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Nguyen HTL, Kohl E, Bade J, Eng SE, Tosevska A, Al Shihabi A, Tebon PJ, Hong JJ, Dry S, Boutros PC, Panossian A, Gosline SJC, Soragni A. A platform for rapid patient-derived cutaneous neurofibroma organoid establishment and screening. CELL REPORTS METHODS 2024; 4:100772. [PMID: 38744290 PMCID: PMC11133839 DOI: 10.1016/j.crmeth.2024.100772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/10/2024] [Accepted: 04/19/2024] [Indexed: 05/16/2024]
Abstract
Localized cutaneous neurofibromas (cNFs) are benign tumors that arise in the dermis of patients affected by neurofibromatosis type 1 syndrome. cNFs are benign lesions: they do not undergo malignant transformation or metastasize. Nevertheless, they can cover a significant proportion of the body, with some individuals developing hundreds to thousands of lesions. cNFs can cause pain, itching, and disfigurement resulting in substantial socio-emotional repercussions. Currently, surgery and laser desiccation are the sole treatment options but may result in scarring and potential regrowth from incomplete removal. To identify effective systemic therapies, we introduce an approach to establish and screen cNF organoids. We optimized conditions to support the ex vivo growth of genomically diverse cNFs. Patient-derived cNF organoids closely recapitulate cellular and molecular features of parental tumors as measured by immunohistopathology, methylation, RNA sequencing, and flow cytometry. Our cNF organoid platform enables rapid screening of hundreds of compounds in a patient- and tumor-specific manner.
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Affiliation(s)
- Huyen Thi Lam Nguyen
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Emily Kohl
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jessica Bade
- Pacific Northwest National Laboratories, Seattle, WA, USA
| | - Stefan E Eng
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Anela Tosevska
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ahmad Al Shihabi
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Department of Pathology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Peyton J Tebon
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jenny J Hong
- Division of Hematology-Oncology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sarah Dry
- Department of Pathology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Paul C Boutros
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA; Department of Urology, University of California, Los Angeles, Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Sara J C Gosline
- Pacific Northwest National Laboratories, Seattle, WA, USA; Department of Biomedical Engineering, Oregon Health and Sciences University, Portland, OR, USA.
| | - Alice Soragni
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA.
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2
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Sundby RT, Rhodes SD, Komlodi-Pasztor E, Sarnoff H, Grasso V, Upadhyaya M, Kim A, Evans DG, Blakeley JO, Hanemann CO, Bettegowda C. Recommendations for the collection and annotation of biosamples for analysis of biomarkers in neurofibromatosis and schwannomatosis clinical trials. Clin Trials 2024; 21:40-50. [PMID: 37904489 PMCID: PMC10922556 DOI: 10.1177/17407745231203330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
INTRODUCTION Neurofibromatosis 1 and schwannomatosis are characterized by potential lifelong morbidity and life-threatening complications. To date, however, diagnostic and predictive biomarkers are an unmet need in this patient population. The inclusion of biomarker discovery correlatives in neurofibromatosis 1/schwannomatosis clinical trials enables study of low-incidence disease. The implementation of a common data model would further enhance biomarker discovery by enabling effective concatenation of data from multiple studies. METHODS The Response Evaluation in Neurofibromatosis and Schwannomatosis biomarker working group reviewed published data on emerging trends in neurofibromatosis 1 and schwannomatosis biomarker research and developed recommendations in a series of consensus meetings. RESULTS Liquid biopsy has emerged as a promising assay for neurofibromatosis 1/schwannomatosis biomarker discovery and validation. In addition, we review recommendations for a range of biomarkers in clinical trials, neurofibromatosis 1/schwannomatosis-specific data annotations, and common data models for data integration. CONCLUSION These Response Evaluation in Neurofibromatosis and Schwannomatosis consensus guidelines are intended to provide best practices for the inclusion of biomarker studies in neurofibromatosis 1/schwannomatosis clinical trials, data, and sample annotation and to lay a framework for data harmonization and concatenation between trials.
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Affiliation(s)
- R Taylor Sundby
- Pediatric Oncology Branch, National Cancer Institute, Bethesda, MD, USA
| | - Steven D Rhodes
- Division of Hematology/Oncology/Stem Cell Transplant, Department of Pediatrics, Herman B Wells Center for Pediatric Research, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Edina Komlodi-Pasztor
- Department of Neurology, MedStar Georgetown University Hospital, Washington, DC, USA
| | - Herb Sarnoff
- Research and Development, Infixion Bioscience, Inc., San Diego, CA, USA
- Patient Representative, REiNS International Collaboration, San Diego, CA, USA
| | - Vito Grasso
- Neural Stem Cell Institute, Rensselaer, NY, USA
- Patient Representative, REiNS International Collaboration, Troy, NY, USA
| | - Meena Upadhyaya
- Division of Cancer and Genetics, Cardiff University, Wales, UK
| | - AeRang Kim
- Center for Cancer and Blood Disorders, Children’s National Hospital, Washington, DC, USA
| | - D Gareth Evans
- Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester Academic Health Sciences Centre (MAHSC), ERN GENTURIS, Division of Evolution, Infection and Genomics, The University of Manchester, Manchester, UK
| | - Jaishri O Blakeley
- Division of Neuro-Oncology, Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | | | - Chetan Bettegowda
- Department of Neurosurgery, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
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3
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Larsson AT, Bhatia H, Calizo A, Pollard K, Zhang X, Conniff E, Tibbitts JF, Rono E, Cummins K, Osum SH, Williams KB, Crampton AL, Jubenville T, Schefer D, Yang K, Lyu Y, Pino JC, Bade J, Gross JM, Lisok A, Dehner CA, Chrisinger JSA, He K, Gosline SJC, Pratilas CA, Largaespada DA, Wood DK, Hirbe AC. Ex vivo to in vivo model of malignant peripheral nerve sheath tumors for precision oncology. Neuro Oncol 2023; 25:2044-2057. [PMID: 37246765 PMCID: PMC10628938 DOI: 10.1093/neuonc/noad097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Indexed: 05/30/2023] Open
Abstract
BACKGROUND Malignant peripheral nerve sheath tumors (MPNST) are aggressive soft tissue sarcomas that often develop in patients with neurofibromatosis type 1 (NF1). To address the critical need for novel therapeutics in MPNST, we aimed to establish an ex vivo 3D platform that accurately captured the genomic diversity of MPNST and could be utilized in a medium-throughput manner for drug screening studies to be validated in vivo using patient-derived xenografts (PDX). METHODS Genomic analysis was performed on all PDX-tumor pairs. Selected PDX were harvested for assembly into 3D microtissues. Based on prior work in our labs, we evaluated drugs (trabectedin, olaparib, and mirdametinib) ex vivo and in vivo. For 3D microtissue studies, cell viability was the endpoint as assessed by Zeiss Axio Observer. For PDX drug studies, tumor volume was measured twice weekly. Bulk RNA sequencing was performed to identify pathways enriched in cells. RESULTS We developed 13 NF1-associated MPNST-PDX and identified mutations or structural abnormalities in NF1 (100%), SUZ12 (85%), EED (15%), TP53 (15%), CDKN2A (85%), and chromosome 8 gain (77%). We successfully assembled PDX into 3D microtissues, categorized as robust (>90% viability at 48 h), good (>50%), or unusable (<50%). We evaluated drug response to "robust" or "good" microtissues, namely MN-2, JH-2-002, JH-2-079-c, and WU-225. Drug response ex vivo predicted drug response in vivo, and enhanced drug effects were observed in select models. CONCLUSIONS These data support the successful establishment of a novel 3D platform for drug discovery and MPNST biology exploration in a system representative of the human condition.
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Affiliation(s)
- Alex T Larsson
- Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Himanshi Bhatia
- Division of Oncology, Department of Internal Medicine, Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Ana Calizo
- Division of Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins; Department of Oncology and Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kai Pollard
- Division of Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins; Department of Oncology and Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Xiaochun Zhang
- Division of Oncology, Department of Internal Medicine, Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Eric Conniff
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - Justin F Tibbitts
- Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Elizabeth Rono
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - Katherine Cummins
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - Sara H Osum
- Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Kyle B Williams
- Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Alexandra L Crampton
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - Tyler Jubenville
- Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Daniel Schefer
- Division of Oncology, Department of Internal Medicine, Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Kuangying Yang
- Division of Oncology, Department of Internal Medicine, Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Yang Lyu
- Division of Oncology, Department of Internal Medicine, Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri, USA
| | - James C Pino
- Pacific Northwest National Laboratory, Seattle, Washington, USA
| | - Jessica Bade
- Pacific Northwest National Laboratory, Seattle, Washington, USA
| | - John M Gross
- Department of Pathology, Division of Surgical Pathology, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Alla Lisok
- Division of Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins; Department of Oncology and Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Carina A Dehner
- Department of Pathology and Immunology, Washington University in St. Louis, Missouri, USA
| | - John S A Chrisinger
- Department of Pathology and Immunology, Washington University in St. Louis, Missouri, USA
| | - Kevin He
- Division of Oncology, Department of Internal Medicine, Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri, USA
| | | | - Christine A Pratilas
- Division of Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins; Department of Oncology and Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - David A Largaespada
- Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - David K Wood
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - Angela C Hirbe
- Division of Oncology, Department of Internal Medicine, Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri, USA
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Clayton A, DeFelice M, Zalmanek B, Hodgson J, Morin C, Simon S, Bletz JA, Eddy JA, Nikolov M, Banerjee J, Vinnakota K, Marasca M, Boske KJ, Hoff B, Bradic L, Kim Y, Goss JR, Allaway RJ. Centralizing neurofibromatosis experimental tool knowledge with the NF Research Tools Database. Database (Oxford) 2022; 2022:6613566. [PMID: 35735230 PMCID: PMC9218993 DOI: 10.1093/database/baac045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/05/2022] [Accepted: 06/01/2022] [Indexed: 11/14/2022]
Abstract
Abstract
Experimental tools and resources, such as animal models, cell lines, antibodies, genetic reagents and biobanks, are key ingredients in biomedical research. Investigators face multiple challenges when trying to understand the availability, applicability and accessibility of these tools. A major challenge is keeping up with current information about the numerous tools available for a particular research problem. A variety of disease-agnostic projects such as the Mouse Genome Informatics database and the Resource Identification Initiative curate a number of types of research tools. Here, we describe our efforts to build upon these resources to develop a disease-specific research tool resource for the neurofibromatosis (NF) research community. This resource, the NF Research Tools Database, is an open-access database that enables the exploration and discovery of information about NF type 1-relevant animal models, cell lines, antibodies, genetic reagents and biobanks. Users can search and explore tools, obtain detailed information about each tool as well as read and contribute their observations about the performance, reliability and characteristics of tools in the database. NF researchers will be able to use the NF Research Tools Database to promote, discover, share, reuse and characterize research tools, with the goal of advancing NF research.
Database URL: https://tools.nf.synapse.org/.
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Affiliation(s)
- Ashley Clayton
- Sage Bionetworks, 2901 Third Ave., Suite 330 , Seattle, WA 98121, USA
| | - Mialy DeFelice
- Sage Bionetworks, 2901 Third Ave., Suite 330 , Seattle, WA 98121, USA
| | - Brynn Zalmanek
- Sage Bionetworks, 2901 Third Ave., Suite 330 , Seattle, WA 98121, USA
| | - Jay Hodgson
- Sage Bionetworks, 2901 Third Ave., Suite 330 , Seattle, WA 98121, USA
| | - Caroline Morin
- Gilbert Family Foundation, 1074 Woodward Ave. , Detroit, MI 48226, USA
| | - Stockard Simon
- Sage Bionetworks, 2901 Third Ave., Suite 330 , Seattle, WA 98121, USA
| | - Julie A Bletz
- Sage Bionetworks, 2901 Third Ave., Suite 330 , Seattle, WA 98121, USA
| | - James A Eddy
- Sage Bionetworks, 2901 Third Ave., Suite 330 , Seattle, WA 98121, USA
| | - Milen Nikolov
- Sage Bionetworks, 2901 Third Ave., Suite 330 , Seattle, WA 98121, USA
| | - Jineta Banerjee
- Sage Bionetworks, 2901 Third Ave., Suite 330 , Seattle, WA 98121, USA
| | - Kalyan Vinnakota
- Gilbert Family Foundation, 1074 Woodward Ave. , Detroit, MI 48226, USA
| | - Marco Marasca
- Sage Bionetworks, 2901 Third Ave., Suite 330 , Seattle, WA 98121, USA
| | - Kevin J Boske
- Sage Bionetworks, 2901 Third Ave., Suite 330 , Seattle, WA 98121, USA
| | - Bruce Hoff
- Sage Bionetworks, 2901 Third Ave., Suite 330 , Seattle, WA 98121, USA
| | - Ljubomir Bradic
- Sage Bionetworks, 2901 Third Ave., Suite 330 , Seattle, WA 98121, USA
| | - YooRi Kim
- Gilbert Family Foundation, 1074 Woodward Ave. , Detroit, MI 48226, USA
| | - James R Goss
- Gilbert Family Foundation, 1074 Woodward Ave. , Detroit, MI 48226, USA
| | - Robert J Allaway
- Sage Bionetworks, 2901 Third Ave., Suite 330 , Seattle, WA 98121, USA
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5
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Brown RM, Farouk Sait S, Dunn G, Sullivan A, Bruckert B, Sun D. Integrated Drug Mining Reveals Actionable Strategies Inhibiting Plexiform Neurofibromas. Brain Sci 2022; 12:brainsci12060720. [PMID: 35741605 PMCID: PMC9221468 DOI: 10.3390/brainsci12060720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/24/2022] [Accepted: 05/26/2022] [Indexed: 12/10/2022] Open
Abstract
Neurofibromatosis Type 1 (NF1) is one of the most common genetic tumor predisposition syndromes, affecting up to 1 in 2500 individuals. Up to half of patients with NF1 develop benign nerve sheath tumors called plexiform neurofibromas (PNs), characterized by biallelic NF1 loss. PNs can grow to immense sizes, cause extensive morbidity, and harbor a 15% lifetime risk of malignant transformation. Increasingly, molecular sequencing and drug screening data from various preclinical murine and human PN cell lines, murine models, and human PN tissues are available to help identify salient treatments for PNs. Despite this, Selumetinib, a MEK inhibitor, is the only currently FDA-approved pharmacotherapy for symptomatic and inoperable PNs in pediatric NF1 patients. The discovery of alternative and additional treatments has been hampered by the rarity of the disease, which makes prioritizing drugs to be tested in future clinical trials immensely important. Here, we propose a gene regulatory network-based integrated analysis to mine high-throughput cell line-based drug data combined with transcriptomes from resected human PN tumors. Conserved network modules were characterized and served as drug fingerprints reflecting the biological connections among drug effects and the inherent properties of PN cell lines and tissue. Drug candidates were ranked, and the therapeutic potential of drug combinations was evaluated via computational predication. Auspicious therapeutic agents and drug combinations were proposed for further investigation in preclinical and clinical trials.
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Affiliation(s)
- Rebecca M. Brown
- Medicine, Hematology and Medical Oncology, Neurosurgery, The Mount Sinai Hospital, New York, NY 10029, USA;
| | - Sameer Farouk Sait
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA;
| | - Griffin Dunn
- Department of Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI 53226, USA; (G.D.); (A.S.); (B.B.)
| | - Alanna Sullivan
- Department of Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI 53226, USA; (G.D.); (A.S.); (B.B.)
| | - Benjamin Bruckert
- Department of Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI 53226, USA; (G.D.); (A.S.); (B.B.)
| | - Daochun Sun
- Department of Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI 53226, USA; (G.D.); (A.S.); (B.B.)
- Department of Pediatrics, The Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Cancer Center, The Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Correspondence: ; Tel.: +1-414-955-8158
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6
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Pollard K, Banerjee J, Doan X, Wang J, Guo X, Allaway R, Langmead S, Slobogean B, Meyer CF, Loeb DM, Morris CD, Belzberg AJ, Blakeley JO, Rodriguez FJ, Guinney J, Gosline SJC, Pratilas CA. A clinically and genomically annotated nerve sheath tumor biospecimen repository. Sci Data 2020; 7:184. [PMID: 32561749 PMCID: PMC7305302 DOI: 10.1038/s41597-020-0508-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 05/12/2020] [Indexed: 12/28/2022] Open
Abstract
Nerve sheath tumors occur as a heterogeneous group of neoplasms in patients with neurofibromatosis type 1 (NF1). The malignant form represents the most common cause of death in people with NF1, and even when benign, these tumors can result in significant disfigurement, neurologic dysfunction, and a range of profound symptoms. Lack of human tissue across the peripheral nerve tumors common in NF1 has been a major limitation in the development of new therapies. To address this unmet need, we have created an annotated collection of patient tumor samples, patient-derived cell lines, and patient-derived xenografts, and carried out high-throughput genomic and transcriptomic characterization to serve as a resource for further biologic and preclinical therapeutic studies. In this work, we release genomic and transcriptomic datasets comprised of 55 tumor samples derived from 23 individuals, complete with clinical annotation. All data are publicly available through the NF Data Portal and at http://synapse.org/jhubiobank. Measurement(s) | gene expression • gene_variant | Technology Type(s) | RNA sequencing • exome sequencing • DNA sequencing | Factor Type(s) | tumor type | Sample Characteristic - Organism | Homo sapiens • Homo sapiens/Mus musculus xenograft |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.12037599
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Affiliation(s)
- Kai Pollard
- Sidney Kimmel Comprehensive Cancer Center and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, USA
| | | | | | - Jiawan Wang
- Sidney Kimmel Comprehensive Cancer Center and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, USA
| | | | | | - Shannon Langmead
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Bronwyn Slobogean
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Christian F Meyer
- Sidney Kimmel Comprehensive Cancer Center and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - David M Loeb
- Albert Einstein College of Medicine, New York, USA
| | - Carol D Morris
- Sidney Kimmel Comprehensive Cancer Center and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, USA.,Department of Orthopedic Surgery, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Allan J Belzberg
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, USA.,Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Jaishri O Blakeley
- Sidney Kimmel Comprehensive Cancer Center and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, USA.,Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Fausto J Rodriguez
- Sidney Kimmel Comprehensive Cancer Center and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, USA.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, USA
| | | | | | - Christine A Pratilas
- Sidney Kimmel Comprehensive Cancer Center and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, USA.
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7
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Banerjee J, Allaway RJ, Taroni JN, Baker A, Zhang X, Moon CI, Pratilas CA, Blakeley JO, Guinney J, Hirbe A, Greene CS, Gosline SJC. Integrative Analysis Identifies Candidate Tumor Microenvironment and Intracellular Signaling Pathways that Define Tumor Heterogeneity in NF1. Genes (Basel) 2020; 11:E226. [PMID: 32098059 PMCID: PMC7073563 DOI: 10.3390/genes11020226] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/15/2020] [Accepted: 02/19/2020] [Indexed: 12/12/2022] Open
Abstract
Neurofibromatosis type 1 (NF1) is a monogenic syndrome that gives rise to numerous symptoms including cognitive impairment, skeletal abnormalities, and growth of benign nerve sheath tumors. Nearly all NF1 patients develop cutaneous neurofibromas (cNFs), which occur on the skin surface, whereas 40-60% of patients develop plexiform neurofibromas (pNFs), which are deeply embedded in the peripheral nerves. Patients with pNFs have a ~10% lifetime chance of these tumors becoming malignant peripheral nerve sheath tumors (MPNSTs). These tumors have a severe prognosis and few treatment options other than surgery. Given the lack of therapeutic options available to patients with these tumors, identification of druggable pathways or other key molecular features could aid ongoing therapeutic discovery studies. In this work, we used statistical and machine learning methods to analyze 77 NF1 tumors with genomic data to characterize key signaling pathways that distinguish these tumors and identify candidates for drug development. We identified subsets of latent gene expression variables that may be important in the identification and etiology of cNFs, pNFs, other neurofibromas, and MPNSTs. Furthermore, we characterized the association between these latent variables and genetic variants, immune deconvolution predictions, and protein activity predictions.
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Affiliation(s)
- Jineta Banerjee
- Computational Oncology, Sage Bionetworks, Seattle, WA 98121, USA
| | - Robert J Allaway
- Computational Oncology, Sage Bionetworks, Seattle, WA 98121, USA
| | - Jaclyn N Taroni
- Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Philadelphia, PA 19102, USA
| | - Aaron Baker
- Computational Oncology, Sage Bionetworks, Seattle, WA 98121, USA
- Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI 53715, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Xiaochun Zhang
- Division of Oncology, Washington University Medical School, St. Louis, MO 63110, USA
| | - Chang In Moon
- Division of Oncology, Washington University Medical School, St. Louis, MO 63110, USA
| | - Christine A Pratilas
- Sidney Kimmel Comprehensive Cancer Center and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jaishri O Blakeley
- Sidney Kimmel Comprehensive Cancer Center and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Neurology, Neurosurgery and Oncology, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Justin Guinney
- Computational Oncology, Sage Bionetworks, Seattle, WA 98121, USA
| | - Angela Hirbe
- Division of Oncology, Washington University Medical School, St. Louis, MO 63110, USA
| | - Casey S Greene
- Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Philadelphia, PA 19102, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sara JC Gosline
- Computational Oncology, Sage Bionetworks, Seattle, WA 98121, USA
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