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Golub D, Lynch DG, Pan PC, Liechty B, Slocum C, Bale T, Pisapia DJ, Juthani R. Polymorphous low-grade neuroepithelial tumor of the young with FGFR3-TACC3 fusion mimicking high-grade glioma: case report and series of high-grade correlates. Front Oncol 2023; 13:1307591. [PMID: 38074682 PMCID: PMC10698862 DOI: 10.3389/fonc.2023.1307591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 11/02/2023] [Indexed: 02/15/2024] Open
Abstract
Background Polymorphous low-grade neuroepithelial tumor of the young (PLNTY) is a recently described entity that can mimic high-grade glioma (HGG) in histologic and molecular features; however, factors predicting aggressive behavior in these tumors are unclear. Methods We present an indolent neuroepithelial neoplasm in a 59-year-old female with imaging initially suggestive of HGG, and a series of adult patients with HGG harboring FGFR3-TACC3 fusions are also presented for comparison. Results Pathology in the case patient revealed low-grade cytomorphology, microcalcifications, unusual neovascularization, and a low proliferation index. The lesion was diffusely CD34+ and harbored an FGFR3-TACC3 fusion and TERT promoter mutation. A diagnosis of PLNTY was therefore favored and the patient was observed with no progression at 15-month follow-up. In patients with HGG with FGFR3-TACC3 fusions, molecular findings included IDH-wildtype status, absence of 1p19q codeletion, CDKN2A loss, TERT promoter mutations and lack of MGMT promoter methylation. These patients demonstrated a median 15-month overall survival and a 6-month progression-free survival. Conclusion PLNTY is a rare low-grade entity that can display characteristics of HGG, particularly in adults. Presence of FGFR3-TACC3 fusions and other high-grade features should raise concern for a more malignant precursor lesion when a diagnosis of PLNTY is considered.
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Affiliation(s)
- Danielle Golub
- Department of Neurosurgery, Weill Cornell Medicine, New York, NY, United States
- Department of Neurosurgery, Northwell Health, Manhasset, NY, United States
| | - Daniel G. Lynch
- Zucker School of Medicine at Hofstra/Northwell Health, Hempstead, NY, United States
| | - Peter C. Pan
- Department of Neurology, Weill Cornell Medicine, New York, NY, United States
- Department of Neurology, Columbia University, New York, NY, United States
| | - Benjamin Liechty
- Department of Pathology, Weill Cornell Medicine, New York, NY, United States
| | - Cheyanne Slocum
- Department of Pathology, Weill Cornell Medicine, New York, NY, United States
| | - Tejus Bale
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - David J. Pisapia
- Department of Pathology, Weill Cornell Medicine, New York, NY, United States
| | - Rupa Juthani
- Department of Neurosurgery, Weill Cornell Medicine, New York, NY, United States
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Levy JJ, Chen Y, Azizgolshani N, Petersen CL, Titus AJ, Moen EL, Vaickus LJ, Salas LA, Christensen BC. MethylSPWNet and MethylCapsNet: Biologically Motivated Organization of DNAm Neural Networks, Inspired by Capsule Networks. NPJ Syst Biol Appl 2021; 7:33. [PMID: 34417465 PMCID: PMC8379254 DOI: 10.1038/s41540-021-00193-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 07/01/2021] [Indexed: 02/07/2023] Open
Abstract
DNA methylation (DNAm) alterations have been heavily implicated in carcinogenesis and the pathophysiology of diseases through upstream regulation of gene expression. DNAm deep-learning approaches are able to capture features associated with aging, cell type, and disease progression, but lack incorporation of prior biological knowledge. Here, we present modular, user-friendly deep-learning methodology and software, MethylCapsNet and MethylSPWNet, that group CpGs into biologically relevant capsules-such as gene promoter context, CpG island relationship, or user-defined groupings-and relate them to diagnostic and prognostic outcomes. We demonstrate these models' utility on 3,897 individuals in the classification of central nervous system (CNS) tumors. MethylCapsNet and MethylSPWNet provide an opportunity to increase DNAm deep-learning analyses' interpretability by enabling a flexible organization of DNAm data into biologically relevant capsules.
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Affiliation(s)
- Joshua J Levy
- Program in Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.
- Emerging Diagnostic and Investigative Technologies, Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH, USA.
| | - Youdinghuan Chen
- Program in Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Nasim Azizgolshani
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Curtis L Petersen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- The Dartmouth Institute for Health Policy and Clinical Practice, Lebanon, NH, USA
| | - Alexander J Titus
- Department of Life Sciences, University of New Hampshire, Manchester, NH, USA
| | - Erika L Moen
- The Dartmouth Institute for Health Policy and Clinical Practice, Lebanon, NH, USA
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Louis J Vaickus
- Emerging Diagnostic and Investigative Technologies, Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH, USA
| | - Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
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Nannapaneni S, Griffith CC, Magliocca KR, Chen W, Lyu X, Chen Z, Wang D, Wang X, Shin DM, Chen ZG, Saba NF. Co-expression of fibroblast growth factor receptor 3 with mutant p53, and its association with worse outcome in oropharyngeal squamous cell carcinoma. PLoS One 2021; 16:e0247498. [PMID: 33626078 PMCID: PMC7904228 DOI: 10.1371/journal.pone.0247498] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 02/08/2021] [Indexed: 02/06/2023] Open
Abstract
Fibroblast growth factor receptor 3 (FGFR3) is expressed in squamous cell carcinoma of the head and neck (SCCHN) including oropharyngeal squamous cell carcinoma (OPSCC) and is a potential therapeutic target. However, information on its correlation with other relevant cancer related proteins stratified by p16 status and its prognostic significance in OPSCC is limited. We examined FGFR3 expression and its correlation with clinical characteristics, p16 status, and mutant p53 (mp53) among 220 retrospectively collected OPSCC cases and 40 prospectively collected SCCHN cases, including a majority of OPSCC. Correlations of FGFR3 Weighted Index (WI) with p16 status and mp53 WI as well as its association with disease-free survival (DFS) and overall survival (OS) were evaluated. FGFR3 expression was detected in 61% and 70% of cases in cohorts 1 and 2, respectively. FGFR3 level was significantly higher in p16-negative tumors in both cohorts (p<0.001 and 0.006). FGFR3 expression was highly correlated with mp53 expression in both p16 + and p16- OPSCC (p<0.0001 and p = 0.0006, respectively). In cohort 1, univariate analysis showed that FGFR3 was associated with DFS but not OS. Kaplan-Meier analysis showed that higher FGFR3 and mp53 level correlated with worse DFS (p = 0.025) and OS (p = 0.009). As expected, p16 positive status was associated with improved OS and DFS (p<0.001 for both). Our results suggest that high FGFR3 expression is associated with p16 negative status and mp53 expression in OPSCC and correlates with a worse clinical outcome. The biological relationship between FGFR3 and mp53 in OPSCC deserves further investigation.
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Affiliation(s)
- Sreenivas Nannapaneni
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University School of Medicine, Atlanta, Georgia, United States of America
| | | | - Kelly R. Magliocca
- Department of Pathology & Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Wanqi Chen
- Department of Biostatistics and Bioinformatics, Emory University School of Public Health, Atlanta, Georgia, United States of America
| | - Xueying Lyu
- Department of Biostatistics and Bioinformatics, Emory University School of Public Health, Atlanta, Georgia, United States of America
| | - Zhengjia Chen
- Department of Epidemiology & Biostatistics, University of Illinois Cancer Center, Chicago, Illinois, United States of America
| | - Dongsheng Wang
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Xu Wang
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Dong M. Shin
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Zhuo G. Chen
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University School of Medicine, Atlanta, Georgia, United States of America
- * E-mail: (NFS); (ZGC)
| | - Nabil F. Saba
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University School of Medicine, Atlanta, Georgia, United States of America
- * E-mail: (NFS); (ZGC)
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Wang H, Xu T, Jiang Y, Xu H, Yan Y, Fu D, Chen J. The challenges and the promise of molecular targeted therapy in malignant gliomas. Neoplasia 2015; 17:239-55. [PMID: 25810009 PMCID: PMC4372648 DOI: 10.1016/j.neo.2015.02.002] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 02/06/2015] [Indexed: 11/18/2022] Open
Abstract
Malignant gliomas are the most common malignant primary brain tumors and one of the most challenging forms of cancers to treat. Despite advances in conventional treatment, the outcome for patients remains almost universally fatal. This poor prognosis is due to therapeutic resistance and tumor recurrence after surgical removal. However, over the past decade, molecular targeted therapy has held the promise of transforming the care of malignant glioma patients. Significant progress in understanding the molecular pathology of gliomagenesis and maintenance of the malignant phenotypes will open opportunities to rationally develop new molecular targeted therapy options. Recently, therapeutic strategies have focused on targeting pro-growth signaling mediated by receptor tyrosine kinase/RAS/phosphatidylinositol 3-kinase pathway, proangiogenic pathways, and several other vital intracellular signaling networks, such as proteasome and histone deacetylase. However, several factors such as cross-talk between the altered pathways, intratumoral molecular heterogeneity, and therapeutic resistance of glioma stem cells (GSCs) have limited the activity of single agents. Efforts are ongoing to study in depth the complex molecular biology of glioma, develop novel regimens targeting GSCs, and identify biomarkers to stratify patients with the individualized molecular targeted therapy. Here, we review the molecular alterations relevant to the pathology of malignant glioma, review current advances in clinical targeted trials, and discuss the challenges, controversies, and future directions of molecular targeted therapy.
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Affiliation(s)
- Hongxiang Wang
- Department of Neurosurgery, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Tao Xu
- Department of Neurosurgery, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Ying Jiang
- Department of Neurosurgery, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Hanchong Xu
- Department of Neurosurgery, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Yong Yan
- Department of Neurosurgery, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Da Fu
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Juxiang Chen
- Department of Neurosurgery, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China.
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