make-up of these tumors, in an attempt to identify potential therapeutic targets. These studies have resulted in ever mounting evidence that inflammatory processes and the immune response play a critical role in the pathogenesis of both the solid and cystic portion of ACPs. Several inflammatory and immune markers have been identified in both the cyst fluid and solid tumor tissue of ACP. Due to the existence of effective agents that target them, IL-6 and immune checkpoint inhibitors seem to present the most likely immediate candidates for clinical trials of targeted immune-related therapy in ACP. If effective, such agents may result in a paradigm shift in treatment that ultimately reduces morbidity and results in better outcomes for our patients.
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Affiliation(s)
- Ros Whelan
- Department of Neurosurgery, University of Colorado Hospital, Aurora, CO 80045, USA; (E.P.); (T.H.)
- Correspondence:
| | - Eric Prince
- Department of Neurosurgery, University of Colorado Hospital, Aurora, CO 80045, USA; (E.P.); (T.H.)
- Department of Pediatric neurosurgery, Children’s Hospital Colorado, University of Colorado, Aurora, CO 80045, USA
- Morgan Adams Foundation Pediatric Brain Tumor Program, Aurora, CO 80045, USA
| | - Ahmed Gilani
- Department of Neuropathology, University of Colorado Hospital, Aurora, CO 80045, USA;
| | - Todd Hankinson
- Department of Neurosurgery, University of Colorado Hospital, Aurora, CO 80045, USA; (E.P.); (T.H.)
- Department of Pediatric neurosurgery, Children’s Hospital Colorado, University of Colorado, Aurora, CO 80045, USA
- Morgan Adams Foundation Pediatric Brain Tumor Program, Aurora, CO 80045, USA
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24
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Lake JA, Donson AM, Prince E, Davies KD, Nellan A, Green AL, Mulcahy Levy J, Dorris K, Vibhakar R, Hankinson TC, Foreman NK, Ewalt MD, Kleinschmidt-DeMasters BK, Hoffman LM, Gilani A. Targeted fusion analysis can aid in the classification and treatment of pediatric glioma, ependymoma, and glioneuronal tumors. Pediatr Blood Cancer 2020; 67:e28028. [PMID: 31595628 PMCID: PMC7560962 DOI: 10.1002/pbc.28028] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 08/26/2019] [Accepted: 09/18/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND The use of next-generation sequencing for fusion identification is being increasingly applied and aids our understanding of tumor biology. Some fusions are responsive to approved targeted agents, while others have future potential for therapeutic targeting. Although some pediatric central nervous system tumors may be cured with surgery alone, many require adjuvant therapy associated with acute and long-term toxicities. Identification of targetable fusions can shift the treatment paradigm toward earlier integration of molecularly targeted agents. METHODS Patients diagnosed with glial, glioneuronal, and ependymal tumors between 2002 and 2019 were retrospectively reviewed for fusion testing. Testing was done primarily using the ArcherDx FusionPlex Solid Tumor panel, which assesses fusions in 53 genes. In contrast to many previously published series chronicling fusions in pediatric patients, we compared histological features and the tumor classification subtype with the specific fusion identified. RESULTS We report 24 cases of glial, glioneuronal, or ependymal tumors from pediatric patients with identified fusions. With the exception of BRAF:KIAA1549 and pilocytic/pilomyxoid astrocytoma morphology, and possibly QKI-MYB and angiocentric glioma, there was not a strong correlation between histological features/tumor subtype and the specific fusion. We report the unusual fusions of PPP1CB-ALK, CIC-LEUTX, FGFR2-KIAA159, and MN1-CXXC5 and detail their morphological features. CONCLUSIONS Fusion testing proved to be informative in a high percentage of cases. A large majority of fusion events in pediatric glial, glioneuronal, and ependymal tumors can be identified by relatively small gene panels.
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Affiliation(s)
- Jessica A Lake
- Center for Cancer and Blood Disorders, Children's Hospital Colorado, Aurora, Colorado
| | - Andrew M Donson
- The Morgan Adams Foundation Pediatric Brain Tumor Research Program, Department of Pediatrics, Center for Cancer and Blood Disorders, Children's Hospital Colorado, Aurora, Colorado
| | - Eric Prince
- Department of Neurosurgery, University of Colorado, Aurora, Colorado
| | - Kurtis D Davies
- Department of Pathology, University of Colorado, Aurora, Colorado
| | - Anandani Nellan
- The Morgan Adams Foundation Pediatric Brain Tumor Research Program, Department of Pediatrics, Center for Cancer and Blood Disorders, Children's Hospital Colorado, Aurora, Colorado
| | - Adam L Green
- The Morgan Adams Foundation Pediatric Brain Tumor Research Program, Department of Pediatrics, Center for Cancer and Blood Disorders, Children's Hospital Colorado, Aurora, Colorado
| | - Jean Mulcahy Levy
- The Morgan Adams Foundation Pediatric Brain Tumor Research Program, Department of Pediatrics, Center for Cancer and Blood Disorders, Children's Hospital Colorado, Aurora, Colorado
| | - Kathleen Dorris
- The Morgan Adams Foundation Pediatric Brain Tumor Research Program, Department of Pediatrics, Center for Cancer and Blood Disorders, Children's Hospital Colorado, Aurora, Colorado
| | - Rajeev Vibhakar
- The Morgan Adams Foundation Pediatric Brain Tumor Research Program, Department of Pediatrics, Center for Cancer and Blood Disorders, Children's Hospital Colorado, Aurora, Colorado
| | - Todd C Hankinson
- The Morgan Adams Foundation Pediatric Brain Tumor Research Program, Department of Pediatrics, Center for Cancer and Blood Disorders, Children's Hospital Colorado, Aurora, Colorado
- Department of Neurosurgery, University of Colorado, Aurora, Colorado
| | - Nicholas K Foreman
- The Morgan Adams Foundation Pediatric Brain Tumor Research Program, Department of Pediatrics, Center for Cancer and Blood Disorders, Children's Hospital Colorado, Aurora, Colorado
| | - Mark D Ewalt
- Department of Pathology, University of Colorado, Aurora, Colorado
| | | | - Lindsey M Hoffman
- The Morgan Adams Foundation Pediatric Brain Tumor Research Program, Department of Pediatrics, Center for Cancer and Blood Disorders, Children's Hospital Colorado, Aurora, Colorado
| | - Ahmed Gilani
- Department of Pathology, Children's Hospital Colorado, University of Colorado, Aurora, Colorado
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25
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Whelan R, Prince E, Mirsky DM, Naftel R, Bhatia A, Pettorini B, Avula S, Staulcup S, Alexander AL, Meier M, Hankinson TC. Interrater reliability of a method to assess hypothalamic involvement in pediatric adamantinomatous craniopharyngioma. J Neurosurg Pediatr 2019; 25:37-42. [PMID: 31604324 DOI: 10.3171/2019.8.peds19295] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 08/05/2019] [Indexed: 11/06/2022]
Abstract
OBJECTIVE Pediatric adamantinomatous craniopharyngiomas (ACPs) are histologically benign brain tumors that confer significant neuroendocrine morbidity. Previous studies have demonstrated that injury to the hypothalamus is associated with worsened quality of life and a shorter lifespan. This insight helps many surgeons define the goals of surgery for patients with ACP. Puget and colleagues proposed a 3-tiered preoperative and postoperative grading system based on the degree of hypothalamic involvement identified on MRI. In a prospective cohort from their institution, the authors found that use of the system to guide operative goals was associated with decreased morbidity. To date, however, the Puget system has not been externally validated. Here, the authors present an interrater reliability study that assesses the generalizability of this system for surgeons planning initial operative intervention for children with craniopharyngiomas. METHODS A panel of 6 experts, consisting of pediatric neurosurgeons and pediatric neuroradiologists, graded 30 preoperative and postoperative MRI scans according to the Puget system. Interrater reliability was calculated using Fleiss' κ and Krippendorff's α statistics. RESULTS Interrater reliability in the preoperative context demonstrated moderate agreement (κ = 0.50, α = 0.51). Interrater reliability in the postoperative context was 0.27 for both methods of statistical evaluation. CONCLUSIONS Interrater reliability for the system as defined is moderate. Slight refinements of the Puget MRI grading system, such as collapsing the 3 grades into 2, may improve its reliability, making the system more generalizable.
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Affiliation(s)
- Ros Whelan
- 1Department of Neurosurgery, University of Colorado, Aurora
| | - Eric Prince
- 2Department of Neurosurgery, Children's Hospital Colorado, Aurora
| | - David M Mirsky
- 4Department of Neuro-Radiology, Children's Hospital Colorado, Aurora, Colorado
| | | | - Aashim Bhatia
- 6Radiology, Vanderbilt University Medical Center, Nashville, Tennessee; and
| | | | - Shivaram Avula
- 8Radiology, Alder Hey Children's Hospital NHS Foundation Trust, Liverpool, United Kingdom
| | - Susan Staulcup
- 2Department of Neurosurgery, Children's Hospital Colorado, Aurora
- 3Children's Hospital Center for Research in Outcomes for Children's Surgery, Children's Hospital Colorado Center for Children's Surgery, Aurora
| | - Allyson L Alexander
- 1Department of Neurosurgery, University of Colorado, Aurora
- 2Department of Neurosurgery, Children's Hospital Colorado, Aurora
- 3Children's Hospital Center for Research in Outcomes for Children's Surgery, Children's Hospital Colorado Center for Children's Surgery, Aurora
| | - Maxene Meier
- 3Children's Hospital Center for Research in Outcomes for Children's Surgery, Children's Hospital Colorado Center for Children's Surgery, Aurora
| | - Todd C Hankinson
- 1Department of Neurosurgery, University of Colorado, Aurora
- 2Department of Neurosurgery, Children's Hospital Colorado, Aurora
- 3Children's Hospital Center for Research in Outcomes for Children's Surgery, Children's Hospital Colorado Center for Children's Surgery, Aurora
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26
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Prince E, Whelan R, Vijmasi T, Staulcup S, Klimo P, Mirsky D, Stence N, Hankinson T. THER-19. MACHINE LEARNING APPROACH TO TUMOR DIAGNOSIS USING SMALL DATASETS: PROOF OF PRINCIPLE USING PEDIATRIC ADAMANTINOMATOUS CRANIOPHARYNGIOMA. Neuro Oncol 2019. [DOI: 10.1093/neuonc/noz036.225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Eric Prince
- Children’s Hospital Colorado, Aurora, CO, USA
| | - Ros Whelan
- Children’s Hospital Colorado, Aurora, CO, USA
| | | | | | - Paul Klimo
- St. Jude Children’s Research Hospital, Memphis, TN, USA
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27
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Grob S, Donson A, Prince E, Vijmasi T, Foreman N, Dahl N, Vibhakar R, Mirsky D, Hankinson T, Levy JM. THER-33. TOCILIZUMAB AS A POTENTIAL NOVEL THERAPY IN PATIENTS DIAGNOSED WITH ADAMANTINOMATOUS CRANIOPHARYNGIOMA. Neuro Oncol 2019. [DOI: 10.1093/neuonc/noz036.237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Sydney Grob
- University of Colorado and Children’s Hospital Colorado, Department of Pediatrics, Aurora, CO, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Aurora, CO, USA
| | - Andrew Donson
- University of Colorado and Children’s Hospital Colorado, Department of Pediatrics, Aurora, CO, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Aurora, CO, USA
| | - Eric Prince
- University of Colorado and Children’s Hospital Colorado, Department of Neurosurgery, Aurora, CO, USA
| | - Trinka Vijmasi
- University of Colorado and Children’s Hospital Colorado, Department of Neurosurgery, Aurora, CO, USA
| | - Nicholas Foreman
- University of Colorado and Children’s Hospital Colorado, Department of Pediatrics, Aurora, CO, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Aurora, CO, USA
| | - Nathan Dahl
- University of Colorado and Children’s Hospital Colorado, Department of Pediatrics, Aurora, CO, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Aurora, CO, USA
| | - Rajeev Vibhakar
- University of Colorado and Children’s Hospital Colorado, Department of Pediatrics, Aurora, CO, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Aurora, CO, USA
| | - David Mirsky
- University of Colorado and Children’s Hospital Colorado, Department of Radiology, Aurora, CO, USA
| | - Todd Hankinson
- University of Colorado and Children’s Hospital Colorado, Department of Neurosurgery, Aurora, CO, USA
| | - Jean Mulcahy Levy
- University of Colorado and Children’s Hospital Colorado, Department of Pediatrics, Aurora, CO, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Aurora, CO, USA
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28
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Vijmasi T, Prince E, Whelan R, Griesinger A, Donson A, Staulcup S, Hoffman L, Foreman N, Handler M, Hankinson T. IMMU-11. RESPONSE OF T-CELLS UNDER THE INFLUENCE OF ADAMANTINOMATOUS CRANIOPHARYNGIOMA CYST FLUID. Neuro Oncol 2019. [DOI: 10.1093/neuonc/noz036.132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Trinka Vijmasi
- Department of Neurosurgery, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
| | - Eric Prince
- Department of Neurosurgery, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
| | - Ros Whelan
- Department of Neurosurgery, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
| | - Andrea Griesinger
- Department of Pediatrics, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
| | - Andrew Donson
- Department of Pediatrics, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
| | - Susan Staulcup
- Department of Neurosurgery, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
| | - Lindsay Hoffman
- Department of Pediatrics, Children’s Hospital Colorado, Aurora, CO, USA
| | - Nicholas Foreman
- Department of Pediatrics, Children’s Hospital Colorado, Aurora, CO, USA
| | - Michael Handler
- Department of Neurosurgery, Children’s Hospital Colorado, Aurora, CO, USA
| | - Todd Hankinson
- Department of Neurosurgery, Children’s Hospital Colorado, Aurora, CO, USA
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29
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Prince E, Whelan R, Vijmasi T, Donson A, Staulcup S, Lillehei K, Foreman N, Johnston J, Massimi L, Handler M, Hankinson T. BIOL-03. TRANSCRIPTIONAL ANALYSIS OF ADULT AND PEDIATRIC CRANIOPHARYNGIOMA REVEALS SIMILAR EXPRESSION SIGNATURES REGARDING POTENTIAL THERAPEUTIC TARGETS. Neuro Oncol 2019. [DOI: 10.1093/neuonc/noz036.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Eric Prince
- Children’s Hospital Colorado, Aurora, CO, USA
| | - Ros Whelan
- Children’s Hospital Colorado, Aurora, CO, USA
| | | | | | | | - Kevin Lillehei
- University of Colorado School of Medicine, Aurora, CO, USA
| | | | | | - Luca Massimi
- Institute of Neurosurgery, A, Gemelli Hospital, Rome, Italy
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30
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Whelan R, Prince E, Mirsky D, Naftel R, Bhatia A, Pettorini B, Avula S, Staulcup S, Cox-Martin M, Hankinson T. NSRG-13. INTER-RATER RELIABILITY OF A METHOD FOR DETERMINING THE PRE-OPERATIVE HYPOTHALAMIC INVOLVEMENT OF PEDIATRIC CRANIOPHARYNGIOMA. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy059.535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ros Whelan
- University of Colorado Hospital, Aurora, CO, USA
| | - Eric Prince
- University of Colorado Hospital, Aurora, CO, USA
- Children’s Hospital Colorado, Aurora, CO, USA
| | | | - Robert Naftel
- Vanderbilt University Medical Center, Nashville, TN, USA
| | - Aashim Bhatia
- Vanderbilt University Medical Center, Nashville, TN, USA
| | | | | | | | - Matthew Cox-Martin
- Adult and Child Consortium for Health Outcomes Research and Delivery Science (ACCORDS) University of Colorado School of Medicine, Aurora, CO, USA
| | - Todd Hankinson
- University of Colorado Hospital, Aurora, CO, USA
- Children’s Hospital Colorado, Aurora, CO, USA
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Prince E, Whelan R, Donson A, Staulcup S, Lillehei K, Foreman N, Massimi L, Handler M, Hankinson T. CRAN-34. TRANSCRIPTOMIC AND PROTEOMIC COMPARISON OF PEDIATRIC AND ADULT ADAMANTINOMATOUS CRANIOPHARYNGIOMA. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy059.070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Eric Prince
- University of Colorado Denver, Denver, CO, USA
- Children’s Hospital Colorado, Aurora, CO, USA
| | - Ros Whelan
- University of Colorado Denver, Denver, CO, USA
- Children’s Hospital Colorado, Aurora, CO, USA
| | - Andrew Donson
- University of Colorado Denver, Denver, CO, USA
- Children’s Hospital Colorado, Aurora, CO, USA
| | - Susan Staulcup
- University of Colorado Denver, Denver, CO, USA
- Children’s Hospital Colorado, Aurora, CO, USA
| | | | - Nicholas Foreman
- University of Colorado Denver, Denver, CO, USA
- Children’s Hospital Colorado, Aurora, CO, USA
| | | | - Michael Handler
- University of Colorado Denver, Denver, CO, USA
- Children’s Hospital Colorado, Aurora, CO, USA
| | - Todd Hankinson
- University of Colorado Denver, Denver, CO, USA
- Children’s Hospital Colorado, Aurora, CO, USA
- Children’s Hospital of Alabama, Birmingham, AL, USA
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Prince E, Whelan R, Staulcup S, Jones K, Yang M, Hoffman L, Handler M, Stence N, Hankinson T. PCLN-09. LEVERAGING CONVOLUTIONAL NEURAL NETWORKS TO PREDICT ADAMANTINOMATOUS CRANIOPHARYNGIOMA DIAGNOSIS FROM PREOPERATIVE PARAMETERS. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy059.578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Eric Prince
- University of Colorado Denver, Denver, CO, USA
- Children’s Hospital Colorado, Denver, CO, USA
| | - Ros Whelan
- University of Colorado Denver, Denver, CO, USA
- Children’s Hospital Colorado, Denver, CO, USA
| | - Susan Staulcup
- University of Colorado Denver, Denver, CO, USA
- Children’s Hospital Colorado, Denver, CO, USA
| | | | | | - Lindsey Hoffman
- University of Colorado Denver, Denver, CO, USA
- Children’s Hospital Colorado, Denver, CO, USA
| | - Michael Handler
- University of Colorado Denver, Denver, CO, USA
- Children’s Hospital Colorado, Denver, CO, USA
| | - Nicholas Stence
- University of Colorado Denver, Denver, CO, USA
- Children’s Hospital Colorado, Denver, CO, USA
| | - Todd Hankinson
- University of Colorado Denver, Denver, CO, USA
- Children’s Hospital Colorado, Denver, CO, USA
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Balakrishnan I, Madhavan K, Pierce A, Dahl N, Lemma R, Fosmire S, Wang D, Prince E, Alimova I, Hashizume R, Huellman E, Hawkins C, Carcaboso AM, Gupta N, Monje M, Jones K, Green A, Foreman N, Vibhakar R, Venkataraman S. DIPG-55. TARGETING SENESCENT CELLS WITH ABT-263 ENHANCES CELL DEATH INDUCED BY BMI1 INHIBITION AND IONIZING RADIATION IN DIPG. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy059.148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | - Krishna Madhavan
- University of Colorado, Denver, CO, USA
- Morgan Adams Foundation, Denver, CO, USA
| | | | - Nathan Dahl
- Childrens Hospital of Colorado, Denver, CO, USA
- Morgan Adams Foundation, Denver, CO, USA
| | | | | | - Dong Wang
- University of Colorado, Denver, CO, USA
| | | | | | - Rintaro Hashizume
- Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | | | | | | | | | | | | | - Adam Green
- Childrens Hospital of Colorado, Denver, CO, USA
- Morgan Adams Foundation, Denver, CO, USA
| | - Nicholas Foreman
- Childrens Hospital of Colorado, Denver, CO, USA
- Morgan Adams Foundation, Denver, CO, USA
| | - Rajeev Vibhakar
- Childrens Hospital of Colorado, Denver, CO, USA
- Morgan Adams Foundation, Denver, CO, USA
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Alimova I, Pierce AM, Harris P, Donson A, Birks DK, Prince E, Balakrishnan I, Foreman NK, Kool M, Hoffman L, Venkataraman S, Vibhakar R. Targeting Polo-like kinase 1 in SMARCB1 deleted atypical teratoid rhabdoid tumor. Oncotarget 2017; 8:97290-97303. [PMID: 29228610 PMCID: PMC5722562 DOI: 10.18632/oncotarget.21932] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 08/15/2017] [Indexed: 12/15/2022] Open
Abstract
Atypical teratoid rhabdoid tumor (ATRT) is an aggressive and malignant pediatric brain tumor. Polo-like kinase 1 (PLK1) is highly expressed in many cancers and essential for mitosis. Overexpression of PLK1 promotes chromosome instability and aneuploidy by overriding the G2-M DNA damage and spindle checkpoints. Recent studies suggest that targeting PLK1 by small molecule inhibitors is a promising approach to tumor therapy. We investigated the effect of PLK1 inhibition in ATRT. Gene expression analysis showed that PLK1 was overexpressed in ATRT patient samples and tumor cell lines. Genetic inhibition of PLK1 with shRNA potently suppressed ATRT cell growth in vitro. Treatment with the PLK1 inhibitor BI 6727 (Volasertib) significantly decreased cell growth, inhibited clonogenic potential, and induced apoptosis. BI6727 treatment led to G2-M phase arrest, consistent with PLK1's role as a critical regulator of mitosis. Moreover, inhibition of PLK1 by BI6727 suppressed the tumor-sphere formation of ATRT cells. Treatment also significantly decreased levels of the DNA damage proteins Ku80 and RAD51 and increased γ-H2AX expression, indicating that BI 6727 can induce DNA damage. Importantly, BI6727 significantly enhanced radiation sensitivity of ATRT cells. In vivo, BI6727 slowed growth of ATRT tumors and prolonged survival in a xenograft model. PLK1 inhibition is a compelling new therapeutic approach for treating ATRT, and the use of BI6727 should be evaluated in clinical studies.
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Affiliation(s)
- Irina Alimova
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Angela M Pierce
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Peter Harris
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Andrew Donson
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Diane K Birks
- Department of Neurosurgery, University of Colorado Denver, Aurora, CO, United States
| | - Eric Prince
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Ilango Balakrishnan
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Nicholas K Foreman
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.,Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, United States.,Department of Neurosurgery, University of Colorado Denver, Aurora, CO, United States
| | - Marcel Kool
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lindsey Hoffman
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Sujatha Venkataraman
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.,Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, United States
| | - Rajeev Vibhakar
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.,Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, United States.,Department of Neurosurgery, University of Colorado Denver, Aurora, CO, United States
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Balakrishnan I, Venkataraman S, Pierce AM, Alimova I, Prince E, Moreira DC, Fosmire S, Madhavan K, Foreman N, Vibhakar R. MEDU-33. PLK1 INHIBITION IN COMBINATION WITH STANDARD THERAPIES FOR MYC-DRIVEN MEDULLOBLASTOMA. Neuro Oncol 2017. [DOI: 10.1093/neuonc/nox083.183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Moreira D, Venkataraman S, Balakrishnan I, Prince E, Foreman N, Vibhakar R. MB-71THE ROLE OF WEE1 IN Myc-DRIVEN MEDULLOBLASTOMA. Neuro Oncol 2016. [DOI: 10.1093/neuonc/now076.67] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Venkataraman S, Davidson N, Samson J, Balakrishnan I, Birks D, Alimova I, Amani V, Prince E, Donson A, Mulcahy-levy J, Green A, Gupta N, Hashizume R, Huellman E, Monje M, Foreman N, Vibhakar R. HG-78SYNTHETIC LETHAL EPIGENETIC INTERACTIONS IN K27M MUTATED DIPG. Neuro Oncol 2016. [DOI: 10.1093/neuonc/now073.74] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Alimova I, Pierce AM, Venkataraman S, Harris P, Birks DK, Amani VM, Prince E, Balakrishnan I, Foreman NK, Vibhakar R. AT-07PLK1 AS A THERAPEUTIC TARGET IN ATRT. Neuro Oncol 2016. [DOI: 10.1093/neuonc/now065.06] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Parise J, Shannon R, Prince E, Cox D. The crystal structures of the synthetic zeolites (Cs, K)-ZK5 and (Cs, D)-ZK5 determined from neutron powder diffraction data. Z KRIST-CRYST MATER 2015. [DOI: 10.1524/zkri.1983.165.14.175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Shah M, Prince E, Venkataraman S, Balakrishnan I, Alimova I, Harris P, Remeke M, Taylor MD, Handler MH, Foreman NK, Vibhakar R. Abstract 496: Checkpoint kinase 1 inhibition suppresses cell growth and enhances cisplatin sensitivity in medulloblastoma cells. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Medulloblastoma is the most common malignant brain tumor in children and remains a therapeutic challenge due to its significant therapy-related morbidity. Checkpoint kinase 1 (CHK1) is highly expressed in many cancers and regulates critical steps in mitotic progression and DNA-damage response. Activation of CHK1 pathway promotes treatment resistance in tumor cells. Recent studies suggest that targeting CHK1 with a small molecule inhibitor, to sensitize tumors to a variety of DNA-damaging agents, is a promising approach to tumor therapy.
Methods: The expression of CHK1 mRNA in medulloblastoma patient samples and cell lines were examined using microarray analysis and qRT-PCR respectively. Western blot analysis was conducted on medulloblastoma cell lines to analyze expression level of CHK1 protein. The effect of AZD7762, a small molecule inhibitor of CHK1, on colony forming ability of medulloblastoma cell lines in combination with cisplatin was examined using colony formation assay and methylcellulose assay. The impact of AZD7762 in combination with cisplatin on tumor cell proliferation was further evaluated in real-time using xCELLigence. The effect of AZD7762 on cell viability was assessed using Guava ViaCount assay. Furthermore, the effects on key signaling pathways were analyzed using immunofluorescence, senescence assay, and apoptosis assay.
Results: Analysis of gene expression and western blot experiments revealed that CHK1 mRNA and protein levels are over expressed in all medulloblastoma patient samples and in cell lines when compared to normal pediatric cerebellum. High CHK1 expression correlates with adverse outcomes in a large cohort of medulloblastoma patients. Inhibition of CHK1 by a low nanomolar concentration of AZD7762 potently inhibited cell growth, suppressed the colony-forming ability, and increased cellular apoptosis of medulloblastoma cells. Furthermore, AZD7762 pretreatment sensitized medulloblastoma cells to cisplatin synergistically.
Conclusions: CHK1 expression is a prognostic marker in medulloblastoma and targeting CHK1 with a small molecule inhibitor, in combination with cisplatin, is an attractive strategy in treatment of medulloblastoma that warrants further investigation.
Citation Format: Monil Shah, Eric Prince, Sujatha Venkataraman, Ilango Balakrishnan, Irina Alimova, Peter Harris, Marc Remeke, Michael D. Taylor, Michael H. Handler, Nicholas K. Foreman, Rajeev Vibhakar. Checkpoint kinase 1 inhibition suppresses cell growth and enhances cisplatin sensitivity in medulloblastoma cells. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 496. doi:10.1158/1538-7445.AM2015-496
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Affiliation(s)
- Monil Shah
- 1University of Colorado School of Medicine, Denver, CO
| | - Eric Prince
- 2Children's Hospital Colorado; University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Sujatha Venkataraman
- 2Children's Hospital Colorado; University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Ilango Balakrishnan
- 2Children's Hospital Colorado; University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Irina Alimova
- 2Children's Hospital Colorado; University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Peter Harris
- 2Children's Hospital Colorado; University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Marc Remeke
- 3Hospital for Sick Children, Toronto, Ontario, Canada
| | | | | | - Nicholas K. Foreman
- 2Children's Hospital Colorado; University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Rajeev Vibhakar
- 2Children's Hospital Colorado; University of Colorado Anschutz Medical Campus, Aurora, CO
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Prince E, Shah M, Venkataraman S, Balakrishnan I, Alimova I, Harris P, Birks D, Donson A, Taylor M, Handler M, Foreman N, Vibhakar R. MB-22 * CHECKPOINT KINASE 1 EXPRESSION IS AN ADVERSE PROGNOSTIC MARKER AND THERAPEUTIC TARGET IN MYC-DRIVEN MEDULLOBLASTOMA. Neuro Oncol 2015. [DOI: 10.1093/neuonc/nov061.98] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Amani V, Venkataraman S, Prince E, Birks D, Balakrishnan I, Donson A, Griesinger A, Harris P, Foreman N, Vibhakar R. BT-06 * PLK1 AS A POTENTIAL THERAPEUTIC TARGET FOR DIPG. Neuro Oncol 2015. [DOI: 10.1093/neuonc/nov061.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Foreman B, Alimova I, Harris P, Balakrishnan I, Prince E, Foreman N, Vibhakar R, Venkataraman S. MB-26 * TARGETING MEDULLOBLASTOMA WITH A NEW SMALL-MOLECULE DRUG THAT INHIBITS MYC MEDIATED TRANSLATION. Neuro Oncol 2015. [DOI: 10.1093/neuonc/nov061.102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Strobel K, Simpson P, Donohoue P, Firat S, Jogal S, Lai JS, Beaumont J, Goldman S, Huang C, Barrera M, Rokeach A, Hancock K, Cataudella D, Schulte F, Chung J, Bartels U, Janzen L, Sung L, Strother D, Hukin J, Downie A, Zelcer S, Atenafu E, Schiavello E, Biassoni V, Meazza C, Podda M, Massimino M, Wells EM, Ullrich NJ, Seidel K, Leisenring W, Sklar C, Armstrong GT, Diller L, King A, krull K, Neglia JP, Stovall M, Whelan K, Robison LL, Packer RJ, Remes T, Harila-Saari A, Suo-Palosaari M, Lahteenmaki P, Arikoski P, Riikonen P, Rantala H, Ojaniemi M, Bull K, Kennedy C, Bailey S, Ellison D, Clifford S, Dembowska-Baginska B, Brozyna A, Drogosiewicz M, Perek-Polnik M, Swieszkowska E, Filipek I, Tarasinska M, Korzeniewska J, Perek D, Salgado D, Nunes S, Pereira P, Vinhais S, Salih S, Elsarrag S, Prange E, Contreas K, Possin P, Frierdich S, Eickhoff J, Puccetti D, Huang C, Ladas E, Buck C, Arbit N, Gudrunardottir T, Lannering B, Remke M, Taylor MD, Wells EM, Keating RF, Packer RJ, Stapleton S, Flanary J, Hamblin F, Amankwah E, Ghazarian S, Jagt CT, van de Wetering M, Schouten-van Meeteren AYN, Lai JS, Nowinski C, Hartsell W, Chang JHC, Cella D, Goldman S, Krishna U, Nagrulkar A, Takle M, Kannan S, Gupta T, Jalali R, Northman L, Morris M, Ross S, Guo D, Chordas C, Liptak C, Delaney B, Ullrich N, Manley P, Avula S, Pizer B, Ong CC, Harave S, Mallucci C, Kumar R, Margol A, Finlay J, Dhall G, Robison N, Krieger M, Kiehna E, Coates T, Nelson M, Grimm J, Evans A, Nelson MB, Britt B, Margol A, Robison N, Dhall G, Finlay J, Cooksey R, Wu S, Gode A, Klesse L, Oden J, Vega G, Gargan L, Bowers D, Madden JR, Prince E, Zeitler P, Foreman NK, Liu AK. QUALITY OF LIFE/AFTERCARE. Neuro Oncol 2014. [DOI: 10.1093/neuonc/nou079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Vaidyanathan G, Gururangan S, Bigner D, Zalutsky M, Morfouace M, Shelat A, Megan J, Freeman BB, Robinson S, Throm S, Olson JM, Li XN, Guy KR, Robinson G, Stewart C, Gajjar A, Roussel M, Sirachainan N, Pakakasama S, Anurathapan U, Hansasuta A, Dhanachai M, Khongkhatithum C, Hongeng S, Feroze A, Lee KS, Gholamin S, Wu Z, Lu B, Mitra S, Cheshier S, Northcott P, Lee C, Zichner T, Lichter P, Korbel J, Wechsler-Reya R, Pfister S, Project IPT, Li KKW, Xia T, Ma FMT, Zhang R, Zhou L, Lau KM, Ng HK, Lafay-Cousin L, Chi S, Madden J, Smith A, Wells E, Owens E, Strother D, Foreman N, Packer R, Bouffet E, Wataya T, Peacock J, Taylor MD, Ivanov D, Garnett M, Parker T, Alexander C, Meijer L, Grundy R, Gellert P, Ashford M, Walker D, Brent J, Cader FZ, Ford D, Kay A, Walsh R, Solanki G, Peet A, English M, Shalaby T, Fiaschetti G, Baulande S, Gerber N, Baumgartner M, Grotzer M, Hayase T, Kawahara Y, Yagi M, Minami T, Kanai N, Yamaguchi T, Gomi A, Morimoto A, Hill R, Kuijper S, Lindsey J, Schwalbe E, Barker K, Boult J, Williamson D, Ahmad Z, Hallsworth A, Ryan S, Poon E, Robinson S, Ruddle R, Raynaud F, Howell L, Kwok C, Joshi A, Nicholson SL, Crosier S, Wharton S, Robson K, Michalski A, Hargrave D, Jacques T, Pizer B, Bailey S, Swartling F, Petrie K, Weiss W, Chesler L, Clifford S, Kitanovski L, Prelog T, Kotnik BF, Debeljak M, Fiaschetti G, Shalaby T, Baumgartner M, Grotzer MA, Gevorgian A, Morozova E, Kazantsev I, Iukhta T, Safonova S, Kumirova E, Punanov Y, Afanasyev B, Zheludkova O, Grajkowska W, Pronicki M, Cukrowska B, Dembowska-Baginska B, Lastowska M, Murase A, Nobusawa S, Gemma Y, Yamazaki F, Masuzawa A, Uno T, Osumi T, Shioda Y, Kiyotani C, Mori T, Matsumoto K, Ogiwara H, Morota N, Hirato J, Nakazawa A, Terashima K, Fay-McClymont T, Walsh K, Mabbott D, Smith A, Wells E, Madden J, Chi S, Owens E, Strother D, Packer R, Foreman N, Bouffet E, Lafay-Cousin L, Sturm D, Northcott PA, Jones DTW, Korshunov A, Lichter P, Pfister SM, Kool M, Hooper C, Hawes S, Kees U, Gottardo N, Dallas P, Siegfried A, Bertozzi AI, Sevely A, Loukh N, Munzer C, Miquel C, Bourdeaut F, Pietsch T, Dufour C, Delisle MB, Kawauchi D, Rehg J, Finkelstein D, Zindy F, Phoenix T, Gilbertson R, Pfister S, Roussel M, Trubicka J, Borucka-Mankiewicz M, Ciara E, Chrzanowska K, Perek-Polnik M, Abramczuk-Piekutowska D, Grajkowska W, Jurkiewicz D, Luczak S, Kowalski P, Krajewska-Walasek M, Lastowska M, Sheila C, Lee S, Foster C, Manoranjan B, Pambit M, Berns R, Fotovati A, Venugopal C, O'Halloran K, Narendran A, Hawkins C, Ramaswamy V, Bouffet E, Taylor M, Singhal A, Hukin J, Rassekh R, Yip S, Northcott P, Singh S, Duhman C, Dunn S, Chen T, Rush S, Fuji H, Ishida Y, Onoe T, Kanda T, Kase Y, Yamashita H, Murayama S, Nakasu Y, Kurimoto T, Kondo A, Sakaguchi S, Fujimura J, Saito M, Arakawa T, Arai H, Shimizu T, Lastowska M, Jurkiewicz E, Daszkiewicz P, Drogosiewicz M, Trubicka J, Grajkowska W, Pronicki M, Kool M, Sturm D, Jones DTW, Hovestadt V, Buchhalter I, Jager NN, Stuetz A, Johann P, Schmidt C, Ryzhova M, Landgraf P, Hasselblatt M, Schuller U, Yaspo ML, von Deimling A, Korbel J, Eils R, Lichter P, Korshunov A, Pfister S, Modi A, Patel M, Berk M, Wang LX, Plautz G, Camara-Costa H, Resch A, Lalande C, Kieffer V, Poggi G, Kennedy C, Bull K, Calaminus G, Grill J, Doz F, Rutkowski S, Massimino M, Kortmann RD, Lannering B, Dellatolas G, Chevignard M, Lindsey J, Kawauchi D, Schwalbe E, Solecki D, McKinnon P, Olson J, Hayden J, Grundy R, Ellison D, Williamson D, Bailey S, Roussel M, Clifford S, Buss M, Remke M, Lee J, Caspary T, Taylor M, Castellino R, Lannering B, Sabel M, Gustafsson G, Fleischhack G, Benesch M, Doz F, Kortmann RD, Massimino M, Navajas A, Reddingius R, Rutkowski S, Miquel C, Delisle MB, Dufour C, Lafon D, Sevenet N, Pierron G, Delattre O, Bourdeaut F, Ecker J, Oehme I, Mazitschek R, Korshunov A, Kool M, Lodrini M, Deubzer HE, von Deimling A, Kulozik AE, Pfister SM, Witt O, Milde T, Phoenix T, Patmore D, Boulos N, Wright K, Boop S, Gilbertson R, Janicki T, Burzynski S, Burzynski G, Marszalek A, Triscott J, Green M, Foster C, Fotovati A, Berns R, O'Halloran K, Singhal A, Hukin J, Rassekh SR, Yip S, Toyota B, Dunham C, Dunn SE, Liu KW, Pei Y, Wechsler-Reya R, Genovesi L, Ji P, Davis M, Ng CG, Remke M, Taylor M, Cho YJ, Jenkins N, Copeland N, Wainwright B, Tang Y, Schubert S, Nguyen B, Masoud S, Gholamin S, Lee A, Willardson M, Bandopadhayay P, Bergthold G, Atwood S, Whitson R, Cheshier S, Qi J, Beroukhim R, Tang J, Wechsler-Reya R, Oro A, Link B, Bradner J, Cho YJ, Vallero SG, Bertin D, Basso ME, Milanaccio C, Peretta P, Cama A, Mussano A, Barra S, Morana G, Morra I, Nozza P, Fagioli F, Garre ML, Darabi A, Sanden E, Visse E, Stahl N, Siesjo P, Cho YJ, Vaka D, Schubert S, Vasquez F, Weir B, Cowley G, Keller C, Hahn W, Gibbs IC, Partap S, Yeom K, Martinez M, Vogel H, Donaldson SS, Fisher P, Perreault S, Cho YJ, Guerrini-Rousseau L, Dufour C, Pujet S, Kieffer-Renaux V, Raquin MA, Varlet P, Longaud A, Sainte-Rose C, Valteau-Couanet D, Grill J, Staal J, Lau LS, Zhang H, Ingram WJ, Cho YJ, Hathout Y, Brown K, Rood BR, Sanden E, Visse E, Stahl N, Siesjo P, Darabi A, Handler M, Hankinson T, Madden J, Kleinschmidt-Demasters BK, Foreman N, Hutter S, Northcott PA, Kool M, Pfister S, Kawauchi D, Jones DT, Kagawa N, Hirayama R, Kijima N, Chiba Y, Kinoshita M, Takano K, Eino D, Fukuya S, Yamamoto F, Nakanishi K, Hashimoto N, Hashii Y, Hara J, Taylor MD, Yoshimine T, Wang J, Guo C, Yang Q, Chen Z, Perek-Polnik M, Lastowska M, Drogosiewicz M, Dembowska-Baginska B, Grajkowska W, Filipek I, Swieszkowska E, Tarasinska M, Perek D, Kebudi R, Koc B, Gorgun O, Agaoglu FY, Wolff J, Darendeliler E, Schmidt C, Kerl K, Gronych J, Kawauchi D, Lichter P, Schuller U, Pfister S, Kool M, McGlade J, Endersby R, Hii H, Johns T, Gottardo N, Sastry J, Murphy D, Ronghe M, Cunningham C, Cowie F, Jones R, Sastry J, Calisto A, Sangra M, Mathieson C, Brown J, Phuakpet K, Larouche V, Hawkins C, Bartels U, Bouffet E, Ishida T, Hasegawa D, Miyata K, Ochi S, Saito A, Kozaki A, Yanai T, Kawasaki K, Yamamoto K, Kawamura A, Nagashima T, Akasaka Y, Soejima T, Yoshida M, Kosaka Y, Rutkowski S, von Bueren A, Goschzik T, Kortmann R, von Hoff K, Friedrich C, Muehlen AZ, Gerber N, Warmuth-Metz M, Soerensen N, Deinlein F, Benesch M, Zwiener I, Faldum A, Kuehl J, Pietsch T, KRAMER K, -Taskar NP, Zanzonico P, Humm JL, Wolden SL, Cheung NKV, Venkataraman S, Alimova I, Harris P, Birks D, Balakrishnan I, Griesinger A, Remke M, Taylor MD, Handler M, Foreman NK, Vibhakar R, Margol A, Robison N, Gnanachandran J, Hung L, Kennedy R, Vali M, Dhall G, Finlay J, Erdrich-Epstein A, Krieger M, Drissi R, Fouladi M, Gilles F, Judkins A, Sposto R, Asgharzadeh S, Peyrl A, Chocholous M, Holm S, Grillner P, Blomgren K, Azizi A, Czech T, Gustafsson B, Dieckmann K, Leiss U, Slavc I, Babelyan S, Dolgopolov I, Pimenov R, Mentkevich G, Gorelishev S, Laskov M, Friedrich C, Warmuth-Metz M, von Bueren AO, Nowak J, von Hoff K, Pietsch T, Kortmann RD, Rutkowski S, Mynarek M, von Hoff K, Muller K, Friedrich C, von Bueren AO, Gerber NU, Benesch M, Pietsch T, Warmuth-Metz M, Ottensmeier H, Kwiecien R, Faldum A, Kuehl J, Kortmann RD, Rutkowski S, Mynarek M, von Hoff K, Muller K, Friedrich C, von Bueren AO, Gerber NU, Benesch M, Pietsch T, Warmuth-Metz M, Ottensmeier H, Kwiecien R, Faldum A, Kuehl J, Kortmann RD, Rutkowski S, Yankelevich M, Laskov M, Boyarshinov V, Glekov I, Pimenov R, Ozerov S, Gorelyshev S, Popa A, Dolgopolov I, Subbotina N, Mentkevich G, Martin AM, Nirschl C, Polanczyk M, Bell R, Martinez D, Sullivan LM, Santi M, Burger PC, Taube JM, Drake CG, Pardoll DM, Lim M, Li L, Wang WG, Pu JX, Sun HD, Remke M, Taylor MD, Ruggieri R, Symons MH, Vanan MI, Bandopadhayay P, Bergthold G, Nguyen B, Schubert S, Gholamin S, Tang Y, Bolin S, Schumacher S, Zeid R, Masoud S, Yu F, Vue N, Gibson W, Paolella B, Mitra S, Cheshier S, Qi J, Liu KW, Wechsler-Reya R, Weiss W, Swartling FJ, Kieran MW, Bradner JE, Beroukhim R, Cho YJ, Maher O, Khatua S, Tarek N, Zaky W, Gupta T, Mohanty S, Kannan S, Jalali R, Kapitza E, Denkhaus D, Muhlen AZ, Rutkowski S, Pietsch T, von Hoff K, Pizer B, Dufour C, van Vuurden DG, Garami M, Massimino M, Fangusaro J, Davidson TB, da Costa MJG, Sterba J, Benesch M, Gerber NU, Mynarek M, Kwiecien R, Clifford SC, Kool M, Pietsch T, Finlay JL, Rutkowski S, Pietsch T, Schmidt R, Remke M, Korshunov A, Hovestadt V, Jones DT, Felsberg J, Goschzik T, Kool M, Northcott PA, von Hoff K, von Bueren A, Skladny H, Taylor M, Cremer F, Lichter P, Faldum A, Reifenberger G, Rutkowski S, Pfister S, Kunder R, Jalali R, Sridhar E, Moiyadi AA, Goel A, Goel N, Shirsat N, Othman R, Storer L, Korshunov A, Pfister SM, Kerr I, Coyle B, Law N, Smith ML, Greenberg M, Bouffet E, Taylor MD, Laughlin S, Malkin D, Liu F, Moxon-Emre I, Scantlebury N, Mabbott D, Nasir A, Othman R, Storer L, Onion D, Lourdusamy A, Grabowska A, Coyle B, Cai Y, Othman R, Bradshaw T, Coyle B, de Medeiros RSS, Beaugrand A, Soares S, Epelman S, Jones DTW, Hovestadt V, Wang W, Northcott PA, Kool M, Sultan M, Landgraf P, Reifenberger G, Eils R, Yaspo ML, Wechsler-Reya RJ, Korshunov A, Zapatka M, Radlwimmer B, Pfister SM, Lichter P, Alderete D, Baroni L, Lubinieki F, Auad F, Gonzalez ML, Puya W, Pacheco P, Aurtenetxe O, Gaffar A, Gros L, Cruz O, Calvo C, Navajas A, Shinojima N, Nakamura H, Kuratsu JI, Hanaford A, Eberhart C, Archer T, Tamayo P, Pomeroy S, Raabe E, De Braganca K, Gilheeney S, Khakoo Y, Kramer K, Wolden S, Dunkel I, Lulla RR, Laskowski J, Fangusaro J, Goldman S, Gopalakrishnan V, Ramaswamy V, Remke M, Shih D, Wang X, Northcott P, Faria C, Raybaud C, Tabori U, Hawkins C, Rutka J, Taylor M, Bouffet E, Jacobs S, De Vathaire F, Diallo I, Llanas D, Verez C, Diop F, Kahlouche A, Grill J, Puget S, Valteau-Couanet D, Dufour C, Ramaswamy V, Thompson E, Taylor M, Pomeroy S, Archer T, Northcott P, Tamayo P, Prince E, Amani V, Griesinger A, Foreman N, Vibhakar R, Sin-Chan P, Lu M, Kleinman C, Spence T, Picard D, Ho KC, Chan J, Hawkins C, Majewski J, Jabado N, Dirks P, Huang A, Madden JR, Foreman NK, Donson AM, Mirsky DM, Wang X, Dubuc A, Korshunov A, Ramaswamy V, Remke M, Mack S, Gendoo D, Peacock J, Luu B, Cho YJ, Eberhart C, MacDonald T, Li XN, Van Meter T, Northcott P, Croul S, Bouffet E, Pfister S, Taylor M, Laureano A, Brugmann W, Denman C, Singh H, Huls H, Moyes J, Khatua S, Sandberg D, Silla L, Cooper L, Lee D, Gopalakrishnan V. MEDULLOBLASTOMA. Neuro Oncol 2014. [DOI: 10.1093/neuonc/nou074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Redley M, Prince E, Bateman N, Pennington M, Wood N, Croudace T, Ring H. The involvement of parents in healthcare decisions where adult children are at risk of lacking decision-making capacity: a qualitative study of treatment decisions in epilepsy. J Intellect Disabil Res 2013; 57:531-538. [PMID: 22533531 DOI: 10.1111/j.1365-2788.2012.01556.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
BACKGROUND Patients with intellectual disabilities (ID) receive health care by proxy. It is family members and/or paid support staff who must recognise health problems, communicate with clinicians, and report the benefits, if any, of a particular treatment. At the same time international and national statutes protect and promote the right of people with disabilities to access the highest attainable standards of health on the basis of free and informed consent. METHODS To consider the role of parent-proxies in the management of epilepsy in adult children with ID who are at risk of lacking capacity to make decisions about their health care we interviewed 21 mothers. FINDINGS These mothers are not pursuing changes in treatment that might improve their son or daughter's epilepsy, nor are they willing to countenance changes in treatment. Clinicians concerned to build and sustain therapeutic alliances with these mothers, our evidence suggests, may well avoid going against their wishes. DISCUSSION Our research highlights the interactional contingencies of a hitherto neglected three-way clinical relationship comprising parent-proxy, an adult at risk of lacking decision-making capacity, and a treating clinician. This is a relationship, our findings suggest, where little importance is attached to either patient consent, or involvement in treatment decisions.
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Affiliation(s)
- M Redley
- Department of Developmental Psychiatry, University of Cambridge, Cambridge, UK.
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Stalick JK, Prince E, Santoro A, Schroder IG, Rush JJ. Materials Science Applications of the New National Institute of Standards and Technology Powder Diffractometer. ACTA ACUST UNITED AC 2011. [DOI: 10.1557/proc-376-101] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
ABSTRACTThe new high-resolution neutron powder diffractometer BT-1 at the NIST reactor has proven to be a powerful and versatile instrument in its first year of operation. With 32 detectors arranged at 5° intervals and a 12° 2θ scan range, powder diffraction patterns can be collected to 167° 2θ. There is a choice of three monochromator take-off angles (75°, 90°, and 120°) so that the peak-width minimum can be matched to the rf-spacing range that is most important for each sample; all choices have a wavelength close to 1.54 Å. Data can be collected on sample sizes ranging from 200 mg to 30 g. Temperatures of 0.3 K to 1400 K are routinely available, and a magnetic field of 7T can be applied with a superconducting magnet. Typical data collection times range from 1-12 hours depending upon sample size and desired resolution. Examples are given of a variety of materials applications.
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Haile SM, Wuensch BJ, Prince E. Neutron Rietveld Analysis of Anion and Cation Disorder in the Fast-Ion Conducting Pyrochlore System Y2(ZrxTi1−x)2O7. ACTA ACUST UNITED AC 2011. [DOI: 10.1557/proc-166-81] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
ABSTRACTAll information on the site occupancies and atomic displacements which relate a pyrochlore superstructure to the parent fluorite-type subcell is contained in the normally-weak superstructure diffraction intensities. As Ti has a negative scattering length, the supercell maxima in the present phases are up to three times as intense as the fluorite-like reflections, and neutron diffraction provides an especially sensitive probe of the state of disorder. Y2Ti2O7 is found to have a fullyordered anion array and slight disorder, Y0.984Ti0.015, among the cations. In Y2(Zro.6TiO.4)2O7 the oxygen site normally vacant in pyrochlore is half filled and on the order of 15% exchange between cation sites has occurred.
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Beerkircher L, Arocha F, Barse A, Prince E, Restrepo V, Serafy J, Shivji M. Effects of species misidentification on population assessment of overfished white marlin Tetrapturus albidus and roundscale spearfish T. georgii. ENDANGER SPECIES RES 2009. [DOI: 10.3354/esr00234] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Walli A, Teo SLH, Boustany A, Farwell CJ, Williams T, Dewar H, Prince E, Block BA. Seasonal movements, aggregations and diving behavior of Atlantic bluefin tuna (Thunnus thynnus) revealed with archival tags. PLoS One 2009; 4:e6151. [PMID: 19582150 PMCID: PMC2701635 DOI: 10.1371/journal.pone.0006151] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2009] [Accepted: 05/19/2009] [Indexed: 11/19/2022] Open
Abstract
Electronic tags were used to examine the seasonal movements, aggregations and diving behaviors of Atlantic bluefin tuna (Thunnus thynnus) to better understand their migration ecology and oceanic habitat utilization. Implantable archival tags (n = 561) were deployed in bluefin tuna from 1996 to 2005 and 106 tags were recovered. Movement paths of the fish were reconstructed using light level and sea-surface-temperature-based geolocation estimates. To quantify habitat utilization we employed a weighted kernel estimation technique that removed the biases of deployment location and track length. Throughout the North Atlantic, high residence times (167+/-33 days) were identified in four spatially confined regions on a seasonal scale. Within each region, bluefin tuna experienced distinct temperature regimes and displayed different diving behaviors. The mean diving depths within the high-use areas were significantly shallower and the dive frequency and the variance in internal temperature significantly higher than during transit movements between the high-use areas. Residence time in the more northern latitude high-use areas was significantly correlated with levels of primary productivity. The regions of aggregation are associated with areas of abundant prey and potentially represent critical foraging habitats that have seasonally abundant prey. Throughout the North Atlantic mean diving depth was significantly correlated with the depth of the thermocline, and dive behavior changed in relation to the stratification of the water column. In this study, with numerous multi-year tracks, there appear to be repeatable patterns of clear aggregation areas that potentially are changing with environmental conditions. The high concentrations of bluefin tuna in predictable locations indicate that Atlantic bluefin tuna are vulnerable to concentrated fishing efforts in the regions of foraging aggregations.
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Affiliation(s)
- Andreas Walli
- Tuna Research and Conservation Center, Stanford University, Hopkins Marine Station, Pacific Grove, CA, USA.
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