synapse-react-client
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versionNumber: 897,
values: [
"A 3D Cutaneous Neurofibroma Model for Automated High-Throughput Drug Screenings",
"syn11374354",
"Given the absence of therapeutic options and the heterogeneous nature of cutaneous neurofibromas (cNF), a physiological system that supports the growth of cNF tumor cells is required for drug screening efforts. We aim to adapt our optimized high-throughput 3D ring approach to develop a novel preclinical cNF model. My laboratory has developed a robust high-throughput system to establish tumor organoids using a specific geometry to minimize sample handling and cell seeding density. By seeding cells in Matrigel in a mini-ring format we are able to routinely generate organoids from cell lines and primary samples in a format suitable for automation and high-throughput drug screenings. The approach does not necessitate of a priori cell expansion and allows to pinpoint drug sensitivities in within 5-6 days, hence avoiding most of the issues that arise from sample senescence and/or accumulation of genetic changes that can occur with prolonged time in culture. Our method is particularly suited to sustain growth of clinically relevant heterogeneous primary samples, both malignant as well as benign such as Schwann cells or fibroblasts. A single clinical sample can provide sufficient material to screen hundreds of drugs and identify individual drug susceptibilities. Here we aim to extend our proven method to cNF specimens to establish a reliable pre-clinical model. We will use primary samples obtained from NF1 patients and establish cNF organoids to elucidate disease biology and enable therapeutic testing. We anticipate collecting n=10 samples from adult NF1 patients through established collaborations with the UCLA NF clinic. We will characterize the tissues by histopathology and next generation sequencing (NGS) and determine whether the cNF 3D models recapitulate all the major features of the tumor of origin. While beyond the scope of the current project, the cNF models developed and validated here may be used in the future to perform automated high throughput 3D drug screenings to identify possible new therapeutic options for NF1 patients.",
"Accessing the data from this study requires a Synapse account.",
"Please acknowledge the NF Data Portal like so: “The results published here are in whole or in part based on data obtained from the NF Data Portal (http://www.nf.synapse.org, RRID:SCR_021683) and made available through the NF Open Science Initiative.”",
"syn11374354"
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{
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versionNumber: 897,
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"Synodos NF2",
"syn2343195",
"Synodos for NF2 is a first-of-its-kind neurofibromatosis research collaboration dedicated to defeating the rare genetic disorder neurofibromatosis type 2 (NF2). This unique consortium brings together a multidisciplinary team of scientists from twelve world-class labs at academic and medical centers of excellence, who have pledged to work closely together - sharing information, datasets, results and more - at every step in research development, with the goal of speeding up the drug discovery process. The end goal of this effort is to find new approaches to the diagnosis and treatment of two primary NF2-related tumors: schwannoma and meningioma. The expectation is to take the work from discovery to pre-clinical development, resulting in the development of an Investigational New Drug (IND) for NF2. Presently, two of three data releases have been conducted, with high-throughput drug screening data and more gene expression/kinomics data to be released in the future.",
"Accessing the data from this study requires a Synapse account.",
'If you use data from this study in a publication or talk, please cite the following publication: "The Synodos for NF2 Consortium, et al. (2018) Traditional and systems biology based drug discovery for the rare tumor syndrome neurofibromatosis type 2. PLoS ONE 13(6): e0197350. https://doi.org/10.1371/journal.pone.0197350." In addition, please acknowledge the NF Data Portal using the following statement: "The results published here are in whole or in part based on data obtained from the NF Data Portal (http://www.nf.synapse.org, RRID:SCR_021683) and made available through the NF Open Science Initiative."',
"syn2343195"
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{
rowId: 501,
versionNumber: 897,
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"The Johns Hopkins NF1 biospecimen repository",
"syn4939902",
"Surgery is currently the only treatment option for patients with NF1 with symptomatic plexiform neurofibromas (pNF). Progress developing nonsurgical therapy for pNF has been limited by a number of factors including 1) the lack of cell culture based models of pNF, 2) a limited number of animal models of pNF, and 3) limited access of investigators to primary pNF tissue from NF1 patients. Although progress is being made in the development and utilization of animal models and cell culture models, the limited availability of primary patient tissue remains a gap. The goal of this project is to establish a biospecimen and xenograft bank from NF1 patients with pNF and malignant peripheral nerve sheath tumors (MPNST) and to increase accessibility of these tissues to the research community.",
"Accessing the data from this study requires a Synapse account. You must also [request access](https://www.synapse.org/#!Synapse:syn4939902/wiki/593715) from the study investigators.",
'If you use data from this study in a publication or talk, please cite the following preprint: ""Pollard, K, et al. A clinically and genomically annotated nerve sheath tumor biospecimen repository. bioRxiv 2019.12.19.871897; doi: https://doi.org/10.1101/2019.12.19.871897 .” In addition, please acknowledge the NF Data Portal using the following statement: ""The results published here are in whole or in part based on data obtained from the NF Data Portal (http://www.nf.synapse.org, RRID:SCR_021683) and made available through the NF Open Science Initiative.""',
"syn4939902"
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versionNumber: 897,
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"A Robust Plexiform Neurofibroma Model for Preclinical Drug Screening",
"syn8016635",
"We utilized a genetically engineered mouse model as a tool to identify the cell of origin for plexiform neurofibroma. Using genetic labeling for cell-lineage tracing, we showed that the embryonic GAP43+PLP+ Schwann cell precursors originate from dorsal spinal nerve roots are the cells of origin for plexiform neurofibromas. Our studies point to the importance of stem cells and their immediate progenitors in the initiation of tumors, consistent with the notion that these neoplasms originate in a subset of primitive precursors and that most cells in an organ do not generate tumors. The identity of the tumor cell of origin and facility for isolation and expansion of these DRG/nerve root neurosphere cells (DNSCs), which contain the embryonic GAP43+PLP+ Schwann cell precursors, allow us to reconstruct all the biological steps from the original cells to tumor stage to delineate mechanism of neurofibromagenesis. Most importantly, the ability to isolate embryonic PLP+ GAP43+ cells for ex vivo expansion and Nf1 ablation to generate classic sciatic plexiform neurofibromas provides a reliable and robust non-germline neurofibroma model for in vivo drug screening with a quantifiable and reproducible outcome measure (via bioluminescent scan) to select lead compounds for clinical assessment. In this application, we propose to establish the utility of this non-germline plexiform neurofibroma (pNF) model as a rapid preclinical therapeutic drug screening tool to identify effective therapies for pNF. To achieve this goal, we will first explore the possibility of long term storage of DNSCs to maintain their tumorigenic potential for reliable and rapid plexiform neurofibromagenesis. Next, we will develop it into a robust plexiform neurofibroma model for preclinical drug screening by testing therapeutic effects of different pharmacological interventions.",
"The data from this study is currently under embargo. Please contact the principal investigator for access to the data.",
"The data from this study are still under embargo, therefore, if you have been granted access by the data contributor, you must work with them to determine how to acknowledge your collaboration in any manuscripts that arise. In addition, please acknowledge the NF Data Portal like so: “The results published here are in whole or in part based on data obtained from the NF Data Portal (http://www.nf.synapse.org, RRID:SCR_021683) and made available through the NF Open Science Initiative.”",
"syn8016635"
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versionNumber: 897,
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"Acceptance and Commitment Training for Adolescents and Young Adults with Neurofibromatosis Type I, Plexiform Neurofibromas, and Chronic Pain: A Phase III Clinical Trial",
"syn4939896",
"NF1-related pain is often not well-controlled with medication and many of the medications cause significant side effects. To our knowledge, only one prior study (by our group) has examined the effectiveness of a psychological intervention for chronic pain in adolescents and young adults (AYA) with NF1 and PNs. Acceptance and Commitment Therapy (ACT) is a type of therapy that focuses on encouraging individuals to engage in more adaptive ways of coping with pain. The goal of ACT is not to eliminate the person's pain, but to optimize the person's functioning despite their pain. This study is examining the impact of an 8-week ACT intervention on pain interference and other variables among AYA ages 16-34 years with NF1, one or more PNs, and chronic pain. We also are exploring the role of heart rate variability (HRV), which is a physiological marker of pain, in this population. The goal of this project is to establish ACT's effectiveness as a psychological intervention tool targeting chronic pain in patients with NF1/PN, in order to improve daily functioning and pain interference. Our primary goal is to compare changes in pain interference scores from pre- to post- intervention between the ACT group and the waitlist (WL) group. Secondary aims include examining baseline to post-treatment changes in quality of life, pain severity, depression, pain-related anxiety, and HRV, assessed by electrocardiogram (ECG); comparing the ACT and WL groups on pre-post changes in quality of life, pain intensity, depression, pain-related anxiety, and HRV; and examining the relationships of HRV with pain and psychosocial variables.",
null,
"The data from this study are still under embargo, therefore, if you have been granted access by the data contributor, you must work with them to determine how to acknowledge your collaboration in any manuscripts that arise. In addition, please acknowledge the NF Data Portal like so: “The results published here are in whole or in part based on data obtained from the NF Data Portal (http://www.nf.synapse.org, RRID:SCR_021683) and made available through the NF Open Science Initiative.”",
"syn4939896"
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rowId: 504,
versionNumber: 897,
values: [
"Can targeted therapy prevent neurofibroma growth in mice?",
"syn4939872",
"Preliminary efficacy studies conducted through the NFTC showed that DhhCre;Nf1fl/fl;Stat3fl/fl mice had minimal nerve disruption and, although neurofibromas formed, they were dramatically reduced in size as compared to those in DhhCre;Nf1fl/fl mice. As a result, the hypothesis was formulated that Stat3 inhibition using a Stat3 Antisense RNA will prevent tumor formation in a mouse neurofibroma model. The inhibitor, AZD 9150 / ISIS 481464 showed efficacy in multiple myeloma and is in Phase1/1b trials in other cancers. If this same inhibitor shows efficacy in preventing tumor formation, pre-clinical studies will be executed to assess dosing strategies for limited duration.",
"N/A",
"N/A",
"syn4939872"
]
},
{
rowId: 505,
versionNumber: 897,
values: [
"Development of a Child Neurofibromatosis Type 1 Health Related Quality of Life Measure",
"syn4939878",
"To develop and test the feasibility, reliability and validity of the child self-report and parent proxy-report versions of the Pediatric Quality of Life InventoryTM (PedsQL-TM) NF1 module for pediatric patients ages 5-25 with NF1 from the perspectives of patients and parents. The PedsQL(TM) NF1 Module Scales demonstrated acceptable to excellent measurement properties, and may be utilized as standardized metrics to assess NF1-specific symptoms and problems in clinical research and practice in children, adolescents, and young adults. The PedsQL(TM) NF1 Module will have a significant impact on the design of clinical trials targeted to better understand and improve clinical treatment for NF1.",
"The data from this study is currently under embargo. Please contact the principal investigator for access to the data.",
"The data from this study are still under embargo, therefore, if you have been granted access by the data contributor, you must work with them to determine how to acknowledge your collaboration in any manuscripts that arise. In addition, please acknowledge the NF Data Portal like so: “The results published here are in whole or in part based on data obtained from the NF Data Portal (http://www.nf.synapse.org, RRID:SCR_021683) and made available through the NF Open Science Initiative.”",
"syn4939878"
]
},
{
rowId: 506,
versionNumber: 897,
values: [
"Combination Index Validation Studies (2 drug combinations)",
"syn4939876",
"Preliminary High-throughput screening (HTS) data generated at National Center for Advancing Translational Sciences (NCATS) implicated a number of different compounds as potential candidates and combinations suitable for moving forward to preclinical testing, with nine combinations prioritized for validation in murine primary embryonic Schwann cell lines and/or immortalized cell lines. The goal of these experiments was to validate the results of preliminary HTS at NIH/NCATS by Dr. Ferrer.",
"Accessing the data from this study requires a Synapse account.",
'If you use data from this study, please acknowledge the NF Data Portal using the following statement: "The results published here are in whole or in part based on data obtained from the NF Data Portal (http://www.nf.synapse.org, RRID:SCR_021683) and made available through the NF Open Science Initiative."',
"syn4939876"
]
},
{
rowId: 507,
versionNumber: 897,
values: [
"Cutaneous Neurofibroma - Models, Biology, and Translation",
"syn11374333",
"There are still gaps in our knowledge of cNF pathogenesis that could be addressed by the adoption of a systemic approach to decipher all the biological steps in cNF development from the cell of origin to tumor stage to identify the rate limiting step that can be therapeutically targeted to prevent or delay cNF formation. Therefore, in this application, we propose a set specific aims to fill this knowledge gap: We will define the identity of the cNF cell of origin in mice that will guide us to identify the cells of origin for human cNF. We will next decipher how the cell of origin and the tumor microenvironment contribute to drive cNF initiation that will uncover its pathogenesis to delineate biological steps and mechanisms in tumor development as well as generating of preclinical models system that elucidate cNF biology and enable preclinical therapeutic testing. Our overall project will advance via two parallel but interwoven efforts: (1) Characterize cNF cell of origin to trace their developmental origin as well as to define their phenotypes and interactions with the tumor microenvironment. This will provide a framework for elucidating the functional contributions of cNF cell of origin in neurofibroma development. (2) To determine biological steps that are critical for cNF development. A major innovation in our work is linking these approaches in a synergistic manner to our novel neurofibroma models that can be used broadly to decipher the pathogenesis as well as pre-clinical models for therapeutic testing.",
"Accessing the data from this study requires a Synapse account.",
"Please acknowledge the NF Data Portal like so: “The results published here are in whole or in part based on data obtained from the NF Data Portal (http://www.nf.synapse.org, RRID:SCR_021683) and made available through the NF Open Science Initiative.”",
"syn11374333"
]
},
{
rowId: 508,
versionNumber: 897,
values: [
"Deconstruction and Reconstitution of NF1 Cutaneous Neurofibromas",
"syn11374357",
"Our goal is to substantially increase understanding of the pathophysiology of the cutaneous neurofibromas (cNFs) that are a major burden to many patients with type 1 neurofibromatosis (NF1). We will do this by first deconstructing human cNFs through single-cell transcriptomics (scRNA-Seq) to rigorously define the cell populations and sub-populations in these complex tumors. We will then develop three-dimensional (3D) co-culture models of these tumors as a step toward pathomimetic systems for more accurate preclinical therapeutic screening.The goal of the first aim is to use scRNA-Seq to develop an unbiased portrait of the cellular composition of NF1 cNFs. Each tumor that is deconstructed will be a milestone along the way to reaching that goal. We anticipate that at least 8 tumors will need to be deconstructed to take account of the high degree of heterogeneity in the these tumors. Approximately 10,000 cells from each sample will be subject to scRNA-Seq, with the rest used for development of primary cNF cells and fibroblasts for use in Aim Two. The second aim has the goal of development of pathomimetic avatars of NF1 cNFs that will be useful for therapeutic testing. The number and complexity of the avatars required will be determined by the results of the scRNA-Seq. Milestones will be successful development of 3D culture and co-culture conditions for the cell types and of quantitative assays for their morphology, proliferation, and apoptosis.",
"The data from this study is currently under embargo. Please contact the principal investigator for access to the data.",
"The data from this study are still under embargo, therefore, if you have been granted access by the data contributor, you must work with them to determine how to acknowledge your collaboration in any manuscripts that arise. In addition, please acknowledge the NF Data Portal like so: “The results published here are in whole or in part based on data obtained from the NF Data Portal (http://www.nf.synapse.org, RRID:SCR_021683) and made available through the NF Open Science Initiative.”",
"syn11374357"
]
},
{
rowId: 509,
versionNumber: 897,
values: [
"Development of a needs-based quality of life Patient Reported Outcome measure specific to patients with NF1-associated pNFs",
"syn4939880",
"The goal of this project is to establish that interventions to NF1-associated pNFs improve/benefit a patient's QoL, in addition to clinical status. The study was designed to develop a patient-based measure that determines the impact of plexiforms on need fulfilment in affected individuals. The model underlying the new measure is that illness and its treatment affect individuals by limiting their ability to meet their human needs. Needs are fundamental to life as they motivate us to take appropriate actions. The work is being conducted in parallel in the US and UK. Consequently, the final scale will be valid for use in both countries individually or combined. A secondary aim of the study is to work with the European Medicines Agency (EMA) to gain favourable Qualification Opinion for the new PRO. This will ensure that data generated from the measure in clinical trials will be accepted by the EMA.",
"N/A",
"N/A",
"syn4939880"
]
},
{
rowId: 510,
versionNumber: 897,
values: [
"Development of Patient Reported Outcomes System for Patients with NF1-Associated Plexiform Neurofibromas using Mixed Method Approach",
"syn4939888",
"Patient Reported Outcome (PRO) measures assess the treatment outcomes most relevant to patients, and constitute potential outcomes to evaluate in clinical trials. PROs meeting FDA guidelines are critical to ensuring patient-centered endpoints are incorporated. Historically, NF1-associated plexiform neurofibromas (pNF) treatment trials have under-utilized PROs specific to pNF. A psychometrically sound measure incorporating input from patients, families and clinicians, is critical for inclusion in treatment trials. To address the need for a pNF-specific PRO measure for use in clinical trials, this project sought to develop a PRO measurement system utilizing input from patients, families and clinicians, as well as well as psychometric analysis methods to ensure the developed measures are reliable and valid. Specifically this project designed a PRO system for children and young adults with pNF by (1) establishing a conceptual model describing HRQOL, 2) Developing item pools (e.g., pain, stigma, and organ dysfucntion measures), 3) Evaluating psychometric properties of the pools, 4) affirming clinical differences.",
"Accessing the data from this study requires a Synapse account.",
"The data from this study are still under embargo, therefore, if you have been granted access by the data contributor, you must work with them to determine how to acknowledge your collaboration in any manuscripts that arise. In addition, please acknowledge the NF Data Portal like so: “The results published here are in whole or in part based on data obtained from the NF Data Portal (http://www.nf.synapse.org, RRID:SCR_021683) and made available through the NF Open Science Initiative.”",
"syn4939888"
]
},
{
rowId: 511,
versionNumber: 897,
values: [
"Drug Screening of pNF Cell Lines",
"syn4939906",
"A lack of cellular model systems was identified as a major gap in pNF therapeutics-focused research when NTAP was launched in 2012. Hence, creating a cell culture initiative was an early priority. While current animal models can faithfully mimic some aspects of pNF (tumor histology, imaging characteristics, natural history), they are based on relatively narrow genetically engineered platforms and are not fully representative of human NF1 diversity. Moreover, the tumors in these models are slow growing (requiring 9-12 months for a single compound efficacy study) and costly. Hence, there is a need for in vivo models that allow more rapid drug screening (particularly when considering possible combinatorial therapies) and a need for in vitro models that allow more facile manipulation of the NF1 gene in order to understand the molecular genomics influencing tumor behavior. The goal of this project is to create a panel of cell culture systems that represent pNF complexity and can be utilized to both screen new compounds as well as to identify new therapeutic targets.",
"Accessing the data from this study requires a Synapse account.",
'If you use data from this study in a publication or talk, please cite the following publication: "Ferrer M, Gosline SJC, Stathis M, et al. Pharmacological and genomic profiling of neurofibromatosis type 1 plexiform neurofibroma-derived schwann cells. Sci Data. 2018;5:180106. Published 2018 Jun 12. doi:10.1038/sdata.2018.106." In addition, please acknowledge the NF Data Portal using the following statement: "The results published here are in whole or in part based on data obtained from the NF Data Portal (http://www.nf.synapse.org, RRID:SCR_021683) and made available through the NF Open Science Initiative."',
"syn4939906"
]
},
{
rowId: 512,
versionNumber: 899,
values: [
"Identification of pathways triggered by Schwann cell-fibroblast interactions driving cutaneous neurofibroma growth",
"syn11374353",
"Inactivation of the NF1 gene in SCs is believed to be the cause triggering cNF formation. Extensive analysis has shown that from a genetic and genomic perspective, there is no additional recurrent genetic alteration besides the NF1 inactivation involved in cNFs. Despite its simple genetic etiology, the contribution of the interactions among cells composing cNFs need to be investigated to better understand their role in cNF formation and their potential influence on treatment response. In this work, we propose to use co-cultures of cNF-derived primary SCs and FBs to identify expression signatures in cNFs that are specifically due to SC-FB heterotypic interactions. For this purpose we will compare RNA-Seq data from cNFs, their single cell primary cultures and co-cultures of SCs and FBs. Furthermore, we will identify the genetic variation present in gene coding regions of neurofibroma donors. Since SCs and FBs used in co-cultures will belong to different individuals, we estimate to dissect about 75% of the expression signature due to SC-FB interactions by assigning each differently expressed gene to a specific cell type, according to their genetic variation. Signaling pathways represented by expression signatures will be analyzed and their disruption tested functionally. The goal of this study is to understand the signaling between SCs and FBs within cNFs and their importance and impact on their viability, proliferation capacity and contribution to cNF development.",
"Accessing the data from this study requires a Synapse account.",
null,
"syn11374353"
]
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{
rowId: 513,
versionNumber: 897,
values: [
"Genetic Studies of Neurofibromatosis",
"syn11374339",
"NF1 cutaneous neurofibromas (cNFs) have some similarities to non-cutaneous (plexiform) neurofibromas, but there are also differences whose molecular bases are not well characterized. There is also heterogeneity within cNFs, e.g. NF1 mutations and phenotypes. To improve our understanding of cNF biology, we will develop characterized cNF Schwann cell two-hit cultures/lines, and perform exome RNA sequence analysis in these resources as well as primary tissue (intact and isolated single cells). Heterozygous Schwann cell lines will also be developed and studied from some of the same tumors.",
"The data from this study is currently under embargo. Please contact the principal investigator for access to the data.",
"The data from this study are still under embargo, therefore, if you have been granted access by the data contributor, you must work with them to determine how to acknowledge your collaboration in any manuscripts that arise. In addition, please acknowledge the NF Data Portal like so: “The results published here are in whole or in part based on data obtained from the NF Data Portal (http://www.nf.synapse.org, RRID:SCR_021683) and made available through the NF Open Science Initiative.”",
"syn11374339"
]
},
{
rowId: 515,
versionNumber: 897,
values: [
"Imaging Biomarkers of Neurofibromatosis Type 1-Associated Optic Pathway Glioma",
"syn4939894",
"The mechanism of visual acuity loss in optic pathway gliomas (OPG) involves damage to white matter connections due to tumor infiltration or compression of the visual pathway. Non-invasive methods of investigating white matter tract integrity and tissue microstructure may help measure and predict visual acuity in children with OPG. Research supported by the Francis S. Collins Scholarship examines two innovative and non-invasive measures of tissue microstructure: Diffusion Tensor Imaging (DTI) is a magnetic resonance technique to quantify white matter tracts and assess tract damage by measuring the preferential motion of water molecules along and not across hydrophobic myelin. In preliminary data, measures of white matter integrity in the optic radiations of children with OPG are associated with current visual acuity and may predict visual acuity one year later. Magnetic Resonance Fingerprinting (MRF) uses pseudo-randomized magnetic resonance acquisition parameters and a matching algorithm to rapidly quantify T1, T2, M0 and off-resonance signals. These measures of tissue microstructure have been associated with identification of tissue type and tumor grade, but have never before been available so rapidly and reliably. The goal of this project is to interrogate 2 two promising advanced magnetic resonance techniques, DTI and MRF, investigating tissue microstructure in OPG.",
null,
"The data from this study are still under embargo, therefore, if you have been granted access by the data contributor, you must work with them to determine how to acknowledge your collaboration in any manuscripts that arise. In addition, please acknowledge the NF Data Portal like so: “The results published here are in whole or in part based on data obtained from the NF Data Portal (http://www.nf.synapse.org, RRID:SCR_021683) and made available through the NF Open Science Initiative.”",
"syn4939894"
]
},
{
rowId: 516,
versionNumber: 897,
values: [
"Leveraging human induced pluripotent stem cells (iPSCs) to determine the impact of patient-derived NF1 gene mutations on peripheral sensory neuron-driven Schwann cell growth",
"syn11374345",
"Cutaneous or dermal neurofibromas (cNFs) are composed of neoplastic Schwann cells embedded in a microenvironment containing terminal nerve endings, fibroblasts, mast cells, and macrophages. While caused by loss of NF1 protein function in Schwannian lineage cells, studies in mouse plexiform neurofibroma models have revealed a critical role for non-neoplastic stromal cells (fibroblasts, mast cells, and macrophages) in tumor formation, maintenance, and continued growth. In this regard, inhibition of stromal cell (mast cells, macrophages) function in preclinical genetically-engineered mice resulted in attenuated plexiform neurofibroma growth. In addition to fibroblasts, mast cells, and macrophages, the NF1-deficient Schwann cells in cNFs often grow in proximity to terminal nerve endings. The intimate relationship between neurons and Schwann cells during normal peripheral nervous system development and function raises the intriguing possibility that neurons are important drivers of cNF growth. This notion is supported by recent studies in which the proliferation of myelinating cells in the central nervous system (oligodendrocytes) is regulated by neuronal production of a novel growth factor (neuroligin-3). Based on these provocative findings, we hypothesize that peripheral sensory neurons accelerate NF1-deficient Schwann cell growth through the elaboration of mitogens. To identify these potentially clinically-actionable mitogens, we have designed a series of milestone-driven experiments using a novel collection of patient-derived and isogenic human induced pluripotent stem cells harboring NF1-patient germline NF1 gene mutations.",
"Accessing the data from this study requires a Synapse account.",
'If you use data from this study in a publication or talk, please cite study here: Anastasaki, C., Mo, J., Chen, JK. et al. Neuronal hyperexcitability drives central and peripheral nervous system tumor progression in models of neurofibromatosis-1. Nat Commun 13, 2785 (2022). https://doi.org/10.1038/s41467-022-30466-6. In addition, please acknowledge the NF Data Portal using the following statement: "The results published here are in whole or in part based on data obtained from the NF Data Portal (http://www.nf.synapse.org, RRID:SCR_021683) and made available through the NF Open Science Initiative.',
"syn11374345"
]
},
{
rowId: 517,
versionNumber: 897,
values: [
"Microenvironmental targets of cutaneous neurofibromas: T-cells and mast cells as tumor contributors",
"syn11374341",
"Immunity has a central and complex role in tumor growth, which can be utilized when developing new treatment modalities for tumors. To date, the role of immune system in cNFs has gained little attention. Transformed cells are normally eradicated by cooperation of innate and adaptive immune cells. Immune surveillance could be expected to recognize neurofibromin neoepitopes resulting from the second hit of the NF1 gene, but this is not taking place in cNFs. Mast cells are known to be abundant in cNFs and they are increasingly more interesting as druggable targets in tumor biology and neurogenic itch. It is also not known whether mast cells of cNFs are tumorigenic or anti- tumorigenic. The goal of this project is to prove that T cells and mast cells are valid targets for the treatment of cNF. Elucidating the characteristics, roles and effects of these prominent tumor microenvironment components in promoting tumorigenesis could be used to facilitate finding of targeted therapies for the treatment of cNF. The therapeutic modalities include those already approved and those being developed for tumor biology as well as for inflammatory diseases.",
"A subset of this project has been released: www.doi.org/10.7303/syn25613686.The data from this study is currently under embargo. Please contact the principal investigator for access to the data.",
'If you use data from this study in a publication or talk, please cite the following publication: "Kallionpää R, A, Ahramo K, Martikkala E, Fazeli E, Haapaniemi P, Rokka A, Leivo I, Harvima I, T, Peltonen J, Peltonen S: Mast Cells in Human Cutaneous Neurofibromas: Density, Subtypes, and Association with Clinical Features in Neurofibromatosis 1. Dermatology 2021. doi: 10.1159/000517011." In addition, please acknowledge the NF Data Portal using the following statement: "The results published here are in whole or in part based on data obtained from the NF Data Portal (http://www.nf.synapse.org, RRID:SCR_021683) and made available through the NF Open Science Initiative."',
"syn11374341"
]
},
{
rowId: 518,
versionNumber: 897,
values: [
"Modeling signaling networks of NF1-deficient Schwann cells and plexiform neurofibromas using mass spectrometry-based proteomics",
"syn8016599",
"We aim to identify putative proteomic and/or phosphoproteomic signatures associated with loss of NF1. Recent advances in mass-spectrometry (MS)-based proteomics permit the determination of the extent, localization, and site-specific stoichiometry of protein phosphorylation. We propose using two complementary MS-based approaches to define (i) the proteome and phosphoproteome and (ii) the activated kinome signature of NF1-deficient Schwann cells (SCs). We will perform analyses on a panel of SC lines derived from PNs. Transcriptome profiling of cell lines will complement these data sets, together providing a detailed view of the cellular signaling networks and the molecular targets controlled by neurofibromin in a cell-type relevant to the disease. Finally, we will use small molecule inhibitors to both known and any novel signaling pathways we identify to examine the adaptive kinome in treated cell lines. Combining the use of a novel panel of cell lines with the sensitivity of high-end MS, we expect to identify signaling pathways and targets previously implicated as being important in NF1-associated tumors, as well as new and unexpected targets downstream of NF1.",
null,
"Please acknowledge the NF Data Portal like so: “The results published here are in whole or in part based on data obtained from the NF Data Portal (http://www.nf.synapse.org, RRID:SCR_021683) and made available through the NF Open Science Initiative.”",
"syn8016599"
]
},
{
rowId: 519,
versionNumber: 897,
values: [
"Identification of Neurofibroma Growth and Drug Resistance Pathways",
"syn4939892",
"Up to 50%> of children with NF1 develop plexiform neurofibromas that can cause severe disfigurement and serious morbidity-- and death when they compress vital organs. Most plexiform neurofibromas are resistant to chemotherapy and surgical removal is often impossible due to tumor size, location, and nerve integration. We jo not know why some human neurofibromas grow slowly and some rapidly, nor why some neurofibromas respond to therapy but others do not. Plexiform neurofibromas grow most aggressively in young children, and an appealing (unproven) idea is that transiently blocking growth of plexiform neurofibromas early in tumor development will prevent tumor progression. Models to study these critical issues have been lacking. Our laboratory has recently developed mouse models that recapitulate 1) slow and fast growing neurofibromas, and 2) neurofibromas that respond or fail to respond to targeted molecular therapy. We plan to use new methods in gene expression analysis to identify molecular pathways that correlate with these phenotypes in mouse models, with verification on human tissues. We also plan test if early treatment delays or halts neurofibroma formation by administering drugs before tumors develop in a neurofibroma mouse model.",
null,
"The data from this study are still under embargo, therefore, if you have been granted access by the data contributor, you must work with them to determine how to acknowledge your collaboration in any manuscripts that arise. In addition, please acknowledge the NF Data Portal like so: “The results published here are in whole or in part based on data obtained from the NF Data Portal (http://www.nf.synapse.org, RRID:SCR_021683) and made available through the NF Open Science Initiative.”",
"syn4939892"
]
},
{
rowId: 520,
versionNumber: 897,
values: [
"Neurofibromatosis Type 1 Dermal Neurofibroma Longitudinal Natural History Study and Selumetinib Clinical Trial",
"syn8012530",
"Previous reports have correlated increased burden of dermal neurofibromas (DNs) with age and pregnancy, but longitudinal data are not available to establish a quantitative natural history of these tumors. Moreover, the genomic mechanisms responsible for dermal tumor proliferation are not completely understood, although biallelic inactivation of the NF1 gene is known to be required. The NF1 gene encodes neurofibromin, which negatively regulates the Ras/MAPK signaling cascade that includes the RAF/MEK/ERK and PI3K/AKT/mTOR pro-growth pathways. Current therapeutic development for NF1-related tumors target components of this pathway; however, clinical trials directed at dermal neurofibromas have been hampered by the difficulty in measuring and counting dermal neurofibromas. The overall goal of this project is to complete a longitudinal natural history study of dermal neurofibromas to enhance current knowledge of dermal neurofibroma development as well as improve the design, implementation, and interpretation of clinical trials targeting DNs. To address the clinical trial facet of this project, a trial using the MEK1/2 inhibitor selumetinib will be piloted. We will also evaluate the quality of life impact of dermal neurofibromas before and during Selumetinib treatment. For both facets of this study, we will examine genomic alterations that correlate with DN development and selumetinib response.",
"The data from this study is currently under embargo. Please contact the principal investigator for access to the data.",
"The data from this study are still under embargo, therefore, if you have been granted access by the data contributor, you must work with them to determine how to acknowledge your collaboration in any manuscripts that arise. In addition, please acknowledge the NF Data Portal like so: “The results published here are in whole or in part based on data obtained from the NF Data Portal (http://www.nf.synapse.org, RRID:SCR_021683) and made available through the NF Open Science Initiative.”",
"syn8012530"
]
},
{
rowId: 521,
versionNumber: 897,
values: [
"Cutaneous Neurofibroma Data Resource",
"syn4984604",
"In 2013, CTF began a neurofibromatosis biobank to collect NF samples to better study the disease. With all samples being collected under the same protocol, the biobank enables comprehensive analysis of diverse NF samples. To showcase the value the biobank, CTF has kicked off a pilot project designed to characterize the molecular landscape of cutaneous neurofibromas (NF) that grow in NF1 patients, sponsored by the Children's Tumor Foundation. This project includes high-throughput data from 11 different patient tumors and matched blood samples. These data are then compared with one another to assess the distinct landscape of cutaneous NF for each patient.",
"Accessing the data from this study requires a Synapse account. You must also [request access](https://www.synapse.org/#!Synapse:syn4984604/wiki/594099) from the Children's Tumor Foundation.",
'If you use data from this study in a publication or talk, please cite the following publication: "Gosline SJ� Weinberg H, Knight P, et al. A high-throughput molecular data resource for cutaneous neurofibromas. Sci Data. 2017;4:170045. Published 2017 Apr 11. doi:10.1038/sdata.2017.45." In addition, please acknowledge the NF Data Portal using the following statement: "The results published here are in whole or in part based on data obtained from the NF Data Portal (http://www.nf.synapse.org, RRID:SCR_021683) and made available through the NF Open Science Initiative."',
"syn4984604"
]
},
{
rowId: 522,
versionNumber: 897,
values: [
"Synodos NF1 Preclinical Models (Iowa Sanford Exemplar)",
"syn5610446",
"The aim of Synodos for NF1 is to find solutions to the unique problems that affect NF1 patients in the fastest, most efficient manner by sharing their real-time data and results. In Project 2 of the Synodos for NF1 Consortium, researchers will develop and perfect animal models that will most accurately replicate human reaction to drugs in preclinical testing. Two teams will independently generate models; this project consists of results from the Iowa team, and includes members from the University of Iowa, University of Arizona, Exemplar Genetics and Sanford Health.",
'Accessing animal model data from this project requires a Synapse account. <br><br> Accessing human biospecimen genomics data from this project requires submission of an Intended Data Use Statement and agreement to Data Access Terms of Use. <br><br> To access data from this project, please follow these steps: <br><br> **1**: Register for a Synapse account [here](https://www.synapse.org/#!RegisterAccount:0) (if you do not already have one). <br> **2**: Navigate to the [data files page](https://www.synapse.org/#!Synapse:syn11898002). <br> **3**: Click on "Request Access" next to the "lock" symbol. <br> **4**: Follow the instructions on that page. You will be prompted to "Request access to Data" by clicking the Request Access button and submitting an Intended Data Use statement (1-3 paragraphs in English) to be posted publicly. You will also need to review the Terms of Use and click �Accept Terms of Use". If you have questions about the data access process please post them to the [discussion forum](https://www.synapse.org/#!Synapse:syn5610418/discussion/default). <br>',
'The Data Contributors encourage project results to be made publicly available according to the following terms: <br/> <br/> You will provide any results that are to be publicly disclosed to the Data Contributor for review according to the following timelines: Manuscripts 30 days in advance and abstracts 10 days in advance. <em>The Data Contributor may request in writing that the proposed publication/disclosure be delayed for up to 30 additional days as necessary to protect proprietary information.</em> **Please email materials for review to benjamin-darbro@uiowa.edu**<br/> <br/> You will acknowledge the NF Data Portal using the following statement: "The results published here are in whole or in part based on data obtained from the NF Data Portal (http://www.nf.synapse.org, RRID:SCR_021683) and made available through the NF Open Science Initiative." <br/> <br/> If you use the transcriptomic data provided by the **Synodos NF1 Preclinical Models (Iowa Sanford Exemplar) Study** in a publication or talk, you will cite the following paper: <em>Kohlmeyer JL, Kaemmer CA, Pulliam C, et al. RABL6A Is an Essential Driver of MPNSTs that Negatively Regulates the RB1 Pathway and Sensitizes Tumor Cells to CDK4/6 Inhibitors. Clin Cancer Res. 2020. https://doi.org/10.1158/1078-0432.ccr-19-2706</em>',
"syn5610446"
]
},
{
rowId: 523,
versionNumber: 897,
values: [
"Synodos NF1 Preclinical Models (Minnesota CCHMC Recombinetics)",
"syn5610425",
"The aim of Synodos for NF1 is to find solutions to the unique problems that affect NF1 patients in the fastest, most efficient manner by sharing their real-time data and results. In Project 2 of the Synodos for NF1 Consortium, researchers will develop and perfect animal models that will most accurately replicate human reaction to drugs in preclinical testing. Two teams will independently generate models; this project consists of results from the Minnesota team, and includes members from the University of Minnesota, Cincinnati Children's Hospital, the National Cancer Institute, and Recombinetics Inc.",
"Accessing the data from this study requires a Synapse account.",
"The data from this study are still under embargo, therefore, if you hav