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Xu WX, Song W, Jiang MP, Yang SJ, Zhang J, Wang DD, Tang JH. Systematic Characterization of Expression Profiles and Prognostic Values of the Eight Subunits of the Chaperonin TRiC in Breast Cancer. Front Genet 2021; 12:637887. [PMID: 33815471 PMCID: PMC8009990 DOI: 10.3389/fgene.2021.637887] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 02/22/2021] [Indexed: 01/03/2023] Open
Abstract
Background Chaperonin-containing TCP-1 (TRiC or CCT) was demonstrated to be involved in oncogenesis of cancers carcinogenesis and development of various malignancies. Increasing experimental evidence indicated that dysregulation of TRiC was implicated in the tumor progression of breast cancer (BCa). However, few definitive studies have addressed the diverse expression patterns and prognostic values of eight TRiC subunits. Thus, we aimed to investigate the clinical significance of TRiC subunit expression and prognostic values for their possible implications in diagnosis and treatment of BCa. Methods Based on updated public resources and comprehensive bioinformatics analysis, we used some online databases (e.g., UALCAN, GEPIA, cBioPortal, TIMER, BC-GenExMiner, metascape, and GeneMANIA) to comprehensively explore the expression levels and the prognostic effects of eight TRiC subunits in patients with BCa. Results The transcriptional levels of most subunits of the Chaperonin TRiC (CCT2, CCT3, CCT4, CCT5, CCT6A, and CCT7) were significantly elevated compared with normal breast tissues, whereas TCP1, CCT4, and CCT6B were lower in BCa tissues than in normal tissues. Besides, copy-number alterations (CNA) of eight TRiC subunits positively regulated their mRNA expressions. Furthermore, high mRNA expression of TCP1/CCT2/CCT4/CCT5/CCT6A/CCT7/CCT8 was significantly associated with poor overall survival (OS) in BCa patients. The eight subunits of the chaperonin TRiC was related to tumor purity and immune infiltration levels of BCa. Co-expression analysis showed CCT6B was negatively associated with other subunits of TRiC and other subunits of TRiC were positively correlated with each other. Additionally, TRiC and their interactive proteins were correlated with positive regulation of biological process, localization, and biological regulation. Conclusion This study systematically illustrated the expression profiles and distinct prognostic values of chaperonin TRiC in BCa, providing insights for further investigation of subunits of the chaperonin TRiC as novel therapeutic targets and potential prognostic biomarkers in BCa.
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Affiliation(s)
- Wen-Xiu Xu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wei Song
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Meng-Ping Jiang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Su-Jin Yang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jian Zhang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Dan-Dan Wang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jin-Hai Tang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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2
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Mei J, Cai Y, Xu R, Yang X, Zhou W, Wang H, Liu C. Characterization of the Clinical Significance of PD-1/PD-Ls Expression and Methylation in Patients With Low-Grade Glioma. Technol Cancer Res Treat 2021; 20:15330338211011970. [PMID: 33955303 PMCID: PMC8111557 DOI: 10.1177/15330338211011970] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 02/23/2021] [Accepted: 03/30/2021] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Immune checkpoints play crucial roles in the immune escape of cancer cells. However, the exact prognostic values of expression and methylation of programmed-death 1 (PD-1), programmed-death-ligand 1 (PD-L1) and PD-L2 in low-grade glioma (LGG) have not been well-defined yet. METHODS A total 514 LGG samples from the Cancer Genome Atlas (TCGA) dataset containing gene expression, DNA methylation, and survival data were enrolled in our study. Besides, a total of 137 primary LGG samples from the Chinese Glioma Genome Atlas (CGGA) database were also extracted for the survival analysis of the prognostic values of PD-1/PD-Ls expression. RESULTS PD-1/PD-Ls had distinct co-expression patterns in LGG tissues. The expression and methylation level of PD-1/PD-Ls seemed to be various in different LGG subtypes. Besides, overexpression and hypo-methylation of PD-1/PD-Ls were associated with worse prognosis. In addition, PD-1/PD-Ls expression was positively associated with TIICs infiltration, while their methylation was negatively associated with TIICs infiltration. Moreover, PD-1/PD-Ls and their positively correlated gene mainly participated in immune response related biological processes. CONCLUSION To conclude, overexpression and hypo-methylation of PD-1/PD-Ls predicted unfavorable prognosis in LGG patients, suggesting those patients may benefit from PD1/PD-Ls checkpoint inhibitors treatment.
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Affiliation(s)
- Jie Mei
- Department of Oncology, Wuxi People’s Hospital Affiliated to Nanjing Medical University, Wuxi, China
| | - Yun Cai
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
| | - Rui Xu
- School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Xuejing Yang
- Department of Oncology, Wuxi People’s Hospital Affiliated to Nanjing Medical University, Wuxi, China
| | - Weijian Zhou
- Department of Oncology, Wuxi People’s Hospital Affiliated to Nanjing Medical University, Wuxi, China
| | - Huiyu Wang
- Department of Oncology, Wuxi People’s Hospital Affiliated to Nanjing Medical University, Wuxi, China
| | - Chaoying Liu
- Department of Oncology, Wuxi People’s Hospital Affiliated to Nanjing Medical University, Wuxi, China
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3
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Wang J, Pollard K, Calizo A, Pratilas CA. Activation of Receptor Tyrosine Kinases Mediates Acquired Resistance to MEK Inhibition in Malignant Peripheral Nerve Sheath Tumors. Cancer Res 2020; 81:747-762. [PMID: 33203698 DOI: 10.1158/0008-5472.can-20-1992] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 10/08/2020] [Accepted: 11/12/2020] [Indexed: 11/16/2022]
Abstract
Malignant peripheral nerve sheath tumors often arise in patients with neurofibromatosis type 1 and are among the most treatment-refractory types of sarcoma. Overall survival in patients with relapsed disease remains poor, and thus novel therapeutic approaches are needed. NF1 is essential for negative regulation of RAS activity and is altered in about 90% of malignant peripheral nerve sheath tumors (MPNST). A complex interplay of upstream signaling and parallel RAS-driven pathways characterizes NF1-driven tumorigenesis, and inhibiting more than one RAS effector pathway is therefore necessary. To devise potential combination therapeutic strategies, we identified actionable alterations in signaling that underlie adaptive and acquired resistance to MEK inhibitor (MEKi). Using a series of proteomic, biochemical, and genetic approaches in an in vitro model of MEKi resistance provided a rationale for combination therapies. HGF/MET signaling was elevated in the MEKi-resistant model. HGF overexpression conferred resistance to MEKi in parental cells. Depletion of HGF or MET restored sensitivity of MEKi-resistant cells to MEKi. Finally, a combination of MEK and MET inhibition demonstrated activity in models of MPNST and may therefore be effective in patients with MPNST harboring genetic alterations in NF1. SIGNIFICANCE: This study demonstrates that MEKi plus MET inhibitor may delay or prevent a novel mechanism of acquired MEKi resistance, with clinical implications for MPNST patients harboring NF1 alterations.
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Affiliation(s)
- Jiawan Wang
- 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
| | - 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
| | - 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
| | - 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.
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4
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Mei J, Wang R, Xia D, Yang X, Zhou W, Wang H, Liu C. BRCA1 Is a Novel Prognostic Indicator and Associates with Immune Cell Infiltration in Hepatocellular Carcinoma. DNA Cell Biol 2020; 39:1838-1849. [PMID: 32876480 DOI: 10.1089/dna.2020.5644] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The breast cancer gene 1 (BRCA1) is a tumor suppressor, and mutations or epigenetic inactivation will increase the risk of breast cancer oncogenesis. The current research aimed to explore the relationship between BRCA1 expression, prognosis, and tumor immunity in hepatocellular carcinoma (HCC). In this study, BRCA1 expression was analyzed via multiple online databases and its association with clinical characteristics, prognosis and genetic alterations was identified using the original The Cancer Genome Atlas-liver hepatocellular carcinoma cohorts. DNA methylation sites and their prognostic values were analyzed using MethSurv. The correlations between BRCA1 and immune infiltration were investigated via Tumor Immune Estimation Resource. As results, BRCA1 was significantly upregulated in tumor tissues in multiple HCC cohorts. Besides, high BRCA1 expression was correlated with race, advanced T stage, clinical stage, poor tumor grade, MSI status, and worse prognosis. Notably, BRCA1 expression was positively correlated with infiltration levels of B cells, CD4+ T cells, CD8+ T cells, neutrophils, macrophages, and dendritic cells. The current findings imply that BRCA1 is associated with prognosis and immune infiltration, laying foundations for in-depth research on the role of BRCA1 in HCC.
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Affiliation(s)
- Jie Mei
- Department of Oncology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu, China
| | - Runjie Wang
- Department of Oncology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu, China
| | - Dandan Xia
- Department of Oncology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu, China
| | - Xuejing Yang
- Department of Oncology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu, China
| | - Weijian Zhou
- Department of Oncology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu, China
| | - Huiyu Wang
- Department of Oncology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu, China
| | - Chaoying Liu
- Department of Oncology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu, China
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Pemov A, Li H, Presley W, Wallace MR, Miller DT. Genetics of human malignant peripheral nerve sheath tumors. Neurooncol Adv 2019; 2:i50-i61. [PMID: 32642732 PMCID: PMC7317054 DOI: 10.1093/noajnl/vdz049] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Malignant peripheral nerve sheath tumors (MPNSTs) are heterogeneous, highly aggressive tumors with no widely effective treatment other than surgery. Genomic architecture of MPNST is similar to other soft tissue sarcomas, with a relatively modest burden of single nucleotide variants and an elevated frequency of copy-number alterations. Recent advances in genomic studies identified previously unrecognized critical involvement of polycomb repressor complex 2 (PRC2) core components SUZ12 and EED in transition to malignancy. Notably, somatic changes in NF1, CDKN2A/B, and PRC2 are found in most MPNST regardless of their etiology (e.g. neurofibromatosis type 1-associated vs. sporadic vs. radiation-induced), indicating that similar molecular mechanisms impact pathogenesis in these neoplasms. The timing and specific order of genetic or epigenetic changes may, however, explain the typically poorer prognosis of NF1-associated MPNSTs. Studies that reveal genes and regulatory pathways uniquely altered in malignancies are essential to development of targeted tumor therapies. Characterization of MPNST molecular profiles may also contribute to tools for earlier detection, and prediction of prognosis or drug response. Here we review the genetic discoveries and their implications in understanding MPNST biology.
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Affiliation(s)
- Alexander Pemov
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland
| | - Hua Li
- Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, Florida
| | - William Presley
- Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, Florida
| | - Margaret R Wallace
- Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, Florida.,University of Florida Health Cancer Center, University of Florida, Gainesville, Florida
| | - David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts
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6
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Mei J, Hao L, Liu X, Sun G, Xu R, Wang H, Liu C. Comprehensive analysis of peroxiredoxins expression profiles and prognostic values in breast cancer. Biomark Res 2019; 7:16. [PMID: 31402980 PMCID: PMC6683561 DOI: 10.1186/s40364-019-0168-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 07/12/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The peroxiredoxins (PRDXs) gene family has been demonstrated to participate in carcinogenesis and development of numerous cancers and the prognostic values in several cancers have been evaluated already. Purpose of our research is to explore the expression profiles and prognostic values of PRDXs in breast cancer (BrCa). METHODS The transcriptional levels of PDRX family members in primary BrCa tissues and their association with intrinsic subclasses were analyzed using UALCAN database. Then, the genetic alterations of PDRXs were examined by cBioPortal database. Moreover, the prognostic values of PRDXs in BrCa patients were investigated via the Kaplan-Meier plotter. RESULTS The transcriptional levels of most PRDXs family members in BrCa tissues were significantly elevated compared with normal breast tissues. Meanwhile, dysregulated PRDXs expression was associated with intrinsic subclasses of BrCa. Besides, copy number alterations (CNA) of PRDXs positively regulated their mRNA expressions. Furthermore, high mRNA expression of PRDX4/6 was significantly associated with poor overall survival (OS) in BrCa patients, while high mRNA expression of PRDX3 was notably related to favorable OS. Simultaneously, high mRNA expression of PRDX1/2/4/5/6 was significantly associated with shorter relapse-free survival (RFS) in BrCa patients, while high mRNA expression of PRDX3 was notably related to favorable RFS. In addition, the prognostic value of PRDXs in the different clinicopathological features based on intrinsic subclasses and chemotherapeutic treatment of BrCa patients was further assessed in the KM plotter database. CONCLUSION Our findings systematically elucidate the expression profiles and distinct prognostic values of PRDXs in BrCa, which might provide novel therapeutic targets and potential prognostic biomarkers for BrCa patients.
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Affiliation(s)
- Jie Mei
- Department of Oncology, Wuxi People’s Hospital Affiliated to Nanjing Medical University, Wuxi, 214023 China
| | - Leiyu Hao
- Department of Physiology, Nanjing Medical University, Nanjing, 211166 China
| | - Xiaorui Liu
- School of Pediatrics, Nanjing Medical University, Nanjing, 211166 China
| | - Guangshun Sun
- Department of General Surgery, Wuxi People’s Hospital Affiliated to Nanjing Medical University, Wuxi, 214023 China
| | - Rui Xu
- Department of Physiology, Nanjing Medical University, Nanjing, 211166 China
| | - Huiyu Wang
- Department of Oncology, Wuxi People’s Hospital Affiliated to Nanjing Medical University, Wuxi, 214023 China
| | - Chaoying Liu
- Department of Oncology, Wuxi People’s Hospital Affiliated to Nanjing Medical University, Wuxi, 214023 China
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7
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Krawczyk MA, Karpinsky G, Izycka-Swieszewska E, Gabrych A, Kunc M, Fatyga A, Garstka M, Styczewska M, Sokolewicz EM, Szlagatys-Sidorkiewicz A, Kazanowska B, Bien E. Immunohistochemical assessment of cyclin D1 and p53 is associated with survival in childhood malignant peripheral nerve sheath tumor. Cancer Biomark 2019; 24:351-361. [PMID: 30883338 DOI: 10.3233/cbm-181572] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND Malignant peripheral nerve sheath tumor (MPNST) is rare, aggressive soft tissue sarcoma which may affect children. OBJECTIVE We aimed to assess prognostic significance of immunohistochemical (IHC) markers, osteopontin, fibronectin, survivin, cyclin D1 and p53, in pediatric MPNST. METHODS A total of 26 pediatric MPNST patients were enrolled in the current study with a median follow-up of 51 months. IHC staining using commercially available monoclonal antibodies were employed to detect analyzed antigens on tissue microarrays. Eventually, all markers were subclassified to high (H) and low (L) expression categories in all analyzed tumors. RESULTS High IHC expressions of survivin, cyclin D1, osteopontin, fibronectin, and p53 were detected in 18 (69.2%), 13 (50%), 16 (61.5%), 16 (61.5%), and 13 (50%) tumors, respectively. A significant correlation was demonstrated between cyclin D1 and osteopontin (p= 0.004). Both markers were associated with neurofibromatosis type 1 (NF1) status (p= 0.041 and p= 0.037, respectively). H-fibronectin was more prevalent in deeply located tumors (p= 0.046). None of the markers was associated with IRS stage, age at diagnosis, and tumor size. Univariate analysis identified IRS stage, regional lymph node metastases, NF1, and cyclin D1 as variables associated with overall survival (OS), whereas tumor depth, osteopontin, and cyclin D1 - for relapse-free survival (RFS). Subsequent multivariate analysis identified cyclin D1 and p53 as independent variables predicting RFS, whereas cyclin D1 and regional lymph nodes status were independent predictors for OS.
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Affiliation(s)
- Malgorzata A Krawczyk
- Department of Pediatrics, Hematology and Oncology, Medical University of Gdansk, Gdansk, Poland.,Department of Pediatrics, Hematology and Oncology, Medical University of Gdansk, Gdansk, Poland
| | - Gabrielle Karpinsky
- Children's Hospital of Michigan, Detroit, MI, USA.,Department of Pediatrics, Hematology and Oncology, Medical University of Gdansk, Gdansk, Poland
| | - Ewa Izycka-Swieszewska
- Department of Pathology and Neuropathology, Medical University of Gdansk, Gdansk, Poland
| | - Anna Gabrych
- Department of Pediatrics, Hematology and Oncology, University Clinical Centre, Gdansk, Poland
| | - Michal Kunc
- Department of Pathomorphology, Medical University of Gdansk, Gdansk, Poland
| | - Aleksandra Fatyga
- Department of Pediatrics, Hematology and Oncology, University Clinical Centre, Gdansk, Poland
| | - Monika Garstka
- The English Division Pediatric Oncology Scientific Circle, Medical University of Gdansk, Gdansk, Poland
| | - Malgorzata Styczewska
- The English Division Pediatric Oncology Scientific Circle, Medical University of Gdansk, Gdansk, Poland
| | - Ewa M Sokolewicz
- The English Division Pediatric Oncology Scientific Circle, Medical University of Gdansk, Gdansk, Poland
| | | | - Bernarda Kazanowska
- The English Division Pediatric Oncology Scientific Circle, Medical University of Gdansk, Gdansk, Poland
| | - Ewa Bien
- Department of Pediatrics, Hematology and Oncology, Medical University of Gdansk, Gdansk, Poland
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8
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Pridgeon MG, Grohar PJ, Steensma MR, Williams BO. Wnt Signaling in Ewing Sarcoma, Osteosarcoma, and Malignant Peripheral Nerve Sheath Tumors. Curr Osteoporos Rep 2017. [PMID: 28647886 DOI: 10.1007/s11914-017-0377-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
PURPOSE OF REVIEW Wnt signaling plays a central role in development and homeostasis, and its dysregulation is a common event in many types of human cancer. Here we explore in detail the contributions of Wnt signaling to the initiation and maintenance of three types of saroma: Ewing sarcoma, osteosarcoma, and malignant peripheral nerve sheath tumors. This review provides an overview of the Wnt signaling pathway and explores in detail the current knowledge about its role in the initiation or maintenance of three tumor types: Ewing sarcoma, osteosarcoma, and malignant peripheral nerve sheath tumors. RECENT FINDINGS Recent work has assessed the role(s) of Wnt signaling within these cell types. This review provides an overview of the mechanistic insights that have been gained from a number of recent studies to set the foundation for potential therapeutic applications. Wnt signaling has emerged as a potentially critical pathway in maintaining the growth of these types of tumors. Given the fact that many new inhibitors of the pathway have recently or will soon enter Phase 1 clinical trials, it is likely that assessment of their activity in these tumor types will occur in human patients.
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Affiliation(s)
- Matthew G Pridgeon
- Grand Rapids Medical Education Partners, Grand Rapids, MI, USA
- Spectrum Health Cancer Center, Spectrum Health System, Grand Rapids, MI, USA
- Helen De Vos Children's Hospital, Grand Rapids, MI, USA
| | - Patrick J Grohar
- Spectrum Health Cancer Center, Spectrum Health System, Grand Rapids, MI, USA
- Helen De Vos Children's Hospital, Grand Rapids, MI, USA
- Department of Pediatrics, Michigan State University, Grand Rapids, MI, USA
- Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Matthew R Steensma
- Spectrum Health Cancer Center, Spectrum Health System, Grand Rapids, MI, USA
- Helen De Vos Children's Hospital, Grand Rapids, MI, USA
- Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, MI, USA
- Department of Surgery, Michigan State University College of Human Medicine, Grand Rapids, MI, USA
| | - Bart O Williams
- Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, MI, USA.
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9
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Martínez M, Sorzano COS, Pascual-Montano A, Carazo JM. Gene signature associated with benign neurofibroma transformation to malignant peripheral nerve sheath tumors. PLoS One 2017; 12:e0178316. [PMID: 28542306 PMCID: PMC5443557 DOI: 10.1371/journal.pone.0178316] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 05/11/2017] [Indexed: 11/19/2022] Open
Abstract
Benign neurofibromas, the main phenotypic manifestations of the rare neurological disorder neurofibromatosis type 1, degenerate to malignant tumors associated to poor prognosis in about 10% of patients. Despite efforts in the field of (epi)genomics, the lack of prognostic biomarkers with which to predict disease evolution frustrates the adoption of appropriate early therapeutic measures. To identify potential biomarkers of malignant neurofibroma transformation, we integrated four human experimental studies and one for mouse, using a gene score-based meta-analysis method, from which we obtained a score-ranked signature of 579 genes. Genes with the highest absolute scores were classified as promising disease biomarkers. By grouping genes with similar neurofibromatosis-related profiles, we derived panels of potential biomarkers. The addition of promoter methylation data to gene profiles indicated a panel of genes probably silenced by hypermethylation. To identify possible therapeutic treatments, we used the gene signature to query drug expression databases. Trichostatin A and other histone deacetylase inhibitors, as well as cantharidin and tamoxifen, were retrieved as putative therapeutic means to reverse the aberrant regulation that drives to malignant cell proliferation and metastasis. This in silico prediction corroborated reported experimental results that suggested the inclusion of these compounds in clinical trials. This experimental validation supported the suitability of the meta-analysis method used to integrate several sources of public genomic information, and the reliability of the gene signature associated to the malignant evolution of neurofibromas to generate working hypotheses for prognostic and drug-responsive biomarkers or therapeutic measures, thus showing the potential of this in silico approach for biomarker discovery.
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Affiliation(s)
- Marta Martínez
- Biocomputing Unit, Nacional Center for Biotechnology (CSIC), Campus Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
- * E-mail:
| | - Carlos O. S. Sorzano
- Biocomputing Unit, Nacional Center for Biotechnology (CSIC), Campus Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
- Bioengineering Lab., Universidad CEU San Pablo, Campus Urb. Montepríncipe, Boadilla del Monte, Madrid, Spain
| | - Alberto Pascual-Montano
- Biocomputing Unit, Nacional Center for Biotechnology (CSIC), Campus Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
| | - Jose M. Carazo
- Biocomputing Unit, Nacional Center for Biotechnology (CSIC), Campus Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
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10
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Lai YP, Wang LB, Wang WA, Lai LC, Tsai MH, Lu TP, Chuang EY. iGC-an integrated analysis package of gene expression and copy number alteration. BMC Bioinformatics 2017; 18:35. [PMID: 28088185 PMCID: PMC5237550 DOI: 10.1186/s12859-016-1438-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 12/17/2016] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND With the advancement in high-throughput technologies, researchers can simultaneously investigate gene expression and copy number alteration (CNA) data from individual patients at a lower cost. Traditional analysis methods analyze each type of data individually and integrate their results using Venn diagrams. Challenges arise, however, when the results are irreproducible and inconsistent across multiple platforms. To address these issues, one possible approach is to concurrently analyze both gene expression profiling and CNAs in the same individual. RESULTS We have developed an open-source R/Bioconductor package (iGC). Multiple input formats are supported and users can define their own criteria for identifying differentially expressed genes driven by CNAs. The analysis of two real microarray datasets demonstrated that the CNA-driven genes identified by the iGC package showed significantly higher Pearson correlation coefficients with their gene expression levels and copy numbers than those genes located in a genomic region with CNA. Compared with the Venn diagram approach, the iGC package showed better performance. CONCLUSION The iGC package is effective and useful for identifying CNA-driven genes. By simultaneously considering both comparative genomic and transcriptomic data, it can provide better understanding of biological and medical questions. The iGC package's source code and manual are freely available at https://www.bioconductor.org/packages/release/bioc/html/iGC.html .
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Affiliation(s)
- Yi-Pin Lai
- Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taipei, Taiwan
| | - Liang-Bo Wang
- Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taipei, Taiwan.,Graduate Institute of Biomedical Electronics and Bioinformatics, Department of Electrical Engineering, National Taiwan University, Taipei, Taiwan
| | - Wei-An Wang
- Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taipei, Taiwan
| | - Liang-Chuan Lai
- Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taipei, Taiwan.,Graduate Institute of Physiology, National Taiwan University, Taipei, Taiwan
| | - Mong-Hsun Tsai
- Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taipei, Taiwan.,Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Tzu-Pin Lu
- Department of Public Health, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan.
| | - Eric Y Chuang
- Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taipei, Taiwan. .,Graduate Institute of Biomedical Electronics and Bioinformatics, Department of Electrical Engineering, National Taiwan University, Taipei, Taiwan.
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11
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Jung HS, Lefferts JA, Tsongalis GJ. Utilization of the oncoscan microarray assay in cancer diagnostics. ACTA ACUST UNITED AC 2017. [DOI: 10.1186/s41241-016-0007-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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12
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Neurofibromatosis type 1: Fundamental insights into cell signalling and cancer. Semin Cell Dev Biol 2016; 52:39-46. [PMID: 26860753 DOI: 10.1016/j.semcdb.2016.02.007] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 02/02/2016] [Accepted: 02/03/2016] [Indexed: 11/23/2022]
Abstract
Neurofibromatosis type 1 (NF1) is an autosomal dominant tumour predisposition syndrome that is caused through loss of function mutations of a tumour suppressor gene called Neurofibromin 1. Therapeutic options are currently limited for NF1-associated tumours, where treatment is often restricted to complete surgical resection with clear margins. Herein, we discuss the multifunctional tumour suppressive role of neurofibromin, which is classically known as a GTPase activating protein (GAP) towards the RAS small GTPase. While neurofibromin inhibits proliferative growth through blockade of RAS-mediated signal transduction, neurofibromin should also be considered as a modulator of cell motility and cell adhesion. Through interfacing with the cytoskeleton and membrane structures, neurofibromin acts as a negative regulator of RHO/ROCK signalling pathways involved in cytoskeletal dynamics that are instrumental in proper neuronal development. In the context of cancer, the loss of normal function of neurofibromin via genetic mutation results in heightened cell proliferation and migration, predisposing NF1 patients to cancer. Malignant Peripheral Nerve Sheath Tumours (MPNSTs) can develop from benign neurofibromas and are the main cause of death amongst NF1 patients. Through recent research on MPNSTs, we have gained insight into the key molecular events that drive their malignancy. Advances regarding malignant drivers involved in cell migration, cell invasion and angiogenic signalling are discussed in this review, where these findings will likely influence future therapies for both NF1 and related sporadic cancers.
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Sherborne AL, Davidson PR, Yu K, Nakamura AO, Rashid M, Nakamura JL. Mutational Analysis of Ionizing Radiation Induced Neoplasms. Cell Rep 2015; 12:1915-26. [PMID: 26344771 DOI: 10.1016/j.celrep.2015.08.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Revised: 07/08/2015] [Accepted: 08/05/2015] [Indexed: 10/25/2022] Open
Abstract
Ionizing radiation (IR) is a mutagen that promotes tumorigenesis in multiple exposure contexts. One severe consequence of IR is the development of second malignant neoplasms (SMNs), a radiotherapy-associated complication in survivors of cancers, particularly pediatric cancers. SMN genomes are poorly characterized, and the influence of genetic background on genotoxin-induced mutations has not been examined. Using our mouse models of SMNs, we performed whole exome sequencing of neoplasms induced by fractionated IR in wild-type and Nf1 mutant mice. Using non-negative matrix factorization, we identified mutational signatures that did not segregate by genetic background or histology. Copy-number analysis revealed recurrent chromosomal alterations and differences in copy number that were background dependent. Pathway analysis identified enrichment of non-synonymous variants in genes responsible for cell assembly and organization, cell morphology, and cell function and maintenance. In this model system, ionizing radiation and Nf1 heterozygosity each exerted distinct influences on the mutational landscape.
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Affiliation(s)
- Amy L Sherborne
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Philip R Davidson
- Department of Finance and Statistical Analysis, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Katharine Yu
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alice O Nakamura
- Department of Finance and Statistical Analysis, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Mamunur Rashid
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Jean L Nakamura
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA 94158, USA.
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