1
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Wu P, Pan X, Lu K, Gu N. Screening prognostic genes related to leucovorin, fluorouracil, and irinotecan treatment sensitivity by performing co-expression network analysis for colon cancer. Front Genet 2022; 13:928356. [DOI: 10.3389/fgene.2022.928356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 11/11/2022] [Indexed: 11/30/2022] Open
Abstract
Background: Colon cancer is one of the most common malignant tumors in the world. FOLFIRI (leucovorin, fluorouracil, and irinotecan) is a common combination in chemotherapy regimens. However, insensitivity to FOLFIRI is an important factor in the effectiveness of the treatment for advanced colon cancer. Our study aimed to explore precise molecular targets associated with chemotherapy responses in colon cancer.Methods: Gene expression profiles of 21 patients with advanced colorectal cancer who received chemotherapy based on FOLFIRI were obtained from the Gene Expression Omnibus (GEO) database. The gene co-expression network was constructed by the weighted gene co-expression network analysis (WGCNA) and functional gene modules were screened out. Clinical phenotypic correlation analysis was used to identify key gene modules. Gene Ontology and pathway enrichment analysis were used to screen enriched genes in key modules. Protein–protein interaction (PPI) analysis was used to screen out key node genes. Based on the Gene Expression Profiling Interactive Analysis (GEPIA) database, the correlation between the expression levels of these genes and the overall survival (OS) and disease-free survival (DFS) of colon cancer patients was investigated, and the hub genes were screened out. Immunohistochemistry of candidate hub genes was identified using the Human Protein Atlas database. Finally, clinical information and RNA sequencing data of colon cancer were obtained from The Cancer Genome Atlas project database (TCGA), the GEPIA, and the Human Atlas databases for validation.Results: The WGCNA revealed that three hub genes were closely related to chemotherapy insensitivity of colon cancer: AEBP1, BGN, and TAGLN. The protein expression levels of AEBP1, BGN, and TAGLN in tumor tissues were higher than those in normal tissues. In addition, the gene expression levels of AEBP1, BGN, and TAGLN were negatively correlated with OS and DFS in colon cancer patients. Therefore, AEBP1, BGN, and TAGLN have been identified as potential biomarkers related to the response to FOLFIRI treatment of colon cancer.Conclusion: We found that AEBP1, BGN, and TAGLN, as potential predictive biomarkers, may play an important role in the response to FOLFIRI treatment of colon cancer and as a precise molecular target associated with chemotherapy response in colon cancer.
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Longo JF, Brosius SN, Znoyko I, Alers VA, Jenkins DP, Wilson RC, Carroll AJ, Wolff DJ, Roth KA, Carroll SL. Establishment and genomic characterization of a sporadic malignant peripheral nerve sheath tumor cell line. Sci Rep 2021; 11:5690. [PMID: 33707600 PMCID: PMC7952412 DOI: 10.1038/s41598-021-85055-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 02/17/2021] [Indexed: 12/19/2022] Open
Abstract
Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive Schwann cell-derived neoplasms that occur sporadically or in patients with neurofibromatosis type 1 (NF1). Preclinical research on sporadic MPNSTs has been limited as few cell lines exist. We generated and characterized a new sporadic MPNST cell line, 2XSB, which shares the molecular and genomic features of the parent tumor. These cells have a highly complex karyotype with extensive chromothripsis. 2XSB cells show robust invasive 3-dimensional and clonogenic culture capability and form solid tumors when xenografted into immunodeficient mice. High-density single nucleotide polymorphism array and whole exome sequencing analyses indicate that, unlike NF1-associated MPNSTs, 2XSB cells have intact, functional NF1 alleles with no evidence of mutations in genes encoding components of Polycomb Repressor Complex 2. However, mutations in other genes implicated in MPNST pathogenesis were identified in 2XSB cells including homozygous deletion of CDKN2A and mutations in TP53 and PTEN. We also identified mutations in genes not previously associated with MPNSTs but associated with the pathogenesis of other human cancers. These include DNMT1, NUMA1, NTRK1, PDE11A, CSMD3, LRP5 and ACTL9. This sporadic MPNST-derived cell line provides a useful tool for investigating the biology and potential treatment regimens for sporadic MPNSTs.
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Affiliation(s)
- Jody Fromm Longo
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, 171 Ashley Avenue, MSC 908, Charleston, SC, 29425-9080, USA
| | - Stephanie N Brosius
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35294-0017, USA.,Medical Scientist Training Program, University of Alabama at Birmingham, Birmingham, AL, 35294-0017, USA.,Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Iya Znoyko
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, 171 Ashley Avenue, MSC 908, Charleston, SC, 29425-9080, USA
| | - Victoria A Alers
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, 171 Ashley Avenue, MSC 908, Charleston, SC, 29425-9080, USA
| | - Dorea P Jenkins
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, 171 Ashley Avenue, MSC 908, Charleston, SC, 29425-9080, USA
| | - Robert C Wilson
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, 171 Ashley Avenue, MSC 908, Charleston, SC, 29425-9080, USA.,Center for Genomic Medicine, Medical University of South Carolina, Charleston, SC, 29425-9080, USA
| | - Andrew J Carroll
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 35294-0017, USA
| | - Daynna J Wolff
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, 171 Ashley Avenue, MSC 908, Charleston, SC, 29425-9080, USA
| | - Kevin A Roth
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Steven L Carroll
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, 171 Ashley Avenue, MSC 908, Charleston, SC, 29425-9080, USA. .,Center for Genomic Medicine, Medical University of South Carolina, Charleston, SC, 29425-9080, USA. .,Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35294-0017, USA.
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3
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Liu X, Gygi SP, Paulo JA. Isobaric Tag-Based Protein Profiling across Eight Human Cell Lines Using High-Field Asymmetric Ion Mobility Spectrometry and Real-Time Database Searching. Proteomics 2020; 21:e2000218. [PMID: 33015980 DOI: 10.1002/pmic.202000218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/26/2020] [Indexed: 12/11/2022]
Abstract
A vast number of human cell lines are available for cell culture model-based studies, and as such the potential exists for discrepancies in findings due to cell line selection. To investigate this concept, the authors determine the relative protein abundance profiles of a panel of eight diverse, but commonly studied human cell lines. This panel includes HAP1, HEK293T, HeLa, HepG2, Jurkat, Panc1, SH-SY5Y, and SVGp12. A mass spectrometry-based proteomics workflow designed to enhance quantitative accuracy while maintaining analytical depth is used. To this end, this strategy leverages TMTpro16-based sample multiplexing, high-field asymmetric ion mobility spectrometry, and real-time database searching. The data show that the differences in the relative protein abundance profiles reflect cell line diversity. The authors also determine several hundred proteins to be highly enriched for a given cell line, and perform gene ontology and pathway analysis on these cell line-enriched proteins. An R Shiny application is designed to query protein abundance profiles and retrieve proteins with similar patterns. The workflows used herein can be applied to additional cell lines to aid cell line selection for addressing a given scientific inquiry or for improving an experimental design.
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Affiliation(s)
- Xinyue Liu
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
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4
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Liu J, Zhang Y, Li Q, Wang Y. Transgelins: Cytoskeletal Associated Proteins Implicated in the Metastasis of Colorectal Cancer. Front Cell Dev Biol 2020; 8:573859. [PMID: 33117801 PMCID: PMC7575706 DOI: 10.3389/fcell.2020.573859] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 09/07/2020] [Indexed: 12/20/2022] Open
Abstract
Transgelins, including transgelin-1 (T-1), transgelin-2 (T-2), and transgelin-3 (T-3), are a family of actin-binding proteins (ABPs) that can alter the structure and morphology of the cytoskeleton. These proteins function by regulating migration, proliferation and apoptosis in many different cancers. Several studies have shown that in various types of tumor cells, including colorectal cancer (CRC) cells, and in the tumor microenvironment, the expression and biological effects of transgelins are diverse and may transform during tumor progression. Previous researches have demonstrated that transgelin levels are positively correlated with metastasis in CRC, and down-regulating their expression can inhibit this process. In advanced disease, T-1 is a tumor activator with increasing expression, and T-2 expression increases with the progression of CRC. Finally, T-3 is only expressed in neurons and is not associated with CRC. This evidence suggests that T-1 and T-2 are potential biomarkers and therapeutic targets for CRC metastasis.
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Affiliation(s)
- Jingwen Liu
- Department of Medical Oncology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yingru Zhang
- Department of Medical Oncology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Qi Li
- Department of Medical Oncology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yan Wang
- Department of Medical Oncology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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5
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Yuan Y, Chen J, Wang J, Xu M, Zhang Y, Sun P, Liang L. Identification Hub Genes in Colorectal Cancer by Integrating Weighted Gene Co-Expression Network Analysis and Clinical Validation in vivo and vitro. Front Oncol 2020; 10:638. [PMID: 32426282 PMCID: PMC7203460 DOI: 10.3389/fonc.2020.00638] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/06/2020] [Indexed: 12/15/2022] Open
Abstract
Colorectal cancer (CRC) is the third leading cause of death in the world. However, the key roles of most molecules in CRC remain unclear. This study aimed to identify key modules and hub genes associated with the progression of CRC. The data of the patients with CRC were obtained from the Gene Expression Omnibus (GEO) database and assessed by weighted gene co-expression network analysis (WGCNA), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses performed in R. by WGCNA, several hub genes that regulate the mechanism of tumorigenesis in CRC were identified, which were associated with clinical traits. Next, we screened hub genes related to the progression of CRC authenticated by The Cancer Genome Atlas (TCGA) and Oncomine databases. Three hub genes (HCLS1, EVI2B, and CD48) were identified, and survival analysis was further performed. Moreover, the results of qPCR and immunohistochemistry staining revealed that HCLS1, EVI2B, and CD48 are tumor suppressor genes. Further, the functional study verified that over-expression of HCLS1, EVI2B, and CD48 can reduce the proliferation, migration, and invasion ability of CRC cells and significantly suppress CRC tumor growth in vivo. In summary, we identified three hub genes that were associated with the progression of CRC that can be applied in treatment.
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Affiliation(s)
- Yihang Yuan
- Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ji Chen
- Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jue Wang
- Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ming Xu
- Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yunpeng Zhang
- Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Peng Sun
- Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Leilei Liang
- Department of General Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 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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7
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Liu Y, Wu X, Wang G, Hu S, Zhang Y, Zhao S. CALD1, CNN1, and TAGLN identified as potential prognostic molecular markers of bladder cancer by bioinformatics analysis. Medicine (Baltimore) 2019; 98:e13847. [PMID: 30633156 PMCID: PMC6336601 DOI: 10.1097/md.0000000000013847] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 09/17/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Bladder cancer (BC) is one of the most common malignant neoplasms in the genitourinary tract. We employed the GSE13507 data set from the Gene Expression Omnibus (GEO) database in order to identify key genes related to tumorigenesis, progression, and prognosis in BC patients. METHODS The data set used in this study included 10 normal bladder mucosae tissue samples and 165 primary BC tissue samples. Differentially expressed genes (DEGs) in the 2 types of samples were identified by GEO2R. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using the online website DAVID. The online website STRING was used to construct a protein-protein interaction network. Moreover, the plugins in MCODE and cytoHubba in Cytoscape were employed to find the hub genes and modules in these DEGs. RESULTS We identified 154 DEGs comprising 135 downregulated genes and 19 upregulated genes. The GO enrichment results were mainly related to the contractile fiber part, extracellular region part, actin cytoskeleton, and extracellular region. The KEGG pathway enrichment results mainly comprised type I diabetes mellitus, asthma, systemic lupus erythematosus, and allograft rejection. A module was identified from the protein-protein interaction network. In total, 15 hub genes were selected and 3 of them comprising CALD1, CNN1, and TAGLN were associated with both overall survival and disease-free survival. CONCLUSION CALD1, CNN1, and TAGLN may be potential biomarkers for diagnosis as well as therapeutic targets in BC patients.
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8
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Beyer SJ, Bell EH, McElroy JP, Fleming JL, Cui T, Becker A, Bassett E, Johnson B, Gulati P, Popp I, Staszewski O, Prinz M, Grosu AL, Haque SJ, Chakravarti A. Oncogenic transgelin-2 is differentially regulated in isocitrate dehydrogenase wild-type vs. mutant gliomas. Oncotarget 2018; 9:37097-37111. [PMID: 30647847 PMCID: PMC6324682 DOI: 10.18632/oncotarget.26365] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 10/24/2018] [Indexed: 12/27/2022] Open
Abstract
The presence of an isocitrate dehydrogenase (IDH1/2) mutation in gliomas is associated with favorable outcomes compared to gliomas without the mutation (IDH1/2 wild-type, WT). The underlying biological mechanisms accounting for improved clinical outcomes in IDH1/2 mutant gliomas remain poorly understood, but may, in part, be due to the glioma CpG island methylator phenotype (G-CIMP) and epigenetic silencing of genes. We performed profiling of IDH1/2 WT versus IDH1/2 mutant Grade II and III gliomas and identified transgelin-2 (TAGLN2), an oncogene and actin-polymerizing protein, to be expressed at significantly higher levels in IDH1/2 WT gliomas compared to IDH1/2 mutant gliomas. This differential expression of TAGLN2 was primarily due to promoter hypermethylation in IDH1/2 mutant gliomas, suggesting involvement of TAGLN2 in the G-CIMP. Our results also suggest that TAGLN2 may be involved in progression due to higher expression in glioblastomas compared to IDH1/2 WT gliomas of lower grades. Furthermore, our results suggest that TAGLN2 functions as an oncogene by contributing to proliferation and invasion when overexpressed in IDH1/2 WT glioma cells. Taken together, this study demonstrates a possible link between increased TAGLN2 expression, invasion and poor patient outcomes in IDH1/2 WT gliomas and identifies TAGLN2 as a potential novel therapeutic target for IDH1/2 WT gliomas.
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Affiliation(s)
- Sasha J. Beyer
- Department of Radiation Oncology, Arthur G. James Hospital/The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Erica H. Bell
- Department of Radiation Oncology, Arthur G. James Hospital/The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Joseph P. McElroy
- Center for Biostatistics, The Ohio State University, Columbus, OH, USA
| | - Jessica L. Fleming
- Department of Radiation Oncology, Arthur G. James Hospital/The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Tiantian Cui
- Department of Radiation Oncology, Arthur G. James Hospital/The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Aline Becker
- Department of Radiation Oncology, Arthur G. James Hospital/The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Emily Bassett
- Department of Radiation Oncology, Arthur G. James Hospital/The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Benjamin Johnson
- Department of Radiation Oncology, Arthur G. James Hospital/The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Pooja Gulati
- Department of Radiation Oncology, Arthur G. James Hospital/The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Ilinca Popp
- Department of Radiation Oncology, Medical Center University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site, Freiburg, Germany
| | - Ori Staszewski
- Institute of Neuropathology, Medical Faculty, University of Freiburg, Freiburg, Germany
| | - Marco Prinz
- Institute of Neuropathology, Medical Faculty, University of Freiburg, Freiburg, Germany
- BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
- CIBSS Centre for Integrative Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Anca L. Grosu
- Department of Radiation Oncology, Medical Center University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site, Freiburg, Germany
| | - Saikh Jaharul Haque
- Department of Radiation Oncology, Arthur G. James Hospital/The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Arnab Chakravarti
- Department of Radiation Oncology, Arthur G. James Hospital/The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
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MEK inhibitors enhance therapeutic response towards ATRA in NF1 associated malignant peripheral nerve sheath tumors (MPNST) in-vitro. PLoS One 2017; 12:e0187700. [PMID: 29131833 PMCID: PMC5683628 DOI: 10.1371/journal.pone.0187700] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 10/24/2017] [Indexed: 12/11/2022] Open
Abstract
OBJECTIVE Neurofibromatosis type 1 (NF1) is a hereditary tumor syndrome characterized by an increased risk of malignant peripheral nerve sheath tumors (MPNST). Chemotherapy of MPNST is still insufficient. In this study, we investigated whether human tumor Schwann cells derived from NF1 associated MPNST respond to all-trans retinoic acid (ATRA). We analyzed effects of ATRA and MEK inhibitor (MEKi) combination therapy. METHODS MPNST cell lines S462, T265, NSF1 were treated with ATRA and MEKi U0126 and PD0325901. We assessed cell viability, proliferation, migration, apoptosis and differentiation as well as mRNA expression of RAR and RXR subtypes and ATRA target genes such as CRABP2, CYP26A1, RARB and PDK1. We also analyzed CRABP2 methylation in cell lines and performed immunohistochemistry of human MPNST specimens. RESULTS ATRA therapy reduced viability and proliferation in S462 and T265 cells, accompanied by differentiation, apoptosis and reduced migration. NSF1 cells which lacked RXRG expression did not respond to ATRA. We furthermore demonstrated that ATRA signaling was functional for common targets, and that mRNA expression of CRABP2 and its targets was raised by ATRA therapy, whereas alternative pathways via FABP5 were not induced. Finally, combination of ATRA and MEKi demonstrated additively reduced viability of T265 and S462 cells. CONCLUSIONS We observed therapeutic effects in two of three MPNST cell lines pronounced by combination therapy. These data point to a potentially successful treatment of MPNST by combined application of ATRA and MEK inhibitors such as U0126 or PD0325901.
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Walther C, Mayrhofer M, Nilsson J, Hofvander J, Jonson T, Mandahl N, Øra I, Gisselsson D, Mertens F. Genetic heterogeneity in rhabdomyosarcoma revealed by SNP array analysis. Genes Chromosomes Cancer 2015; 55:3-15. [DOI: 10.1002/gcc.22285] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 06/27/2015] [Indexed: 12/25/2022] Open
Affiliation(s)
- Charles Walther
- Department of Clinical Genetics; University and Regional Laboratories, Skåne University Hospital, Lund University; Lund Sweden
| | - Markus Mayrhofer
- Array & Analysis Facility, Science for Life Laboratory, Uppsala University; Sweden
| | - Jenny Nilsson
- Department of Clinical Genetics; University and Regional Laboratories, Skåne University Hospital, Lund University; Lund Sweden
| | - Jakob Hofvander
- Department of Clinical Genetics; University and Regional Laboratories, Skåne University Hospital, Lund University; Lund Sweden
| | - Tord Jonson
- Department of Clinical Genetics; University and Regional Laboratories, Skåne University Hospital, Lund University; Lund Sweden
| | - Nils Mandahl
- Department of Clinical Genetics; University and Regional Laboratories, Skåne University Hospital, Lund University; Lund Sweden
| | - Ingrid Øra
- Department of Pediatric Oncology; Skåne University Hospital; Lund Sweden
| | - David Gisselsson
- Department of Clinical Genetics; University and Regional Laboratories, Skåne University Hospital, Lund University; Lund Sweden
| | - Fredrik Mertens
- Department of Clinical Genetics; University and Regional Laboratories, Skåne University Hospital, Lund University; Lund Sweden
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11
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Sayar N, Karahan G, Konu O, Bozkurt B, Bozdogan O, Yulug IG. Transgelin gene is frequently downregulated by promoter DNA hypermethylation in breast cancer. Clin Epigenetics 2015; 7:104. [PMID: 26421063 PMCID: PMC4587865 DOI: 10.1186/s13148-015-0138-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Accepted: 09/18/2015] [Indexed: 12/17/2022] Open
Abstract
Background CpG hypermethylation in gene promoters is a frequent mechanism of tumor suppressor gene silencing in various types of cancers. It usually occurs at early steps of cancer progression and can be detected easily, giving rise to development of promising biomarkers for both detection and progression of cancer, including breast cancer. 5-aza-2′-deoxycytidine (AZA) is a DNA demethylating and anti-cancer agent resulting in induction of genes suppressed via DNA hypermethylation. Results Using microarray expression profiling of AZA- or DMSO-treated breast cancer and non-tumorigenic breast (NTB) cells, we identified for the first time TAGLN gene as a target of DNA hypermethylation in breast cancer. TAGLN expression was significantly and frequently downregulated via promoter DNA hypermethylation in breast cancer cells compared to NTB cells, and also in 13/21 (61.9 %) of breast tumors compared to matched normal tissues. Analyses of public microarray methylation data showed that TAGLN was also hypermethylated in 63.02 % of tumors compared to normal tissues; relapse-free survival of patients was worse with higher TAGLN methylation; and methylation levels could discriminate between tumors and healthy tissues with 83.14 % sensitivity and 100 % specificity. Additionally, qRT-PCR and immunohistochemistry experiments showed that TAGLN expression was significantly downregulated in two more independent sets of breast tumors compared to normal tissues and was lower in tumors with poor prognosis. Colony formation was increased in TAGLN silenced NTB cells, while decreased in overexpressing BC cells. Conclusions TAGLN gene is frequently downregulated by DNA hypermethylation, and TAGLN promoter methylation profiles could serve as a future diagnostic biomarker, with possible clinical impact regarding the prognosis in breast cancer. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0138-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nilufer Sayar
- Department of Molecular Biology and Genetics, Bilkent University, Faculty of Science, TR-06800 Ankara, Turkey
| | - Gurbet Karahan
- Department of Molecular Biology and Genetics, Bilkent University, Faculty of Science, TR-06800 Ankara, Turkey
| | - Ozlen Konu
- Department of Molecular Biology and Genetics, Bilkent University, Faculty of Science, TR-06800 Ankara, Turkey
| | - Betul Bozkurt
- Department of General Surgery, Ankara Numune Training and Research Hospital, 06100 Ankara, Turkey
| | - Onder Bozdogan
- Department of Pathology, Ankara Numune Training and Research Hospital, 06100 Ankara, Turkey
| | - Isik G Yulug
- Department of Molecular Biology and Genetics, Bilkent University, Faculty of Science, TR-06800 Ankara, Turkey
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12
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Dong LH, Li L, Song Y, Duan ZL, Sun SG, Lin YL, Miao SB, Yin YJ, Shu YN, Li H, Chen P, Zhao LL, Han M. TRAF6-Mediated SM22α K21 Ubiquitination Promotes G6PD Activation and NADPH Production, Contributing to GSH Homeostasis and VSMC Survival In Vitro and In Vivo. Circ Res 2015; 117:684-94. [PMID: 26291555 DOI: 10.1161/circresaha.115.306233] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 08/19/2015] [Indexed: 12/31/2022]
Abstract
RATIONALE Vascular smooth muscle cell (VSMC) survival under stressful conditions is integral to promoting vascular repair, but facilitates plaque stability during the development of atherosclerosis. The cytoskeleton-associated smooth muscle (SM) 22α protein is involved in the regulation of VSMC phenotypes, whereas the pentose phosphate pathway plays an essential role in cell proliferation through the production of dihydronicotinamide adenine dinucleotide phosphate. OBJECTIVE To identify the relationship between dihydronicotinamide adenine dinucleotide phosphate production and SM22α activity in the development and progression of vascular diseases. METHODS AND RESULTS We showed that the expression and activity of glucose-6-phosphate dehydrogenase (G6PD) are promoted in platelet-derived growth factor (PDGF)-BB-induced proliferative VSMCs. PDGF-BB induced G6PD membrane translocation and activation in an SM22α K21 ubiquitination-dependent manner. Specifically, the ubiquitinated SM22α interacted with G6PD and mediated G6PD membrane translocation. Furthermore, we found that tumor necrosis factor receptor-associated factor (TRAF) 6 mediated SM22α K21 ubiquitination in a K63-linked manner on PDGF-BB stimulation. Knockdown of TRAF6 decreased the membrane translocation and activity of G6PD, in parallel with reduced SM22α K21 ubiquitination. Elevated levels of activated G6PD consequent to PDGF-BB induction led to increased dihydronicotinamide adenine dinucleotide phosphate generation through stimulation of the pentose phosphate pathway, which enhanced VSMC viability and reduced apoptosis in vivo and in vitro via glutathione homeostasis. CONCLUSIONS We provide evidence that TRAF6-induced SM22α ubiquitination maintains VSMC survival through increased G6PD activity and dihydronicotinamide adenine dinucleotide phosphate production. The TRAF6-SM22α-G6PD pathway is a novel mechanism underlying the association between glucose metabolism and VSMC survival, which is beneficial for vascular repair after injury but facilitates atherosclerotic plaque stability.
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Affiliation(s)
- Li-Hua Dong
- From the Department of Biochemistry and Molecular Biology, College of Basic Medicine, Key Laboratory of Medical Biotechnology of Hebei Province, Key Laboratory of Neural and Vascular Biology of Ministry of Education, Hebei Medical University, Shijiazhuang, PR China
| | - Liang Li
- From the Department of Biochemistry and Molecular Biology, College of Basic Medicine, Key Laboratory of Medical Biotechnology of Hebei Province, Key Laboratory of Neural and Vascular Biology of Ministry of Education, Hebei Medical University, Shijiazhuang, PR China
| | - Yu Song
- From the Department of Biochemistry and Molecular Biology, College of Basic Medicine, Key Laboratory of Medical Biotechnology of Hebei Province, Key Laboratory of Neural and Vascular Biology of Ministry of Education, Hebei Medical University, Shijiazhuang, PR China
| | - Zhi-Li Duan
- From the Department of Biochemistry and Molecular Biology, College of Basic Medicine, Key Laboratory of Medical Biotechnology of Hebei Province, Key Laboratory of Neural and Vascular Biology of Ministry of Education, Hebei Medical University, Shijiazhuang, PR China
| | - Shao-Guang Sun
- From the Department of Biochemistry and Molecular Biology, College of Basic Medicine, Key Laboratory of Medical Biotechnology of Hebei Province, Key Laboratory of Neural and Vascular Biology of Ministry of Education, Hebei Medical University, Shijiazhuang, PR China
| | - Yan-Ling Lin
- From the Department of Biochemistry and Molecular Biology, College of Basic Medicine, Key Laboratory of Medical Biotechnology of Hebei Province, Key Laboratory of Neural and Vascular Biology of Ministry of Education, Hebei Medical University, Shijiazhuang, PR China
| | - Sui-Bing Miao
- From the Department of Biochemistry and Molecular Biology, College of Basic Medicine, Key Laboratory of Medical Biotechnology of Hebei Province, Key Laboratory of Neural and Vascular Biology of Ministry of Education, Hebei Medical University, Shijiazhuang, PR China
| | - Ya-Juan Yin
- From the Department of Biochemistry and Molecular Biology, College of Basic Medicine, Key Laboratory of Medical Biotechnology of Hebei Province, Key Laboratory of Neural and Vascular Biology of Ministry of Education, Hebei Medical University, Shijiazhuang, PR China
| | - Ya-Nan Shu
- From the Department of Biochemistry and Molecular Biology, College of Basic Medicine, Key Laboratory of Medical Biotechnology of Hebei Province, Key Laboratory of Neural and Vascular Biology of Ministry of Education, Hebei Medical University, Shijiazhuang, PR China
| | - Huan Li
- From the Department of Biochemistry and Molecular Biology, College of Basic Medicine, Key Laboratory of Medical Biotechnology of Hebei Province, Key Laboratory of Neural and Vascular Biology of Ministry of Education, Hebei Medical University, Shijiazhuang, PR China
| | - Peng Chen
- From the Department of Biochemistry and Molecular Biology, College of Basic Medicine, Key Laboratory of Medical Biotechnology of Hebei Province, Key Laboratory of Neural and Vascular Biology of Ministry of Education, Hebei Medical University, Shijiazhuang, PR China
| | - Li-Li Zhao
- From the Department of Biochemistry and Molecular Biology, College of Basic Medicine, Key Laboratory of Medical Biotechnology of Hebei Province, Key Laboratory of Neural and Vascular Biology of Ministry of Education, Hebei Medical University, Shijiazhuang, PR China
| | - Mei Han
- From the Department of Biochemistry and Molecular Biology, College of Basic Medicine, Key Laboratory of Medical Biotechnology of Hebei Province, Key Laboratory of Neural and Vascular Biology of Ministry of Education, Hebei Medical University, Shijiazhuang, PR China.
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Hirbe AC, Dahiya S, Miller CA, Li T, Fulton RS, Zhang X, McDonald S, DeSchryver K, Duncavage EJ, Walrath J, Reilly KM, Abel HJ, Pekmezci M, Perry A, Ley TJ, Gutmann DH. Whole Exome Sequencing Reveals the Order of Genetic Changes during Malignant Transformation and Metastasis in a Single Patient with NF1-plexiform Neurofibroma. Clin Cancer Res 2015; 21:4201-11. [PMID: 25925892 DOI: 10.1158/1078-0432.ccr-14-3049] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 04/14/2015] [Indexed: 11/16/2022]
Abstract
PURPOSE Malignant peripheral nerve sheath tumors (MPNST) occur at increased frequency in individuals with neurofibromatosis type 1 (NF1), where they likely arise from benign plexiform neurofibroma precursors. While previous studies have used a variety of discovery approaches to discover genes associated with MPNST pathogenesis, it is currently unclear what molecular events are associated with the evolution of MPNST from plexiform neurofibroma. EXPERIMENTAL DESIGN Whole-exome sequencing was performed on biopsy materials representing plexiform neurofibroma (n = 3), MPNST, and metastasis from a single individual with NF1 over a 14-year period. Additional validation cases were used to assess candidate genes involved in malignant progression, while a murine MPNST model was used for functional analysis. RESULTS There was an increasing proportion of cells with a somatic NF1 gene mutation as the tumors progressed from benign to malignant, suggesting a clonal process in MPNST development. Copy number variations, including loss of one copy of the TP53 gene, were identified in the primary tumor and the metastatic lesion, but not in benign precursor lesions. A limited number of genes with nonsynonymous somatic mutations (βIII-spectrin and ZNF208) were discovered, several of which were validated in additional primary and metastatic MPNST samples. Finally, increased βIII-spectrin expression was observed in the majority of MPNSTs, and shRNA-mediated knockdown reduced murine MPNST growth in vivo. CONCLUSIONS Collectively, the ability to track the molecular evolution of MPNST in a single individual with NF1 offers new insights into the sequence of genetic events important for disease pathogenesis and progression for future mechanistic study.
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Affiliation(s)
- Angela C Hirbe
- Division of Medical Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Sonika Dahiya
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Christopher A Miller
- Department of Genetics, The Genome Institute at Washington University, St. Louis, Missouri
| | - Tiandao Li
- Department of Genetics, The Genome Institute at Washington University, St. Louis, Missouri
| | - Robert S Fulton
- Department of Genetics, The Genome Institute at Washington University, St. Louis, Missouri
| | - Xiaochun Zhang
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Sandra McDonald
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Katherine DeSchryver
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Eric J Duncavage
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Jessica Walrath
- Rare Tumors Initiative, National Cancer Institute, Bethesda, Maryland. Division of Statistical Genomics, St. Louis, Missouri
| | - Karlyne M Reilly
- Rare Tumors Initiative, National Cancer Institute, Bethesda, Maryland. Division of Statistical Genomics, St. Louis, Missouri
| | | | - Melike Pekmezci
- Neurological Surgery, UCSF School of Medicine, San Francisco, California
| | - Arie Perry
- Neurological Surgery, UCSF School of Medicine, San Francisco, California. Department of Neurology, Washington University, St. Louis, Missouri
| | - Timothy J Ley
- Department of Genetics, The Genome Institute at Washington University, St. Louis, Missouri
| | - David H Gutmann
- Department of Neurology, Washington University, St. Louis, Missouri.
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