{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,25]],"date-time":"2026-04-25T11:51:05Z","timestamp":1777117865280,"version":"3.51.4"},"reference-count":81,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2020,2,21]],"date-time":"2020-02-21T00:00:00Z","timestamp":1582243200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>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\u201360% 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.<\/jats:p>","DOI":"10.3390\/genes11020226","type":"journal-article","created":{"date-parts":[[2020,2,25]],"date-time":"2020-02-25T08:12:22Z","timestamp":1582618342000},"page":"226","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":20,"title":["Integrative Analysis Identifies Candidate Tumor Microenvironment and Intracellular Signaling Pathways that Define Tumor Heterogeneity in NF1"],"prefix":"10.3390","volume":"11","author":[{"given":"Jineta","family":"Banerjee","sequence":"first","affiliation":[{"name":"Computational Oncology, Sage Bionetworks, Seattle, WA 98121, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3573-3565","authenticated-orcid":false,"given":"Robert J","family":"Allaway","sequence":"additional","affiliation":[{"name":"Computational Oncology, Sage Bionetworks, Seattle, WA 98121, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jaclyn N","family":"Taroni","sequence":"additional","affiliation":[{"name":"Childhood Cancer Data Lab, Alex\u2019s Lemonade Stand Foundation, Philadelphia, PA 19102, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aaron","family":"Baker","sequence":"additional","affiliation":[{"name":"Computational Oncology, Sage Bionetworks, Seattle, WA 98121, USA"},{"name":"Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI 53715, USA"},{"name":"Morgridge Institute for Research, Madison, WI 53715, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaochun","family":"Zhang","sequence":"additional","affiliation":[{"name":"Division of Oncology, Washington University Medical School, St. Louis, MO 63110, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chang In","family":"Moon","sequence":"additional","affiliation":[{"name":"Division of Oncology, Washington University Medical School, St. Louis, MO 63110, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christine A","family":"Pratilas","sequence":"additional","affiliation":[{"name":"Sidney Kimmel Comprehensive Cancer Center and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jaishri O","family":"Blakeley","sequence":"additional","affiliation":[{"name":"Sidney Kimmel Comprehensive Cancer Center and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA"},{"name":"Neurology, Neurosurgery and Oncology, Johns Hopkins University, Baltimore, MD 21287, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Justin","family":"Guinney","sequence":"additional","affiliation":[{"name":"Computational Oncology, Sage Bionetworks, Seattle, WA 98121, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1719-0771","authenticated-orcid":false,"given":"Angela","family":"Hirbe","sequence":"additional","affiliation":[{"name":"Division of Oncology, Washington University Medical School, St. Louis, MO 63110, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8713-9213","authenticated-orcid":false,"given":"Casey S","family":"Greene","sequence":"additional","affiliation":[{"name":"Childhood Cancer Data Lab, Alex\u2019s Lemonade Stand Foundation, Philadelphia, PA 19102, USA"},{"name":"Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6534-4774","authenticated-orcid":false,"given":"Sara JC","family":"Gosline","sequence":"additional","affiliation":[{"name":"Computational Oncology, Sage Bionetworks, Seattle, WA 98121, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2020,2,21]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1002\/(SICI)1096-8628(19990326)89:1<1::AID-AJMG3>3.0.CO;2-8","article-title":"Epidemiology of neurofibromatosis type 1","volume":"89","author":"Friedman","year":"1999","journal-title":"Am. 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