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Tavlas P, Nikou S, Geramoutsou C, Bosgana P, Tsaniras SC, Melachrinou M, Maroulis I, Bravou V. CUL4A Ubiquitin Ligase Is an Independent Predictor of Overall Survival in Pancreatic Adenocarcinoma. Cancer Genomics Proteomics 2024; 21:166-177. [PMID: 38423594 PMCID: PMC10905276 DOI: 10.21873/cgp.20438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/22/2024] [Accepted: 02/06/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND/AIM Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy with dismal prognosis. Genomic instability due to defects in cell-cycle regulation/mitosis or deficient DNA-damage repair is a major driver of PDAC progression with clinical relevance. Deregulation of licensing of DNA replication leads to DNA damage and genomic instability, predisposing cells to malignant transformation. While overexpression of DNA replication-licensing factors has been reported in several human cancer types, their role in PDAC remains largely unknown. We aimed here to examine the expression and prognostic significance of the DNA replication-licensing factors chromatin licensing and DNA replication factor 1 (CDT1), cell-division cycle 6 (CDC6), minichromosome maintenance complex component 7 (MCM7) and also of the ubiquitin ligase regulator of CDT1, cullin 4A (CUL4A), in PDAC. MATERIALS AND METHODS Expression levels of CUL4, CDT1, CDC6 and MCM7 were evaluated by immunohistochemistry in 76 formalin-fixed paraffin-embedded specimens of PDAC patients in relation to DNA-damage response marker H2AX, clinicopathological parameters and survival. We also conducted bioinformatics analysis of data from online available databases to corroborate our findings. RESULTS CUL4A and DNA replication-licensing factors were overexpressed in patients with PDAC and expression of CDT1 positively correlated with H2AX. Expression of CUL4A and CDT1 positively correlated with lymph node metastasis. Importantly, elevated CUL4A expression was associated with reduced overall survival and was an independent indicator of poor prognosis on multivariate analysis. CONCLUSION Our findings implicate CUL4A, CDT1, CDC6 and MCM7 in PDAC progression and identify CUL4A as an independent prognostic factor for this disease.
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Affiliation(s)
- Panagiotis Tavlas
- Department of Anatomy-Histology-Embryology, Medical School, University of Patras, Patras, Greece
- Department of Surgery, University General Hospital of Patras, Patras, Greece
| | - Sofia Nikou
- Department of Anatomy-Histology-Embryology, Medical School, University of Patras, Patras, Greece
| | - Christina Geramoutsou
- Department of Anatomy-Histology-Embryology, Medical School, University of Patras, Patras, Greece
| | - Pinelopi Bosgana
- Department of Pathology, School of Medicine, University of Patras, Patras, Greece
| | - Spyridon Champeris Tsaniras
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, U.S.A
- International Institute of Anticancer Research, Kapandriti, Greece
| | - Maria Melachrinou
- Department of Pathology, School of Medicine, University of Patras, Patras, Greece
| | - Ioannis Maroulis
- Department of Surgery, University General Hospital of Patras, Patras, Greece
| | - Vasiliki Bravou
- Department of Anatomy-Histology-Embryology, Medical School, University of Patras, Patras, Greece;
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Song Y, Ma R. Comprehensive Analysis Reveals the Potential Roles of Transcription Factor Dp-1 in Lung Adenocarcinoma. World J Oncol 2023; 14:205-223. [PMID: 37350808 PMCID: PMC10284640 DOI: 10.14740/wjon1595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/22/2023] [Indexed: 06/24/2023] Open
Abstract
Background Transcription factor Dp-1 (TFDP1) was overexpressed and interacted with other genes to impact multiple signaling pathways in various human cancers. However, there is less research about the TFDP1 specific roles in lung adenocarcinoma (LUAD). Methods We first explored TFDP1 expression levels and relative diseases from a pan-cancer perspective using the ONCOMINE, TIMER, and Open Targets Platform databases. Then, we used UALCAN, GEPIA 2, TCGA-LUAD data, and Kaplan-Meier plotter to examine TFDP1 clinicopathological features and prognosis in LUAD patients. Genomic alterations and DNA methylation analysis were performed by cBioPortal and MethSurv, respectively. Then, we used a cancer single-cell state atlas (CancerSEA) to find TFDP1 functions at a single-cell resolution. LinkedOmics was used to find TFDP1 coexpressed genes, biological processes, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Then, Gene Set Cancer Analysis (GSCA) was used to examine the drug resistence of TFDP1 in LUAD. Results We found that TFDP1 was overexpressed in most human cancers and related to various diseases, including LUAD. Moreover, LUAD patients with high TFDP1 expression levels might be significantly associated with individual cancer stages and have a poor prognosis. Multivariate analysis revealed that the American Joint Committee on Cancer (AJCC) pathologic stage, AJCC stage T, and AJCC stage N were the independent prognostic factors. LUAD patients with TFDP1 alterations suggested poor overall survival (OS), and disease-free survival (DFS), while hypermethylation might lead to a good prognosis. TFDP1 and its coexpressed genes were enriched in multiple signaling pathways and biological processes involved in the cell cycle, spliceosome, and DNA replication. Furthermore, TFDP1 was strongly positively related to the half-maximal inhibitory concentration (IC50) values of multiple drugs. Conclusions In summary, TFDP1 was a possible biomarker and potential therapeutic target for LUAD patients.
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Affiliation(s)
- Yipeng Song
- School of Law and Criminal Justice, East China University of Political Science and Law, Songjiang University Town, Shanghai 201620, China
| | - Rongna Ma
- Shanghai Institute of Blood Transfusion, Shanghai Blood Center, Shanghai 200051, China
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3
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Routh ED, Van Swearingen AED, Sambade MJ, Vensko S, McClure MB, Woodcock MG, Chai S, Cuaboy LA, Wheless A, Garrett A, Carey LA, Hoyle AP, Parker JS, Vincent BG, Anders CK. Comprehensive Analysis of the Immunogenomics of Triple-Negative Breast Cancer Brain Metastases From LCCC1419. Front Oncol 2022; 12:818693. [PMID: 35992833 PMCID: PMC9387304 DOI: 10.3389/fonc.2022.818693] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 05/30/2022] [Indexed: 11/23/2022] Open
Abstract
Background Triple negative breast cancer (TNBC) is an aggressive variant of breast cancer that lacks the expression of estrogen and progesterone receptors (ER and PR) and HER2. Nearly 50% of patients with advanced TNBC will develop brain metastases (BrM), commonly with progressive extracranial disease. Immunotherapy has shown promise in the treatment of advanced TNBC; however, the immune contexture of BrM remains largely unknown. We conducted a comprehensive analysis of TNBC BrM and matched primary tumors to characterize the genomic and immune landscape of TNBC BrM to inform the development of immunotherapy strategies in this aggressive disease. Methods Whole-exome sequencing (WES) and RNA sequencing were conducted on formalin-fixed, paraffin-embedded samples of BrM and primary tumors of patients with clinical TNBC (n = 25, n = 9 matched pairs) from the LCCC1419 biobank at UNC—Chapel Hill. Matched blood was analyzed by DNA sequencing as a comparison for tumor WES for the identification of somatic variants. A comprehensive genomics assessment, including mutational and copy number alteration analyses, neoantigen prediction, and transcriptomic analysis of the tumor immune microenvironment were performed. Results Primary and BrM tissues were confirmed as TNBC (23/25 primaries, 16/17 BrM) by immunohistochemistry and of the basal intrinsic subtype (13/15 primaries and 16/19 BrM) by PAM50. Compared to primary tumors, BrM demonstrated a higher tumor mutational burden. TP53 was the most frequently mutated gene and was altered in 50% of the samples. Neoantigen prediction showed elevated cancer testis antigen- and endogenous retrovirus-derived MHC class I-binding peptides in both primary tumors and BrM and predicted that single-nucleotide variant (SNV)-derived peptides were significantly higher in BrM. BrM demonstrated a reduced immune gene signature expression, although a signature associated with fibroblast-associated wound healing was elevated in BrM. Metrics of T and B cell receptor diversity were also reduced in BrM. Conclusions BrM harbored higher mutational burden and SNV-derived neoantigen expression along with reduced immune gene signature expression relative to primary TNBC. Immune signatures correlated with improved survival, including T cell signatures. Further research will expand these findings to other breast cancer subtypes in the same biobank. Exploration of immunomodulatory approaches including vaccine applications and immune checkpoint inhibition to enhance anti-tumor immunity in TNBC BrM is warranted.
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Affiliation(s)
- Eric D. Routh
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Amanda E. D. Van Swearingen
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Maria J. Sambade
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Steven Vensko
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Marni B. McClure
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- National Cancer Center Research Institute, Tokyo, Japan
| | - Mark G. Woodcock
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Medicine, Division of Medical Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Shengjie Chai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine, Chapel Hill, NC, United States
| | - Luz A. Cuaboy
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Amy Wheless
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Amy Garrett
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Lisa A. Carey
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Medicine, Division of Medical Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Alan P. Hoyle
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Joel S. Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Benjamin G. Vincent
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Medicine, Division of Medical Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Curriculum in Bioinformatics and Computational Biology, UNC School of Medicine, Chapel Hill, NC, United States
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Division of Hematology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Carey K. Anders
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Medicine, Division of Medical Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- *Correspondence: Carey K. Anders,
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Taylor AM, Sun JM, Yu A, Voicu H, Shen J, Barkauskas DA, Triche TJ, Gastier-Foster JM, Man TK, Lau CC. Integrated DNA Copy Number and Expression Profiling Identifies IGF1R as a Prognostic Biomarker in Pediatric Osteosarcoma. Int J Mol Sci 2022; 23:ijms23148036. [PMID: 35887382 PMCID: PMC9319262 DOI: 10.3390/ijms23148036] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/17/2022] [Accepted: 07/18/2022] [Indexed: 11/25/2022] Open
Abstract
Osteosarcoma is a primary malignant bone tumor arising from bone-forming mesenchymal cells in children and adolescents. Despite efforts to understand the biology of the disease and identify novel therapeutics, the survival of osteosarcoma patients remains dismal. We have concurrently profiled the copy number and gene expression of 226 osteosarcoma samples as part of the Strategic Partnering to Evaluate Cancer Signatures (SPECS) initiative. Our results demonstrate the heterogeneous landscape of osteosarcoma in younger populations by showing the presence of genome-wide copy number abnormalities occurring both recurrently among samples and in a high frequency. Insulin growth factor receptor 1 (IGF1R) is a receptor tyrosine kinase which binds IGF1 and IGF2 to activate downstream pathways involved in cell apoptosis and proliferation. We identify prevalent amplification of IGF1R corresponding with increased gene expression in patients with poor survival outcomes. Our results substantiate previously tenuously associated copy number abnormalities identified in smaller datasets (13q34+, 20p13+, 4q35-, 20q13.33-), and indicate the significance of high fibroblast growth factor receptor 2 (FGFR2) expression in distinguishing patients with poor prognosis. FGFR2 is involved in cellular proliferation processes such as division, growth and angiogenesis. In summary, our findings demonstrate the prognostic significance of several genes associated with osteosarcoma pathogenesis.
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Affiliation(s)
- Aaron M. Taylor
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA;
- Department of Pediatrics-Oncology, Baylor College of Medicine, Houston, TX 77030, USA; (J.M.S.); (A.Y.); (J.S.); (T.-K.M.)
- Program of Quantitative & Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jiayi M. Sun
- Department of Pediatrics-Oncology, Baylor College of Medicine, Houston, TX 77030, USA; (J.M.S.); (A.Y.); (J.S.); (T.-K.M.)
- Program of Quantitative & Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alexander Yu
- Department of Pediatrics-Oncology, Baylor College of Medicine, Houston, TX 77030, USA; (J.M.S.); (A.Y.); (J.S.); (T.-K.M.)
| | - Horatiu Voicu
- Dan L. Duncan Cancer Center-Bioinformatics, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Jianhe Shen
- Department of Pediatrics-Oncology, Baylor College of Medicine, Houston, TX 77030, USA; (J.M.S.); (A.Y.); (J.S.); (T.-K.M.)
| | - Donald A. Barkauskas
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA;
| | - Timothy J. Triche
- Pathology and Laboratory Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA;
| | | | - Tsz-Kwong Man
- Department of Pediatrics-Oncology, Baylor College of Medicine, Houston, TX 77030, USA; (J.M.S.); (A.Y.); (J.S.); (T.-K.M.)
- Dan L. Duncan Cancer Center-Bioinformatics, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Ching C. Lau
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA;
- Department of Pediatrics-Oncology, Baylor College of Medicine, Houston, TX 77030, USA; (J.M.S.); (A.Y.); (J.S.); (T.-K.M.)
- Program of Quantitative & Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L. Duncan Cancer Center-Bioinformatics, Baylor College of Medicine, Houston, TX 77030, USA;
- Cancer and Hematology Center, Texas Children’s Hospital, Houston, TX 77030, USA;
- Correspondence: ; Tel.: +1-207-288-6000
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5
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Takeuchi Y, Yoshida K, Halik A, Kunitz A, Suzuki H, Kakiuchi N, Shiozawa Y, Yokoyama A, Inoue Y, Hirano T, Yoshizato T, Aoki K, Fujii Y, Nannya Y, Makishima H, Pfitzner BM, Bullinger L, Hirata M, Jinnouchi K, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Okamoto T, Haga H, Ogawa S, Damm F. The landscape of genetic aberrations in myxofibrosarcoma. Int J Cancer 2022; 151:565-577. [PMID: 35484982 DOI: 10.1002/ijc.34051] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/25/2022] [Accepted: 04/08/2022] [Indexed: 11/08/2022]
Abstract
Myxofibrosarcoma (MFS) is a rare subtype of sarcoma, whose genetic basis is poorly understood. We analyzed 69 MFS cases using whole-genome (WGS), whole-exome (WES), and/or targeted-sequencing (TS). Newly sequenced genomic data were combined with additional deposited 116 MFS samples. WGS identified a high number of structural variations (SVs) per tumor most frequently affecting the TP53 and RB1 loci, 40% of tumors showed a BRCAness-associated mutation signature, and evidence of chromothripsis was found in all cases. Most frequently mutated /copy number altered genes affected known disease drivers such as TP53 (56.2%), CDKN2A/B (29.7%), RB1 (27.0%), ATRX (19.5%), and HDLBP (18.9%). Several previously unappreciated genetic aberrations including MUC17, FLG, and ZNF780A were identified in more than 20% of patients. Longitudinal analysis of paired diagnosis and relapse time points revealed a 1.2-fold mutation number increase accompanied with substantial changes in clonal composition over time. This study highlights the genetic complexity underlying sarcomagenesis of MFS. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yasuhide Takeuchi
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.,Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan.,Research Fellowships of Japan Society for the Promotion of Science for Young Scientists
| | - Kenichi Yoshida
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Adriane Halik
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Annegret Kunitz
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Hiromichi Suzuki
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Nobuyuki Kakiuchi
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Yusuke Shiozawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akira Yokoyama
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshikage Inoue
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Tomonori Hirano
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Tetsuichi Yoshizato
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kosuke Aoki
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoichi Fujii
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Yasuhito Nannya
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Hideki Makishima
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | | | - Lars Bullinger
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Masahiro Hirata
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
| | - Keita Jinnouchi
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
| | - Yuichi Shiraishi
- Center for Cancer Genomic and Advanced Therapeutics, National Cancer Center, Tokyo, Japan
| | - Kenichi Chiba
- Center for Cancer Genomic and Advanced Therapeutics, National Cancer Center, Tokyo, Japan
| | - Hiroko Tanaka
- M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Satoru Miyano
- M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takeshi Okamoto
- Department of Orthopaedic Surgery, Kyoto University Hospital, Kyoto, Japan
| | - Hironori Haga
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.,Department of Medicine, Centre for Haematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Frederik Damm
- Department of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
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6
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Lung J, Chen YC, Lin YC, Li YC, You L, Jablons DM, Mao JH, Yang CT, Hung MS. The effect of cullin 4A on lung cancer cell chemosensitivity to paclitaxel through p33ING1b regulation. Am J Transl Res 2021; 13:11194-11208. [PMID: 34786051 PMCID: PMC8581858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 08/12/2021] [Indexed: 06/13/2023]
Abstract
Cullin 4A (Cul4A) reportedly has oncogenic roles in several cancer types by regulating tumor suppressors through the ubiquitination and proteolysis of the tumor suppressor. In addition, Cul4A is associated with chemosensitivity to chemotherapy drugs. This study investigated the association between Cul4A and lung cancer cell chemosensitivity to paclitaxel, particularly with respect to the role of the p33 inhibitor of the growth 1 (p33ING1b) tumor suppressor. The results showed that the Cul4A knockdown upregulated the p33ING1b expression in lung cancer cells and increased the lung cancer cell and mice tumor xenograft chemosensitivity to paclitaxel. The Cul4A knockdown also inhibited the growth and increased the apoptosis in the tumor xenografts treated with paclitaxel. Notably, the p33ING1b overexpression increased the lung cancer cell chemosensitivity to paclitaxel, but the p33ING1b knockdown reduced the chemosensitivity. A further analysis demonstrated that Cul4A regulates the expression of p33ING1b through protein-protein interactions, ubiquitination, and protein degradation. In conclusion, the present findings suggest that Cul4A mediates the chemosensitivity of lung cancer cells to paclitaxel by regulating p33ING1b. These findings may offer novel insights into future therapeutic strategies for lung cancer that target Cul4A.
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Affiliation(s)
- Jrhau Lung
- Department of Medical Research, Chang Gung Memorial Hospital, Chiayi BranchChiayi 61363, Taiwan
| | - Yi-Chuan Chen
- Department of Emergency Medicine, Madou Sin-Lau Hospital, The Presbyterian Church in TaiwanTainan 72100, Taiwan
| | - Yu-Ching Lin
- Department of Medicine, College of Medicine, Chang Gung UniversityTaoyuan 33323, Taiwan
- Department of Pulmonary and Critical Care Medicine, Chang Gung Memorial Hospital, Chiayi BranchChiayi 61363, Taiwan
- Department of Respiratory Care, Chang Gung University of Science and Technology, Chiayi CampusChiayi 61363, Taiwan
| | - Ya-Chin Li
- Department of Pulmonary and Critical Care Medicine, Chang Gung Memorial Hospital, Chiayi BranchChiayi 61363, Taiwan
| | - Liang You
- Thoracic Oncology Laboratory, Department of Surgery, Comprehensive Cancer Center, University of CaliforniaSan Francisco, CA 94143, USA
| | - David M Jablons
- Thoracic Oncology Laboratory, Department of Surgery, Comprehensive Cancer Center, University of CaliforniaSan Francisco, CA 94143, USA
| | - Jian-Hua Mao
- Lawrence Berkeley National Laboratory, Life Sciences DivisionOne Cyclotron Road, Berkeley, California, CA 94720, USA
| | - Cheng-Ta Yang
- Department of Respiratory Care, College of Medicine, Chang Gung UniversityTaoyuan 33323, Taiwan
- Department of Pulmonary and Critical Care Medicine, Chang Gung Memorial Hospital, Taoyuan BranchTaoyuan 33378, Taiwan
| | - Ming-Szu Hung
- Department of Medicine, College of Medicine, Chang Gung UniversityTaoyuan 33323, Taiwan
- Department of Pulmonary and Critical Care Medicine, Chang Gung Memorial Hospital, Chiayi BranchChiayi 61363, Taiwan
- Department of Respiratory Care, Chang Gung University of Science and Technology, Chiayi CampusChiayi 61363, Taiwan
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7
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A novel amplification gene PCI domain containing 2 (PCID2) promotes colorectal cancer through directly degrading a tumor suppressor promyelocytic leukemia (PML). Oncogene 2021; 40:6641-6652. [PMID: 34625711 PMCID: PMC8660639 DOI: 10.1038/s41388-021-01941-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 06/18/2021] [Accepted: 07/01/2021] [Indexed: 11/25/2022]
Abstract
Using whole genome sequencing, PCI Domain Containing 2 (PCID2) was identified to be amplified in colorectal cancer (CRC). In this study, we investigated the expression, biological function, molecular mechanism, and clinical implication of PCID2 in CRC. PCID2 mRNA and protein expression were higher in CRC cells and tumor tissues compared to healthy colonic tissues. The copy number of PCID2 was positively correlated with its mRNA expression. Multivariate analysis revealed that PCID2 is an independent prognostic factor for CRC recurrence. Functional studies showed that PCID2 promoted cell growth, cell cycle progression, and cell migration/invasion, while apoptosis was suppressed. Moreover, PCID2 promoted xenograft growth and lung metastasis in nude mice. Using co-immunoprecipitation and mass spectroscopy, we showed that PCID2 binds to promyelocytic leukemia (PML), a tumor suppressor involved in non-canonical β-catenin signaling. PCID2 promoted the degradation of PML via poly-ubiquitination, which in turn, induced Wnt/β-catenin signaling while simultaneously repressing ARF-p53 pathway. Thus, these results demonstrated that PCID2 functions as an oncogene in CRC by enhancing canonical Wnt/β-catenin signaling and inhibition of CTNNB1-ARF-p53 axis. PCID2 promoted canonical Wnt/β-catenin signaling in CRC via degradation of PML. PCID2 may serve as an independent prediction marker for CRC recurrence.
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8
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Wang Y, Yan F, Nasar A, Chen ZS, Altorki NK, Stiles B, Narula N, Zhou P. CUL4 high Lung Adenocarcinomas Are Dependent on the CUL4-p21 Ubiquitin Signaling for Proliferation and Survival. THE AMERICAN JOURNAL OF PATHOLOGY 2021; 191:1638-1650. [PMID: 34119472 PMCID: PMC8420861 DOI: 10.1016/j.ajpath.2021.05.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 05/16/2021] [Accepted: 05/21/2021] [Indexed: 11/20/2022]
Abstract
Cullin (CUL) 4A and 4B ubiquitin ligases are often highly accumulated in human malignant neoplasms and are believed to possess oncogenic properties. However, the underlying mechanisms by which CUL4A and CUL4B promote pulmonary tumorigenesis remain largely elusive. This study reports that CUL4A and CUL4B are highly expressed in patients with non-small cell lung cancer (NSCLC), and their high expression is associated with disease progression, chemotherapy resistance, and poor survival in adenocarcinomas. Depletion of CUL4A (CUL4Ak/d) or CUL4B (CUL4Bk/d) leads to cell cycle arrest at G1 and loss of proliferation and viability of NSCLC cells in culture and in a lung cancer xenograft model, suggesting that CUL4A and 4B are oncoproteins required for tumor maintenance of certain NSCLCs. Mechanistically, increased accumulation of the cell cycle-dependent kinase inhibitor p21/Cip1/WAF1 was observed in lung cancer cells on CUL4 silencing. Knockdown of p21 rescued the G1 arrest of CUL4Ak/d or CUL4Bk/d NSCLC cells, and allowed proliferation to resume. These findings reveal that p21 is the primary downstream effector of lung adenocarcinoma dependence on CUL4, highlight the notion that not all substrates respond equally to abrogation of the CUL4 ubiquitin ligase in NSCLCs, and imply that CUL4Ahigh/CUL4Bhigh may serve as a prognostic marker and therapeutic target for patients with NSCLC.
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Affiliation(s)
- Yannan Wang
- Department of Pathology and Laboratory Medicine, The Joan and Stanford I. Weill Medical College of Cornell University, New York, New York
| | - Fan Yan
- Department of Pathology and Laboratory Medicine, The Joan and Stanford I. Weill Medical College of Cornell University, New York, New York
| | - Abu Nasar
- Division of Thoracic Surgery, Department of Cardiothoracic Surgery, Weill Cornell Medicine - New York Presbyterian Hospital, New York, New York
| | - Zhe-Sheng Chen
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St John's University, Queens, New York
| | - Nasser Khaled Altorki
- Division of Thoracic Surgery, Department of Cardiothoracic Surgery, Weill Cornell Medicine - New York Presbyterian Hospital, New York, New York
| | - Brendon Stiles
- Division of Thoracic Surgery, Department of Cardiothoracic Surgery, Weill Cornell Medicine - New York Presbyterian Hospital, New York, New York
| | - Navneet Narula
- Department of Pathology and Laboratory Medicine, The Joan and Stanford I. Weill Medical College of Cornell University, New York, New York
| | - Pengbo Zhou
- Department of Pathology and Laboratory Medicine, The Joan and Stanford I. Weill Medical College of Cornell University, New York, New York.
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9
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Wang Q, Li J, Wang S, Deng Q, Wang K, Dai X, An Y, Dong G, Ke W, Chen F, Liu L, Yang H, Du Y, Zhao W, Shang Z. Single-cell transcriptome profiling reveals molecular heterogeneity in human umbilical cord tissue and culture-expanded mesenchymal stem cells. FEBS J 2021; 288:5311-5330. [PMID: 33763993 DOI: 10.1111/febs.15834] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/24/2021] [Accepted: 03/22/2021] [Indexed: 01/08/2023]
Abstract
Human umbilical cord-derived mesenchymal stem/stromal cells (UMSCs) demonstrate great therapeutic potential in regenerative medicine. The use of UMSCs for clinical applications requires high quantity and good quality of cells usually by in vitro expansion. However, the heterogeneity and the characteristics of cultured UMSCs and the cognate human umbilical cord tissue at single-cell resolution remain poorly defined. In this study, we created a single-cell transcriptome profile of human umbilical cord tissue and the cognate culture-expanded UMSCs. Based on the inferred characteristics of cell clusters and trajectory analysis, we identified three subgroups in culture-expanded UMSCs and putative novel transcription factors (TFs) in regulating UMSC state transition. Further, putative ligand-receptor interaction analysis demonstrated that cellular interactions most frequently occurred in epithelial-like cells with other cell groups in umbilical cord tissue. Moreover, we dissected the transcriptomic differences of in vitro and in vivo subgroups and inferred the telomere-related molecules and pathways that might be activated in UMSCs for cell expansion in vitro. Our study provides a comprehensive and integrative study of the transcriptomics of human umbilical cord tissue and their cognate-cultured counterparts, which paves the way for a deeper understanding of cellular heterogeneity and offers fundamental biological insight of UMSCs-based cell therapy.
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Affiliation(s)
- Quanlei Wang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, China.,Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics, BGI-Shenzhen, China
| | - Jinlu Li
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, China
| | - Shengpeng Wang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, China
| | - Qiuting Deng
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, China
| | - Kuixing Wang
- BGI-Shenzhen, China.,Shenzhen BGI Cell Technology Co., Ltd, China
| | - Xi Dai
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, China
| | | | - Guoyi Dong
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, China
| | - Weilin Ke
- Department of Obstetrics, Shenzhen Second People's Hospital, Shenzhen University 1st Affiliated Hospital, China
| | - Fang Chen
- BGI-Shenzhen, China.,MGI, BGI-Shenzhen, China
| | | | - Huanming Yang
- BGI-Shenzhen, China.,James D. Watson Institute of Genome Sciences, Hangzhou, China
| | | | - Weihua Zhao
- Department of Obstetrics, Shenzhen Second People's Hospital, Shenzhen University 1st Affiliated Hospital, China
| | - Zhouchun Shang
- BGI-Shenzhen, China.,Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics, BGI-Shenzhen, China.,MGI, BGI-Shenzhen, China.,BGI College, Northwest University, Xi'an, China
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10
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Erbaba B, Arslan-Ergul A, Adams MM. Effects of caloric restriction on the antagonistic and integrative hallmarks of aging. Ageing Res Rev 2021; 66:101228. [PMID: 33246078 DOI: 10.1016/j.arr.2020.101228] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 11/09/2020] [Accepted: 11/19/2020] [Indexed: 12/19/2022]
Abstract
Aging is a significant risk factor for cognitive decline associated with neurodegenerative diseases, which makes understanding what promotes 'healthy brain aging' very important. Studies suggest that caloric restriction (CR) is a non-genetic intervention that reliably extends life- and healthspan. Here, we review the CR literature related to both the subject of aging and alterations in cell cycle machinery, especially surrounding the regulation of the E2F/DP1 complex, to elucidate the cellular protection mechanisms in the brain induced via dietary applications. The alterations extending lifespan via CR appear to exert their effects by promoting survival of individual cells, downregulating cell proliferation, and inducing stem cell quiescence, which results in keeping the stem cell reserve for extreme needs. This survival instinct of cells is believed to cause some molecular adaptations for their maintenance of the system. Avoiding energy waste of proliferation machinery promotes the long term survival of the individual cells and this is due to adaptations to the limited nutrient supply in the environment. Such a protective mechanism induced by diet could be promoted via the downregulation of crucial cell cycle-related transcription activators. This review article aims to bring attention to the importance of molecular adaptations induced by diet that promote healthy brain aging. It will provide insights into alternative targets for new treatments or neuroprotective approaches against neurodegenerative pathophysiologies.
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Affiliation(s)
- Begun Erbaba
- Interdisciplinary Graduate Program in Neuroscience, Aysel Sabuncu Brain Research Center, Bilkent University, Ankara, Turkey; National Nanotechnology Research Center (UNAM), Bilkent University, Ankara, Turkey
| | - Ayca Arslan-Ergul
- National Nanotechnology Research Center (UNAM), Bilkent University, Ankara, Turkey
| | - Michelle M Adams
- Interdisciplinary Graduate Program in Neuroscience, Aysel Sabuncu Brain Research Center, Bilkent University, Ankara, Turkey; National Nanotechnology Research Center (UNAM), Bilkent University, Ankara, Turkey; Department of Psychology, Bilkent University, Ankara, Turkey.
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11
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Weng SW, Liu TT, Eng HL, You HL, Huang WT. Autophagy Plays a Role in the CUL4A-Related Poor Prognosis of Intrahepatic Cholangiocarcinoma. Pathol Oncol Res 2021; 27:602714. [PMID: 34257560 PMCID: PMC8262180 DOI: 10.3389/pore.2021.602714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 01/22/2021] [Indexed: 11/13/2022]
Abstract
CUL4A regulate the termination of autophagy in a physical process. However, the relationship between CUL4A and autophagy in cancer is unclear. We retrospectively investigated 99 intrahepatic cholangiocarcinoma (iCCA) cases. Whole sections were used for immunohistochemical analysis for p62, and LC3B expression. Q-score was defined as the sum of the labeling intensity and proportion. The cut-off point for immunoreactivity was set. CUL4A was overexpressed in cell lines and autophagy reflux was compared after manipulation. The iCCA cases with CUL4A overexpression had significantly higher prevalence of intact activated autophagy (42.4 vs. 15.2%; p = 0.003), which was significantly associated with advance tumor stage (34.1% vs. 15.4%; p = 0.032), less extensive necrosis (8.3 vs. 49.3%; p < 0.001), and shortened disease-free survival (mean, 19.6 vs. 65.5 months, p = 0.015). In vitro, iCCA cells with CUL4A overexpression significantly increased LC3II level as compared to the cells under basal condition. Although both cell types showed intact autophagy with increased LC3II expression after bafilomycin A1 treatment, the accumulation of LC3II was higher in CUL4A-overexpressing cells. CUL4A overexpression increased the proliferation of cells as compared with control cells. After treatment with bafilomycin A1, proliferation was inhibited in both cell types, but the effects were more prominent in the cells overexpressing CUL4A. CUL4A promotes autophagy, and exhibits significantly higher autophagic flux which affects the proliferation of iCCA cells; these effects correlated with advance tumor stage and poor prognosis. Thus, targeting autophagy may be potentially therapeutic in iCCA.
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Affiliation(s)
- Shao-Wen Weng
- Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Ting-Ting Liu
- Department of Pathology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Medical Laboratory Science, I-Shou University, Kaohsiung, Taiwan
| | - Hock-Liew Eng
- Department of Pathology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Huey-Ling You
- Department of Laboratory Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Medical Laboratory Sciences and Biotechnology, Fooyin University, Kaohsiung, Taiwan
| | - Wan-Ting Huang
- Department of Pathology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Laboratory Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Medical Laboratory Sciences and Biotechnology, Fooyin University, Kaohsiung, Taiwan
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12
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Charan M, Verma AK, Hussain S, Misri S, Mishra S, Majumder S, Ramaswamy B, Ahirwar D, Ganju RK. Molecular and Cellular Factors Associated with Racial Disparity in Breast Cancer. Int J Mol Sci 2020; 21:ijms21165936. [PMID: 32824813 PMCID: PMC7460595 DOI: 10.3390/ijms21165936] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/10/2020] [Accepted: 08/13/2020] [Indexed: 02/06/2023] Open
Abstract
Recent studies have demonstrated that racial differences can influence breast cancer incidence and survival rate. African American (AA) women are at two to three fold higher risk for breast cancer than other ethnic groups. AA women with aggressive breast cancers show worse prognoses and higher mortality rates relative to Caucasian (CA) women. Over the last few years, effective treatment strategies have reduced mortality from breast cancer. Unfortunately, the breast cancer mortality rate among AA women remains higher compared to their CA counterparts. The focus of this review is to underscore the racial differences and differential regulation/expression of genetic signatures in CA and AA women with breast cancer. Moreover, immune cell infiltration significantly affects the clinical outcome of breast cancer. Here, we have reviewed recent findings on immune cell recruitment in the tumor microenvironment (TME) and documented its association with breast cancer racial disparity. In addition, we have extensively discussed the role of cytokines, chemokines, and other cell signaling molecules among AA and CA breast cancer patients. Furthermore, we have also reviewed the distinct genetic and epigenetic changes in AA and CA patients. Overall, this review article encompasses various molecular and cellular factors associated with breast cancer disparity that affects mortality and clinical outcome.
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Affiliation(s)
- Manish Charan
- Department of Pathology, Ohio State University, Columbus, OH 43210, USA; (M.C.); (A.K.V.); (S.H.); (S.M.); (S.M.)
| | - Ajeet K. Verma
- Department of Pathology, Ohio State University, Columbus, OH 43210, USA; (M.C.); (A.K.V.); (S.H.); (S.M.); (S.M.)
| | - Shahid Hussain
- Department of Pathology, Ohio State University, Columbus, OH 43210, USA; (M.C.); (A.K.V.); (S.H.); (S.M.); (S.M.)
| | - Swati Misri
- Department of Pathology, Ohio State University, Columbus, OH 43210, USA; (M.C.); (A.K.V.); (S.H.); (S.M.); (S.M.)
| | - Sanjay Mishra
- Department of Pathology, Ohio State University, Columbus, OH 43210, USA; (M.C.); (A.K.V.); (S.H.); (S.M.); (S.M.)
| | - Sarmila Majumder
- Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA; (S.M.); (B.R.)
| | - Bhuvaneswari Ramaswamy
- Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA; (S.M.); (B.R.)
| | - Dinesh Ahirwar
- Department of Pathology, Ohio State University, Columbus, OH 43210, USA; (M.C.); (A.K.V.); (S.H.); (S.M.); (S.M.)
- Correspondence: (D.A.); (R.K.G.)
| | - Ramesh K. Ganju
- Department of Pathology, Ohio State University, Columbus, OH 43210, USA; (M.C.); (A.K.V.); (S.H.); (S.M.); (S.M.)
- Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA; (S.M.); (B.R.)
- Correspondence: (D.A.); (R.K.G.)
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13
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Identification of the aberrantly methylated differentially expressed genes in proliferative diabetic retinopathy. Exp Eye Res 2020; 199:108141. [PMID: 32721427 DOI: 10.1016/j.exer.2020.108141] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 06/21/2020] [Accepted: 07/03/2020] [Indexed: 11/23/2022]
Abstract
Diabetic retinopathy (DR) is the most common complication of diabetes. Proliferative DR (PDR) is a more advanced stage of DR, which can cause severe impaired vision and even blindness. However, the precise pathological mechanisms of PDR remain unknown. DNA methylation serves an important role in the initiation and progression of numerous types of disease including PDR. The purpose of this study was to identify the aberrantly methylated differentially expressed genes (DEGs) as potential therapeutic targets of PDR. The gene expression microarray dataset GSE60436 and the methylation profiling microarray dataset GSE57362 were used to determine the aberrantly methylated DEGs in PDR, utilizing normal retinas as controls and fibrovascular membranes (FVMs) in patients with PDR as PDR samples. The functional term and signaling pathway enrichment analysis of the selected genes were subsequently performed. In addition, protein-protein interaction (PPI) networks were constructed to determine the hub genes, and the network of transcriptional factor (TF) and target hub genes was also analyzed. In total, 132 hypomethylated genes were found to be upregulated, whereas 172 hypermethylated genes were discovered to be downregulated in PDR. The hypomethylated upregulated genes were found to be enriched in the pathways, such as "cell-substrate adhesion", "adherens junction", "cell adhesion molecule binding" and "extracellular matrix receptor interactions". Meanwhile, the hypermethylated downregulated genes were enriched in the pathways, such as "visual perception", "presynapse" and the "synaptic vesicle cycle". Based on the PPI analysis, a total of eight hub genes were identified: CTGF, SERPINH1, LOX, RBP3, OTX2, RPE65, OPN1SW and NRL. It was hypothesized that the aberrant methylation of these genes might be related to the possible pathophysiology of PDR. An important transcriptional factor, TFDP1, was discovered to share the closest interactions with the hub genes from the gene-TF network. In conclusion, the present study identified an association among DNA methylation and gene expression in PDR using bioinformatics analysis, and identified the hub genes which might be potential methylation-based diagnosis and treatment targets for PDR in the near future.
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14
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Eyler CE, Matsunaga H, Hovestadt V, Vantine SJ, van Galen P, Bernstein BE. Single-cell lineage analysis reveals genetic and epigenetic interplay in glioblastoma drug resistance. Genome Biol 2020; 21:174. [PMID: 32669109 PMCID: PMC7364565 DOI: 10.1186/s13059-020-02085-1] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 06/25/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Tumors can evolve and adapt to therapeutic pressure by acquiring genetic and epigenetic alterations that may be transient or stable. A precise understanding of how such events contribute to intratumoral heterogeneity, dynamic subpopulations, and overall tumor fitness will require experimental approaches to prospectively label, track, and characterize resistant or otherwise adaptive populations at the single-cell level. In glioblastoma, poor efficacy of receptor tyrosine kinase (RTK) therapies has been alternatively ascribed to genetic heterogeneity or to epigenetic transitions that circumvent signaling blockade. RESULTS We combine cell lineage barcoding and single-cell transcriptomics to trace the emergence of drug resistance in stem-like glioblastoma cells treated with RTK inhibitors. Whereas a broad variety of barcoded lineages adopt a Notch-dependent persister phenotype that sustains them through early drug exposure, rare subclones acquire genetic changes that enable their rapid outgrowth over time. Single-cell analyses reveal that these genetic subclones gain copy number amplifications of the insulin receptor substrate-1 and substrate-2 (IRS1 or IRS2) loci, which activate insulin and AKT signaling programs. Persister-like cells and genomic amplifications of IRS2 and other loci are evident in primary glioblastomas and may underlie the inefficacy of targeted therapies in this disease. CONCLUSIONS A method for combined lineage tracing and scRNA-seq reveals the interplay between complementary genetic and epigenetic mechanisms of resistance in a heterogeneous glioblastoma tumor model.
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Affiliation(s)
- Christine E. Eyler
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA USA
- Broad Institute of Harvard and MIT, Cambridge, MA USA
| | - Hironori Matsunaga
- Broad Institute of Harvard and MIT, Cambridge, MA USA
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA USA
| | - Volker Hovestadt
- Broad Institute of Harvard and MIT, Cambridge, MA USA
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA USA
| | - Samantha J. Vantine
- Broad Institute of Harvard and MIT, Cambridge, MA USA
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA USA
| | - Peter van Galen
- Broad Institute of Harvard and MIT, Cambridge, MA USA
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA USA
| | - Bradley E. Bernstein
- Broad Institute of Harvard and MIT, Cambridge, MA USA
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA USA
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15
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Abstract
Cullin 4A (CUL4A) is a protein of E3 ubiquitin ligase with many cellular processes. CUL4A could regulate cell cycle, development, apoptosis, and genome instability. This study aimed to analyze the expression of CUL4A in nasopharyngeal carcinoma (NPC) tissues and the associations of CUL4A expression with prognostic significance. A total of 115 NPC patients were collected to assess the protein expression of CUL4A by immunohistochemistry, so as to analyze the relationships between CUL4A expression and clinicopathological and prognostic parameters. All patients were followed-up until death or 5 years. The results showed that high expression of CUL4A was significantly associated with larger primary tumor size (P = .026), higher nodal status (P = .013), more distant metastasis (P = .020), and higher TNM stage (P = .005). Kaplan-Meier curves showed that patients with higher CUL4A expression had significantly shorter overall survival (OS) and progression-free survival (PFS) (both P < .001). In multivariate Cox analysis, CUL4A is an independent prognostic factor for OS (P = .016; hazard ratio [HR] = 2.770, 95% CI: 1.208-6.351) and PFS (P = .022; HR = 2.311, 95% CI: 1.126-4.743). In conclusion, high expression of CUL4A was associated with advanced disease status of NPC, and might serve as an independent prognostic factor.
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16
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Fouad S, Wells OS, Hill MA, D'Angiolella V. Cullin Ring Ubiquitin Ligases (CRLs) in Cancer: Responses to Ionizing Radiation (IR) Treatment. Front Physiol 2019; 10:1144. [PMID: 31632280 PMCID: PMC6781834 DOI: 10.3389/fphys.2019.01144] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 08/22/2019] [Indexed: 12/19/2022] Open
Abstract
Treatment with ionizing radiation (IR) remains the cornerstone of therapy for multiple cancer types, including disseminated and aggressive diseases in the palliative setting. Radiotherapy efficacy could be improved in combination with drugs that regulate the ubiquitin-proteasome system (UPS), many of which are currently being tested in clinical trials. The UPS operates through the covalent attachment of ATP-activated ubiquitin molecules onto substrates following the transfer of ubiquitin from an E1, to an E2, and then to the substrate via an E3 enzyme. The specificity of ubiquitin ligation is dictated by E3 ligases, which select substrates to be ubiquitylated. Among the E3s, cullin ring ubiquitin ligases (CRLs) represent prototypical multi-subunit E3s, which use the cullin subunit as a central assembling scaffold. CRLs have crucial roles in controlling the cell cycle, hypoxia signaling, reactive oxygen species clearance and DNA repair; pivotal factors regulating the cancer and normal tissue response to IR. Here, we summarize the findings on the involvement of CRLs in the response of cancer cells to IR, and we discuss the therapeutic approaches to target the CRLs which could be exploited in the clinic.
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Affiliation(s)
- Shahd Fouad
- Medical Research Council Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Owen S Wells
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Mark A Hill
- Medical Research Council Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Vincenzo D'Angiolella
- Medical Research Council Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, United Kingdom
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17
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Cui ZJ, Zhou XH, Zhang HY. DNA Methylation Module Network-Based Prognosis and Molecular Typing of Cancer. Genes (Basel) 2019; 10:genes10080571. [PMID: 31357729 PMCID: PMC6722866 DOI: 10.3390/genes10080571] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/11/2019] [Accepted: 07/26/2019] [Indexed: 12/25/2022] Open
Abstract
Achieving cancer prognosis and molecular typing is critical for cancer treatment. Previous studies have identified some gene signatures for the prognosis and typing of cancer based on gene expression data. Some studies have shown that DNA methylation is associated with cancer development, progression, and metastasis. In addition, DNA methylation data are more stable than gene expression data in cancer prognosis. Therefore, in this work, we focused on DNA methylation data. Some prior researches have shown that gene modules are more reliable in cancer prognosis than are gene signatures and that gene modules are not isolated. However, few studies have considered cross-talk among the gene modules, which may allow some important gene modules for cancer to be overlooked. Therefore, we constructed a gene co-methylation network based on the DNA methylation data of cancer patients, and detected the gene modules in the co-methylation network. Then, by permutation testing, cross-talk between every two modules was identified; thus, the module network was generated. Next, the core gene modules in the module network of cancer were identified using the K-shell method, and these core gene modules were used as features to study the prognosis and molecular typing of cancer. Our method was applied in three types of cancer (breast invasive carcinoma, skin cutaneous melanoma, and uterine corpus endometrial carcinoma). Based on the core gene modules identified by the constructed DNA methylation module networks, we can distinguish not only the prognosis of cancer patients but also use them for molecular typing of cancer. These results indicated that our method has important application value for the diagnosis of cancer and may reveal potential carcinogenic mechanisms.
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Affiliation(s)
- Ze-Jia Cui
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiong-Hui Zhou
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
| | - Hong-Yu Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
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18
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Jibrim RLM, de Carvalho CV, Invitti AL, Schor E. Expression of the TFDP1 gene in the endometrium of women with deep infiltrating endometriosis. Gynecol Endocrinol 2019; 35:490-493. [PMID: 30638096 DOI: 10.1080/09513590.2018.1540569] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
The field of endometriosis etiopathogenesis aims to identify the origin of disease in endometrial disorders. Changes in gene and protein expression related to cell adhesion, collagenases, and, mainly, cell cycle regulators have been identified. We set out to analyze the expression of the transcription factor DP-1 (TFDP1) gene, which encodes a protein that controls the G1/S phase passage of the cell cycle, in the endometrium of women with deep infiltrating endometriosis (DIE). Samples of endometrium from both endometriosis-affected women and healthy women were collected, cultured and maintained at the Cell Bank of the Pelvic Pain and Endometriosis Unit of the Federal University of Sao Paulo. This study analyzed five samples from the endometrium cell culture of healthy patients (i.e. no pelvic disease, as determined by means of laparoscopic tubal ligation) and six samples from women diagnosed with DIE. Samples were evaluated for TFDP1 gene expression by real-time PCR. We observed a downregulation of TFDP1 in the endometrium cells of women with DIE when compared to the control (a fold-change of -2.05, p value=.011). The TFDP1 gene is part of the cell cycle pathway, but its function is not yet clear. Additional studies are necessary to clarify the function of TFDP1 in endometriosis etiopathogenesis.
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Affiliation(s)
- Rodrigo Lopes Meime Jibrim
- a Gynecology Department, Pelvic Pain and Endometriosis Unit , Universidade Federal de São Paulo - Escola Paulista de Medicina (UNIFESP-EPM) , Sao Paulo , Brazil
| | - Cristina Valletta de Carvalho
- a Gynecology Department, Pelvic Pain and Endometriosis Unit , Universidade Federal de São Paulo - Escola Paulista de Medicina (UNIFESP-EPM) , Sao Paulo , Brazil
| | - Adriana Luckow Invitti
- a Gynecology Department, Pelvic Pain and Endometriosis Unit , Universidade Federal de São Paulo - Escola Paulista de Medicina (UNIFESP-EPM) , Sao Paulo , Brazil
| | - Eduardo Schor
- a Gynecology Department, Pelvic Pain and Endometriosis Unit , Universidade Federal de São Paulo - Escola Paulista de Medicina (UNIFESP-EPM) , Sao Paulo , Brazil
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19
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Hung MS, Chen YC, Lin P, Li YC, Hsu CC, Lung JH, You L, Xu Z, Mao JH, Jablons DM, Yang CT. Cul4A Modulates Invasion and Metastasis of Lung Cancer Through Regulation of ANXA10. Cancers (Basel) 2019; 11:cancers11050618. [PMID: 31052599 PMCID: PMC6562482 DOI: 10.3390/cancers11050618] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/15/2019] [Accepted: 04/24/2019] [Indexed: 02/06/2023] Open
Abstract
: Cullin 4A (Cul4A) is overexpressed in a number of cancers and has been established as an oncogene. This study aimed to elucidate the role of Cul4A in lung cancer invasion and metastasis. We observed that Cul4A was overexpressed in non-small cell lung cancer (NSCLC) tissues and the overexpression of Cul4A was associated with poor prognosis after surgical resection and it also decreased the expression of the tumor suppressor protein annexin A10 (ANXA10). The knockdown of Cul4A was associated with the upregulation of ANXA10, and the forced expression of Cul4A was associated with the downregulation of ANXA10 in lung cancer cells. Further studies showed that the knockdown of Cul4A inhibited the invasion and metastasis of lung cancer cells, which was reversed by the further knockdown of ANXA10. In addition, the knockdown of Cul4A inhibited lung tumor metastasis in mouse tail vein injection xenograft models. Notably, Cul4A regulated the degradation of ANXA10 through its interaction with ANXA10 and ubiquitination in lung cancer cells. Our findings suggest that Cul4A is a prognostic marker in NSCLC patients, and Cul4A plays important roles in lung cancer invasion and metastasis through the regulation of the ANXA10 tumor suppressor.
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Affiliation(s)
- Ming-Szu Hung
- Division of Thoracic Oncology, Department of Pulmonary and Critical Care Medicine, Chang Gung Memorial Hospital, Chiayi branch 61363, Taiwan.
- Department of Medicine, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan.
- Department of Respiratory Care, Chang Gung University of Science and Technology, Chiayi Campus, Chiayi 61363, Taiwan.
| | - Yi-Chuan Chen
- Department of Emergency Medicine, Chang Gung Memorial Hospital, Chiayi branch 61363, Taiwan.
| | - PaulYann Lin
- Department of Anatomic Pathology, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Chiayi 62247, Taiwan.
| | - Ya-Chin Li
- Division of Thoracic Oncology, Department of Pulmonary and Critical Care Medicine, Chang Gung Memorial Hospital, Chiayi branch 61363, Taiwan.
| | - Chia-Chen Hsu
- Department of Hematology and Oncology, Chang Gung Memorial Hospital, Chiayi branch 61363, Taiwan.
- Department of Medical Research and Development, Chang Gung Memorial Hospital, Chiayi branch 61363, Taiwan.
| | - Jr-Hau Lung
- Department of Medical Research and Development, Chang Gung Memorial Hospital, Chiayi branch 61363, Taiwan.
| | - Liang You
- Thoracic Oncology Laboratory, Department of Surgery, Comprehensive Cancer Center, University of California, San Francisco, CA 94143, USA.
| | - Zhidong Xu
- Thoracic Oncology Laboratory, Department of Surgery, Comprehensive Cancer Center, University of California, San Francisco, CA 94143, USA.
| | - Jian-Hua Mao
- Life Sciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA.
| | - David M Jablons
- Thoracic Oncology Laboratory, Department of Surgery, Comprehensive Cancer Center, University of California, San Francisco, CA 94143, USA.
| | - Cheng-Ta Yang
- Department of Respiratory Care, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan.
- Department of Pulmonary and Critical Care Medicine, Chang Gung Memorial Hospital, Taoyuan branch 33378, Taiwan.
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20
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Liu H, Lu W, He H, Wu J, Zhang C, Gong H, Yang C. Inflammation-dependent overexpression of c-Myc enhances CRL4 DCAF4 E3 ligase activity and promotes ubiquitination of ST7 in colitis-associated cancer. J Pathol 2019; 248:464-475. [PMID: 30945288 DOI: 10.1002/path.5273] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 03/04/2019] [Accepted: 04/01/2019] [Indexed: 02/05/2023]
Abstract
Inflammation is well known as an important driver of the initiation of colitis-associated cancer (CAC). Some cytokines, such as IL-6 and TNF-α can activate expression of the oncogene c-Myc (MYC) and regulate its downstream effects. Cullin-RING E3 Ligases (CRLs) are emerging as master regulators controlling tumorigenesis. Here, we demonstrate that two cullin genes, CUL4A and CUL4B, but not other members, are specifically overexpressed in CAC tumour samples and positively correlate with levels of the proinflammatory cytokines IL-1β and IL-6. In vitro experiments revealed that the transcription factor c-Myc can specifically activate the expression of CUL4A and CUL4B by binding to a conserved site (CACGTG) located in their promoters. Additionally, we found that both CUL4A and CUL4B can form an E3 complex with DNA damage-binding protein 1 (DDB1) and DDB1-CUL4-associated factor 4 (DCAF4). In vitro and in vivo ubiquitination analyses indicate that CRL4DCAF4 E3 ligase specifically directs degradation of ST7 (suppression of tumorigenicity 7). Overexpression of c-Myc in human colon epithelial cells resulted in the accumulation of CUL4A, CUL4B and DCAF4, but degradation of ST7. In contrast, knockdown of c-Myc, CUL4A or CUL4B in the colon adenocarcinoma cell line HT29 caused accumulation of ST7 and inhibition of cell proliferation, colony formation ability and in vivo tumour growth. Collectively, our results provide in vitro and in vivo evidence that c-Myc regulates CRL4DCAF4 E3 ligase activity to mediate ubiquitination of ST7, whose presence is physiologically essential for CAC tumorigenesis. © 2019 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Hong Liu
- Department of Integrated Traditional and Western Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Wenzhu Lu
- Department of Integrated Traditional and Western Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Hongbo He
- Department of Integrated Traditional and Western Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Jin Wu
- Department of Integrated Traditional and Western Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Caiguo Zhang
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Hanlin Gong
- Department of Integrated Traditional and Western Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Chunmei Yang
- Department of Integrated Traditional and Western Medicine, West China Hospital of Sichuan University, Chengdu, China
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21
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Cul4 E3 ubiquitin ligase regulates ovarian cancer drug resistance by targeting the antiapoptotic protein BIRC3. Cell Death Dis 2019; 10:104. [PMID: 30718461 PMCID: PMC6362125 DOI: 10.1038/s41419-018-1200-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 10/30/2018] [Accepted: 11/02/2018] [Indexed: 02/05/2023]
Abstract
CRL4, a well-defined E3 ligase, has been reported to be upregulated and is proposed to be a potential drug target in ovarian cancers. However, the biological functions of CRL4 and the underlying mechanism regulating cancer chemoresistance are still largely elusive. Here, we show that CRL4 is considerably increased in cisplatin-resistant ovarian cancer cells, and CRL4 knockdown with shRNAs is able to reverse cisplatin-resistance of ovarian cancer cells. Moreover, CRL4 knockdown markedly inhibits the expression of BIRC3, one of the inhibitors of apoptosis proteins (IAPs). Besides, lower expression level of BIRC3 is associated with better prognosis of ovarian cancer patients, and BIRC3 knockdown in ovarian cancer cells can recover their sensitivity to cisplatin. More importantly, we demonstrate that CRL4 regulates BIRC3 expression by mediating the STAT3, but not the PI3K pathway. Therefore, our results identified CRL4 as an important factor in ovarian cancer chemoresistance, suggesting that CRL4 and BIRC3 may serve as novel therapeutic targets for relapsed patients after treatment with cisplatin and its derivative to overcome the bottle neck of ovarian cancer chemoresistance.
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22
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Rajendran BK, Deng CX. Characterization of potential driver mutations involved in human breast cancer by computational approaches. Oncotarget 2018; 8:50252-50272. [PMID: 28477017 PMCID: PMC5564847 DOI: 10.18632/oncotarget.17225] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 03/26/2017] [Indexed: 02/06/2023] Open
Abstract
Breast cancer is the second most frequently occurring form of cancer and is also the second most lethal cancer in women worldwide. A genetic mutation is one of the key factors that alter multiple cellular regulatory pathways and drive breast cancer initiation and progression yet nature of these cancer drivers remains elusive. In this article, we have reviewed various computational perspectives and algorithms for exploring breast cancer driver mutation genes. Using both frequency based and mutational exclusivity based approaches, we identified 195 driver genes and shortlisted 63 of them as candidate drivers for breast cancer using various computational approaches. Finally, we conducted network and pathway analysis to explore their functions in breast tumorigenesis including tumor initiation, progression, and metastasis.
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Affiliation(s)
- Barani Kumar Rajendran
- Cancer Research Centre, Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Chu-Xia Deng
- Cancer Research Centre, Faculty of Health Sciences, University of Macau, Macau SAR, China
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23
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Widespread intronic polyadenylation diversifies immune cell transcriptomes. Nat Commun 2018; 9:1716. [PMID: 29712909 PMCID: PMC5928244 DOI: 10.1038/s41467-018-04112-z] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 04/05/2018] [Indexed: 01/08/2023] Open
Abstract
Alternative cleavage and polyadenylation (ApA) is known to alter untranslated region (3'UTR) length but can also recognize intronic polyadenylation (IpA) signals to generate transcripts that lose part or all of the coding region. We analyzed 46 3'-seq and RNA-seq profiles from normal human tissues, primary immune cells, and multiple myeloma (MM) samples and created an atlas of 4927 high-confidence IpA events represented in these cell types. IpA isoforms are widely expressed in immune cells, differentially used during B-cell development or in different cellular environments, and can generate truncated proteins lacking C-terminal functional domains. This can mimic ectodomain shedding through loss of transmembrane domains or alter the binding specificity of proteins with DNA-binding or protein-protein interaction domains. MM cells display a striking loss of IpA isoforms expressed in plasma cells, associated with shorter progression-free survival and impacting key genes in MM biology and response to lenalidomide.
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24
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Wang Y, Liu X, Zheng H, Wang Q, An L, Wei G. Suppression of CUL4A attenuates TGF-β1-induced epithelial-to-mesenchymal transition in breast cancer cells. Int J Mol Med 2017; 40:1114-1124. [PMID: 28902348 PMCID: PMC5593474 DOI: 10.3892/ijmm.2017.3118] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 07/21/2017] [Indexed: 01/28/2023] Open
Abstract
Transforming growth factor-β1 (TGF-β1) plays a vital role in the process of epithelial-to-mesenchymal transition (EMT) in breast cancer and the cullin 4A (CUL4A) gene is overexpressed in primary breast cancer. However, whether TGF-β1 signaling can induce CUL4A expression has not been investigated to date, at least to the best of our knowledge. In this study, using breast cancer cell lines, we found that the CUL4A expression level was increased following EMT induced by TGF-β1. Silencing CUL4A expression or CUL4A inhibition by thalidomide suppressed the EMT process induced by TGF-β1. We also found that CUL4A was associated with the expression of zinc finger E-box-binding homeobox 1 (ZEB1) which was induced by TGF-β1. These results suggest that CUL4A is upregulated in TGF-β1-induced EMT, and has a regulatory function in this process. The identification of CUL4A as a downstream target of TGF-β1 represents a critical pro-survival mechanism in breast cancer progression and provides another point for therapeutic intervention in breast cancer.
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Affiliation(s)
- Yunshan Wang
- Department of Anatomy and Key Laboratory of Experimental Teratology, Ministry of Education, Shandong University School of Medicine, Jinan, Shandong 250012,Department of International Biotechnology R&D Center, Shandong University School of Ocean, Weihai, Shandong 264209
| | - Xiaoyan Liu
- Department of Anatomy and Key Laboratory of Experimental Teratology, Ministry of Education, Shandong University School of Medicine, Jinan, Shandong 250012
| | - Hui Zheng
- Department of Anatomy and Key Laboratory of Experimental Teratology, Ministry of Education, Shandong University School of Medicine, Jinan, Shandong 250012
| | - Qin Wang
- Department of Anesthesiology, Qilu Hospital, Shandong University, Jinan, Shandong 250012
| | - Li An
- Department of Science and Education, Taian Maternal and Child Health-Care Hospital, Taian, Shandong 271000, P.R. China
| | - Guangwei Wei
- Department of Anatomy and Key Laboratory of Experimental Teratology, Ministry of Education, Shandong University School of Medicine, Jinan, Shandong 250012,Correspondence to: Professor Guangwei Wei, Department of Anatomy and Key Laboratory of Experimental Teratology, Ministry of Education, Shandong University School of Medicine, 44 Wenhua Xi Road, Jinan, Shandong 250012, P.R. China, E-mail:
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25
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Wang Z, Zhu WG, Xu X. Ubiquitin-like modifications in the DNA damage response. Mutat Res 2017; 803-805:56-75. [PMID: 28734548 DOI: 10.1016/j.mrfmmm.2017.07.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 06/03/2017] [Accepted: 07/03/2017] [Indexed: 12/14/2022]
Abstract
Genomic DNA is damaged at an extremely high frequency by both endogenous and environmental factors. An improper response to DNA damage can lead to genome instability, accelerate the aging process and ultimately cause various human diseases, including cancers and neurodegenerative disorders. The mechanisms that underlie the cellular DNA damage response (DDR) are complex and are regulated at many levels, including at the level of post-translational modification (PTM). Since the discovery of ubiquitin in 1975 and ubiquitylation as a form of PTM in the early 1980s, a number of ubiquitin-like modifiers (UBLs) have been identified, including small ubiquitin-like modifiers (SUMOs), neural precursor cell expressed, developmentally down-regulated 8 (NEDD8), interferon-stimulated gene 15 (ISG15), human leukocyte antigen (HLA)-F adjacent transcript 10 (FAT10), ubiquitin-fold modifier 1 (UFRM1), URM1 ubiquitin-related modifier-1 (URM1), autophagy-related protein 12 (ATG12), autophagy-related protein 8 (ATG8), fan ubiquitin-like protein 1 (FUB1) and histone mono-ubiquitylation 1 (HUB1). All of these modifiers have known roles in the cellular response to various forms of stress, and delineating their underlying molecular mechanisms and functions is fundamental in enhancing our understanding of human disease and longevity. To date, however, the molecular mechanisms and functions of these UBLs in the DDR remain largely unknown. This review summarizes the current status of PTMs by UBLs in the DDR and their implication in cancer diagnosis, therapy and drug discovery.
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Affiliation(s)
- Zhifeng Wang
- Guangdong Key Laboratory of Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China
| | - Wei-Guo Zhu
- Guangdong Key Laboratory of Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China
| | - Xingzhi Xu
- Guangdong Key Laboratory of Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China; Beijing Key Laboratory of DNA Damage Response, Capital Normal University College of Life Sciences, Beijing 100048, China.
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26
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Zhang S, Zhang Y, Yu P, Hu Y, Zhou H, Guo L, Xu X, Zhu X, Waqas M, Qi J, Zhang X, Liu Y, Chen F, Tang M, Qian X, Shi H, Gao X, Chai R. Characterization of Lgr5+ Progenitor Cell Transcriptomes after Neomycin Injury in the Neonatal Mouse Cochlea. Front Mol Neurosci 2017; 10:213. [PMID: 28725177 PMCID: PMC5496572 DOI: 10.3389/fnmol.2017.00213] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 06/16/2017] [Indexed: 12/17/2022] Open
Abstract
Lgr5+ supporting cells (SCs) are enriched hair cell (HC) progenitors in the cochlea. Both in vitro and in vivo studies have shown that HC injury can spontaneously activate Lgr5+ progenitors to regenerate HCs in the neonatal mouse cochlea. Promoting HC regeneration requires the understanding of the mechanism of HC regeneration, and this requires knowledge of the key genes involved in HC injury-induced self-repair responses that promote the proliferation and differentiation of Lgr5+ progenitors. Here, as expected, we found that neomycin-treated Lgr5+ progenitors (NLPs) had significantly greater HC regeneration ability, and greater but not significant proliferation ability compared to untreated Lgr5+ progenitors (ULPs) in response to neomycin exposure. Next, we used RNA-seq analysis to determine the differences in the gene-expression profiles between the transcriptomes of NLPs and ULPs from the neonatal mouse cochlea. We first analyzed the genes that were enriched and differentially expressed in NLPs and ULPs and then analyzed the cell cycle genes, the transcription factors, and the signaling pathway genes that might regulate the proliferation and differentiation of Lgr5+ progenitors. We found 9 cell cycle genes, 88 transcription factors, 8 microRNAs, and 16 cell-signaling pathway genes that were significantly upregulated or downregulated after neomycin injury in NLPs. Lastly, we constructed a protein-protein interaction network to show the interaction and connections of genes that are differentially expressed in NLPs and ULPs. This study has identified the genes that might regulate the proliferation and HC regeneration of Lgr5+ progenitors after neomycin injury, and investigations into the roles and mechanisms of these genes in the cochlea should be performed in the future to identify potential therapeutic targets for HC regeneration.
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Affiliation(s)
- Shasha Zhang
- Key Laboratory for Developmental Genes and Human Disease, Ministry of Education, Institute of Life Sciences, Southeast UniversityNanjing, China.,Research Institute of OtolaryngologyNanjing, China.,Co-innovation Center of Neuroregeneration, Nantong UniversityNantong, China
| | - Yuan Zhang
- Key Laboratory for Developmental Genes and Human Disease, Ministry of Education, Institute of Life Sciences, Southeast UniversityNanjing, China
| | - Pengfei Yu
- Bioinformatics Department, Admera Health LLCSouth Plainfield, NJ, United States
| | - Yao Hu
- School of Pharmacy, Institute for Stem Cell and Neural Regeneration, Nanjing Medical UniversityNanjing, China
| | - Han Zhou
- Jiangsu Provincial Key Medical Discipline (Laboratory), Department of Otolaryngology Head and Neck Surgery, Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjing, China
| | - Lingna Guo
- Key Laboratory for Developmental Genes and Human Disease, Ministry of Education, Institute of Life Sciences, Southeast UniversityNanjing, China
| | - Xiaochen Xu
- Key Laboratory for Developmental Genes and Human Disease, Ministry of Education, Institute of Life Sciences, Southeast UniversityNanjing, China
| | - Xiaocheng Zhu
- Jiangsu Provincial Key Medical Discipline (Laboratory), Department of Otolaryngology Head and Neck Surgery, Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjing, China
| | - Muhammad Waqas
- Key Laboratory for Developmental Genes and Human Disease, Ministry of Education, Institute of Life Sciences, Southeast UniversityNanjing, China.,Department of Biotechnology, Federal Urdu University of Arts, Science and TechnologyKarachi, Pakistan
| | - Jieyu Qi
- Key Laboratory for Developmental Genes and Human Disease, Ministry of Education, Institute of Life Sciences, Southeast UniversityNanjing, China
| | - Xiaoli Zhang
- Jiangsu Provincial Key Medical Discipline (Laboratory), Department of Otolaryngology Head and Neck Surgery, Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjing, China
| | - Yan Liu
- School of Pharmacy, Institute for Stem Cell and Neural Regeneration, Nanjing Medical UniversityNanjing, China
| | - Fangyi Chen
- Department of Biomedical Engineering, Southern University of Science and TechnologyShenzhen, China
| | - Mingliang Tang
- Key Laboratory for Developmental Genes and Human Disease, Ministry of Education, Institute of Life Sciences, Southeast UniversityNanjing, China
| | - Xiaoyun Qian
- Jiangsu Provincial Key Medical Discipline (Laboratory), Department of Otolaryngology Head and Neck Surgery, Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjing, China
| | - Haibo Shi
- Department of Otorhinolaryngology Head and Neck Surgery, The Sixth People's Hospital Affiliated to Shanghai Jiao Tong UniversityShanghai, China
| | - Xia Gao
- Research Institute of OtolaryngologyNanjing, China.,Jiangsu Provincial Key Medical Discipline (Laboratory), Department of Otolaryngology Head and Neck Surgery, Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjing, China
| | - Renjie Chai
- Key Laboratory for Developmental Genes and Human Disease, Ministry of Education, Institute of Life Sciences, Southeast UniversityNanjing, China.,Research Institute of OtolaryngologyNanjing, China.,Co-innovation Center of Neuroregeneration, Nantong UniversityNantong, China
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27
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CUL4A overexpression as an independent adverse prognosticator in intrahepatic cholangiocarcinoma. BMC Cancer 2017; 17:395. [PMID: 28576144 PMCID: PMC5457619 DOI: 10.1186/s12885-017-3389-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 05/25/2017] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND CUL4A has been known for its oncogenic properties in various human cancers. However, its role in intrahepatic cholangiocarcinoma (iCCA) has not been explored. METHODS We retrospectively investigated 105 iCCA cases from a single medical institution. Tissue microarrays were used for immunohistochemical analysis of CUL4A expression. CUL4A expression vectors were introduced in cell lines. Cell migration and invasion assays were used to compare the mobility potential of iCCA cells under basal conditions and after manipulation. Then we evaluated the effects of CUL4A on the cell growth by proliferation assay, and further checked the susceptibility to cisplatin in iCCA cells with or without CUL4A overexpression. RESULTS CUL4A overexpression was detected in 34 cases (32.4%). Patients with CUL4A-overexpressing tumors exhibited shortened disease-free survival (mean, 27.7 versus 90.4 months; P = 0.011). In the multivariate analysis model, CUL4A overexpression was shown to be an independent unfavorable predictor for disease-free survival (P = 0.045). Moreover, stably transfected CUL4A-overexpressing iCCA cell lines displayed an increased mobility potential and enhanced cell growth without impact on susceptibility to cisplatin. CONCLUSIONS Our data demonstrate that overexpression of CUL4A plays an oncogenic role in iCCA and adversely affects disease-free survival. Thus, it may prove to be a powerful prognostic factor and a potential therapeutic target.
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28
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Integrative analysis of multi-omics data reveals distinct impacts of DDB1-CUL4 associated factors in human lung adenocarcinomas. Sci Rep 2017; 7:333. [PMID: 28336923 PMCID: PMC5428704 DOI: 10.1038/s41598-017-00512-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 02/28/2017] [Indexed: 12/22/2022] Open
Abstract
Many DDB1-CUL4 associated factors (DCAFs) have been identified and serve as substrate receptors. Although the oncogenic role of CUL4A has been well established, specific DCAFs involved in cancer development remain largely unknown. Here we infer the potential impact of 19 well-defined DCAFs in human lung adenocarcinomas (LuADCs) using integrative omics analyses, and discover that mRNA levels of DTL, DCAF4, 12 and 13 are consistently elevated whereas VBRBP is reduced in LuADCs compared to normal lung tissues. The transcriptional levels of DCAFs are significantly correlated with their gene copy number variations. SKIP2, DTL, DCAF6, 7, 8, 13 and 17 are frequently gained whereas VPRBP, PHIP, DCAF10, 12 and 15 are frequently lost. We find that only transcriptional level of DTL is robustly, significantly and negatively correlated with overall survival across independent datasets. Moreover, DTL-correlated genes are enriched in cell cycle and DNA repair pathways. We also identified that the levels of 25 proteins were significantly associated with DTL overexpression in LuADCs, which include significant decreases in protein level of the tumor supressor genes such as PDCD4, NKX2-1 and PRKAA1. Our results suggest that different CUL4-DCAF axis plays the distinct roles in LuADC development with possible relevance for therapeutic target development.
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29
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Sui X, Zhou H, Zhu L, Wang D, Fan S, Zhao W. CUL4A promotes proliferation and metastasis of colorectal cancer cells by regulating H3K4 trimethylation in epithelial-mesenchymal transition. Onco Targets Ther 2017; 10:735-743. [PMID: 28223829 PMCID: PMC5308582 DOI: 10.2147/ott.s118897] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Increasing evidence suggests that CUL4A, a ubiquitin ligase, is involved in the promotion of cancer malignancy and correlated with worse clinical prognosis in several kinds of human cancers. Although its effect and mechanism on the progression of colorectal cancer (CRC) remain unknown. Our clinical data show that CUL4A protein is overexpressed, positively associated with lymph nodes status, differentiation degree, tumor size, and poor prognosis in 80 CRC patients. CUL4A overexpression promotes cell proliferation and colony formation of CRC cells. Knockdown of CUL4A inhibits cell proliferation and migration. CUL4A can significantly promote the in vitro migration of CRC cells via induction of the epithelial–mesenchymal transition process. And the modulation of CUL4A expression altered the level of H3K4 trimethylation at the E-cadherin, N-cadherin, and vimentin gene promoters, which in turn transcriptionally regulated their expression. Moreover, knockdown of CUL4A also decreased the tumor volume and tumor weight in vivo. Together, our results reveal that CUL4A plays as an oncogene in CRC and may become a potential therapeutic target in the treatment of colorectal cancer.
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Affiliation(s)
- Xuemei Sui
- Clinical Laboratory, The First Affiliated Huai'an Hospital of Nanjing Medical University
| | - Hong Zhou
- Huai'an No 4 People's Hospital, Huai'an
| | - Lei Zhu
- Department of Digestive System, Jiangsu Province Hospital of TCM, Nanjing
| | - Deqiang Wang
- Cancer Therapy Center, Affiliated Hospital of Jiangsu University, Zhenjiang
| | - Sumei Fan
- Geriatric Department, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an
| | - Wei Zhao
- Clinical Laboratory, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
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30
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Potter EA, Dolgova EV, Proskurina AS, Efremov YR, Minkevich AM, Rozanov AS, Peltek SE, Nikolin VP, Popova NA, Seledtsov IA, Molodtsov VV, Zavyalov EL, Taranov OS, Baiborodin SI, Ostanin AA, Chernykh ER, Kolchanov NA, Bogachev SS. Gene expression profiling of tumor-initiating stem cells from mouse Krebs-2 carcinoma using a novel marker of poorly differentiated cells. Oncotarget 2017; 8:9425-9441. [PMID: 28031533 PMCID: PMC5354742 DOI: 10.18632/oncotarget.14116] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 12/15/2016] [Indexed: 12/18/2022] Open
Abstract
Using the ability of poorly differentiated cells to natively internalize fragments of extracellular double-stranded DNA as a marker, we isolated a tumorigenic subpopulation present in Krebs-2 ascites that demonstrated the features of tumor-inducing cancer stem cells. Having combined TAMRA-labeled DNA probe and the power of RNA-seq technology, we identified a set of 168 genes specifically expressed in TAMRA-positive cells (tumor-initiating stem cells), these genes remaining silent in TAMRA-negative cancer cells. TAMRA+ cells displayed gene expression signatures characteristic of both stem cells and cancer cells. The observed expression differences between TAMRA+ and TAMRA- cells were validated by Real Time PCR. The results obtained corroborated the biological data that TAMRA+ murine Krebs-2 tumor cells are tumor-initiating stem cells. The approach developed can be applied to profile any poorly differentiated cell types that are capable of immanent internalization of double-stranded DNA.
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Affiliation(s)
- Ekaterina A. Potter
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Evgenia V. Dolgova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Anastasia S. Proskurina
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Yaroslav R. Efremov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Alexandra M. Minkevich
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Aleksey S. Rozanov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Sergey E. Peltek
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Valeriy P. Nikolin
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Nelly A. Popova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | | | - Vladimir V. Molodtsov
- Novosibirsk State University, Novosibirsk 630090, Russia
- Softberry Inc., New York 10549, USA
| | - Evgeniy L Zavyalov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Oleg S. Taranov
- The State Research Center of Virology and Biotechnology VECTOR, Koltsovo, Novosibirsk 630559, Russia
| | - Sergey I. Baiborodin
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Alexander A. Ostanin
- Institute of Clinical Immunology, Siberian Branch of the Russian Academy of Medical Sciences, Novosibirsk 630099, Russia
| | - Elena R. Chernykh
- Institute of Clinical Immunology, Siberian Branch of the Russian Academy of Medical Sciences, Novosibirsk 630099, Russia
| | - Nikolay A. Kolchanov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Sergey S. Bogachev
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
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Targeting the protein ubiquitination machinery in melanoma by the NEDD8-activating enzyme inhibitor pevonedistat (MLN4924). Invest New Drugs 2016; 35:11-25. [PMID: 27783255 DOI: 10.1007/s10637-016-0398-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 10/09/2016] [Indexed: 01/08/2023]
Abstract
Background The neddylation pathway conjugates NEDD8 to cullin-RING ligases and controls the proteasomal degradation of specific proteins involved in essential cell processes. Pevonedistat (MLN4924) is a selective small molecule targeting the NEDD8-activating enzyme (NAE) and inhibits an early step in neddylation, resulting in DNA re-replication, cell cycle arrest and death. We investigated the anti-tumor potential of pevonedistat in preclinical models of melanoma. Methods Melanoma cell lines and patient-derived tumor xenografts (PDTX) treated with pevonedistat were assessed for viability/apoptosis and tumor growth, respectively, to identify sensitive/resistant models. Gene expression microarray and gene set enrichment analyses were performed in cell lines to determine the expression profiles and pathways of sensitivity/resistance. Pharmacodynamic changes in treated-PDTX were also characterized. Results Pevonedistat effectively inhibited cell viability (IC50 < 0.3 μM) and induced apoptosis in a subset of melanoma cell lines. Sensitive and resistant cell lines exhibited distinct gene expression profiles; sensitive models were enriched for genes involved in DNA repair, replication and cell cycle regulation, while immune response and cell adhesion pathways were upregulated in resistant models. Pevonedistat also reduced tumor growth in melanoma cell line xenografts and PDTX with variable responses. An accumulation of pevonedistat-NEDD8 adduct and CDT1 was observed in sensitive tumors consistent with its mechanism of action. Conclusions This study provided preclinical evidence that NAE inhibition by pevonedistat has anti-tumor activity in melanoma and supports the clinical benefits observed in recent Phase 1 trials of this drug in melanoma patients. Further investigations are warranted to develop rational combinations and determine predictive biomarkers of pevonedistat.
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Sang Y, Yan F, Ren X. The role and mechanism of CRL4 E3 ubiquitin ligase in cancer and its potential therapy implications. Oncotarget 2016; 6:42590-602. [PMID: 26460955 PMCID: PMC4767455 DOI: 10.18632/oncotarget.6052] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 09/23/2015] [Indexed: 12/21/2022] Open
Abstract
CRLs (Cullin-RING E3 ubiquitin ligases) are the largest E3 ligase family in eukaryotes, which ubiquitinate a wide range of substrates involved in cell cycle regulation, signal transduction, transcriptional regulation, DNA damage response, genomic integrity, tumor suppression and embryonic development. CRL4 E3 ubiquitin ligase, as one member of CRLs family, consists of a RING finger domain protein, cullin4 (CUL4) scaffold protein and DDB1–CUL4 associated substrate receptors. The CUL4 subfamily includes two members, CUL4A and CUL4B, which share extensively sequence identity and functional redundancy. Aberrant expression of CUL4 has been found in a majority of tumors. Given the significance of CUL4 in cancer, understanding its detailed aspects of pathogenesis of human malignancy would have significant value for the treatment of cancer. Here, the work provides an overview to address the role of CRL4 E3 ubiquitin ligase in cancer development and progression, and discuss the possible mechanisms of CRL4 ligase involving in many cellular processes associated with tumor. Finally, we discuss its potential value in cancer therapy.
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Affiliation(s)
- Youzhou Sang
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,National Clinical Research Center of Cancer, Tianjin, China.,Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
| | - Fan Yan
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,National Clinical Research Center of Cancer, Tianjin, China.,Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
| | - Xiubao Ren
- Department of Biotherapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,National Clinical Research Center of Cancer, Tianjin, China.,Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
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Zheng N, Dai X, Wang Z, Wei W. A new layer of degradation mechanism for PR-Set7/Set8 during cell cycle. Cell Cycle 2016; 15:3042-3047. [PMID: 27649746 DOI: 10.1080/15384101.2016.1234552] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Set8 is critically involved in transcription regulation, cell cycle progression and genomic stability. Emerging evidence has revealed that E3 ubiquitin ligases such as CRL4cdt2 and SCFSkp2 regulate Set8 protein abundance. However, it is unclear whether other E3 ligase(s) could govern Set8 level for proper cell cycle progression in response to genotoxic stress such as UV irradiation. Recently, we report that the SCFβ-TRCP complex regulates Set8 protein stability by targeting it for ubiquitination and subsequent degradation. Notably, Set8 interacts with the SCFβ-TRCP E3 ligase complex. We further revealed a critical role of CKI in SCFβ-TRCP-mediated degradation of Set8. Mechanistically, CKI-mediated phosphorylation of Set8 at the S253 site promotes its destruction by SCFβ-TRCP. Importantly, SCFβ-TRCP-dependent Set8 destruction also contributes to the tight control of cell proliferation and cell cycle progression, in response to UV irradiation. Here, we summarize our new findings regarding the crucial role of β-TRCP in CKI-mediated Set8 degradation, which could provide new evidence to support that dysregulation of a tight regulatory network of Set8 could lead to aberrant cell cycle process.
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Affiliation(s)
- Nana Zheng
- a The Cyrus Tang Hematology Center and Collaborative Innovation Center of Hematology, Jiangsu Institute of Hematology, the First Affiliated Hospital, Soochow University , Suzhou , P. R. China
| | - Xiangpeng Dai
- b Department of Pathology , Beth Israel Deaconess Medical Center, Harvard Medical School , Boston , MA , USA
| | - Zhiwei Wang
- a The Cyrus Tang Hematology Center and Collaborative Innovation Center of Hematology, Jiangsu Institute of Hematology, the First Affiliated Hospital, Soochow University , Suzhou , P. R. China
| | - Wenyi Wei
- b Department of Pathology , Beth Israel Deaconess Medical Center, Harvard Medical School , Boston , MA , USA
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Ren W, Sun Z, Zeng Q, Han S, Zhang Q, Jiang L. Aberrant Expression of CUL4A Is Associated with IL-6/ STAT3 Activation in Colorectal Cancer Progression. Arch Med Res 2016; 47:214-22. [PMID: 27418574 DOI: 10.1016/j.arcmed.2016.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Accepted: 06/28/2016] [Indexed: 11/15/2022]
Abstract
BACKGROUND AND AIMS Although it has been indicated that the cytokine interleukin-6 (IL-6) promotes colorectal cancer (CRC) tumorigenesis in tumor microenvironment, the mechanisms related to IL-6-induced tumor progression are still not well understood. METHODS First, the correlation between pSTAT3, CUL4A and ZEB1 was analyzed using immunocytochemistry. Logistic regression analysis was then used to observe the relationship between levels of pSTAT3, CUL4A and ZEB1 and clinicopathological characteristics. Finally, the mechanism of the effect of the expression level of pSTAT3, CUL4A and ZEB1 on cell invasion ability was verified by cell experiment. RESULTS We discovered that the increased expression levels of pSTAT3, CUL4A and ZEB1 had significant relationships in CRC patients. These up-regulated expression levels were also closely associated with CRC aggressiveness. Furthermore, in vitro, we discovered that expression levels of CUL4A and ZEB1 were significantly up-regulated when IL-6 stimulated. However, the CUL4A-knockdown, IL-6, could not induce expression of ZEB1. CHIP assay authenticated that pSTAT3 could bind to CUL4A promoter and worked as their transcription factors. We also demonstrated that IL-6 markedly increased the reporter activity using a luciferase reporter gene containing CUL4A promoter. Finally, silencing CUL4A blocked IL-6-driven invasion in matrigel invasion assay. CONCLUSION This study proposed that CUL4A played an oncogene role through ZEB1 in IL-6-induced colorectal carcinoma progression.
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Affiliation(s)
- Weiguo Ren
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
| | - Zhenqiang Sun
- Surgical Gastroenterology, Xinjiang Medical University Cancer Hospital, Urumqi, Xinjiang, China
| | - Qinglei Zeng
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Shuang Han
- Department of Oncology, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, Shandong, China
| | - Qinglin Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Libin Jiang
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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Recurrent Amplification at 13q34 Targets at CUL4A, IRS2, and TFDP1 As an Independent Adverse Prognosticator in Intrahepatic Cholangiocarcinoma. PLoS One 2015; 10:e0145388. [PMID: 26684807 PMCID: PMC4686179 DOI: 10.1371/journal.pone.0145388] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 12/03/2015] [Indexed: 02/06/2023] Open
Abstract
Amplification of genes at 13q34 has been reported to be associated with tumor proliferation and progression in diverse types of cancers. However, its role in intrahepatic cholangiocarcinoma (iCCA) has yet to be explored. We examined two iCCA cell lines and 86 cases of intrahepatic cholangiocarcinoma to analyze copy number of three target genes, including cullin 4A (CUL4A), insulin receptor substrate 2 (IRS2), and transcription factor Dp-1 (TFDP1) at 13q34 by quantitative real-time polymerase chain reaction. The cell lines and all tumor samples were used to test the relationship between copy number (CN) alterations and protein expression by western blotting and immunohistochemical assays, respectively. IRS2 was introduced, and each target gene was silenced in cell lines. The mobility potential of cells was compared in the basal condition and after manipulation using cell migration and invasion assays. CN alterations correlated with protein expression levels. The SNU1079 cell line containing deletions of the target genes demonstrated decreased protein expression levels and significantly lower numbers of migratory and invasive cells, as opposed to the RBE cell line, which does not contain CN alterations. Overexpression of IRS2 by introducing IRS2 in SUN1079 cells increased the mobility potential. In contrast, silencing each target gene showed a trend or statistical significance toward inhibition of migratory and invasive capacities in RBE cells. In tumor samples, the amplification of each of these genes was associated with poor disease-free survival. Twelve cases (13.9%) demonstrated copy numbers > 4 for all three genes tested (CUL4A, IRS2, and TFDP1), and showed a significant difference in disease-free survival by both univariate and multivariate survival analyses (hazard ratio, 2.69; 95% confidence interval, 1.23 to 5.88; P = 0.013). Our data demonstrate that amplification of genes at 13q34 plays an oncogenic role in iCCA featuring adverse disease-free survival, which may provide new directions for targeted therapy.
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HUNG MINGSZU, CHEN ICHUAN, YOU LIANG, JABLONS DAVIDM, LI YACHIN, MAO JIANHUA, XU ZHIDONG, HSIEH MENGJER, LIN YUCHING, YANG CHENGTA, LIU SHIHTUNG, TSAI YINGHUANG. Knockdown of Cul4A increases chemosensitivity to gemcitabine through upregulation of TGFBI in lung cancer cells. Oncol Rep 2015; 34:3187-95. [DOI: 10.3892/or.2015.4324] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Accepted: 08/11/2015] [Indexed: 11/06/2022] Open
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Hannah J, Zhou P. Distinct and overlapping functions of the cullin E3 ligase scaffolding proteins CUL4A and CUL4B. Gene 2015; 573:33-45. [PMID: 26344709 DOI: 10.1016/j.gene.2015.08.064] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 08/03/2015] [Accepted: 08/27/2015] [Indexed: 01/29/2023]
Abstract
The cullin 4 subfamily of genes includes CUL4A and CUL4B, which share a mostly identical amino acid sequence aside from the elongated N-terminal region in CUL4B. Both act as scaffolding proteins for modular cullin RING ligase 4 (CRL4) complexes which promote the ubiquitination of a variety of substrates. CRL4 function is vital to cells as loss of both genes or their shared substrate adaptor protein DDB1 halts proliferation and eventually leads to cell death. Due to their high structural similarity, CUL4A and CUL4B share a substantial overlap in function. However, in some cases, differences in subcellular localization, spatiotemporal expression patterns and stress-inducibility preclude functional compensation. In this review, we highlight the most essential functions of the CUL4 genes in: DNA repair and replication, chromatin-remodeling, cell cycle regulation, embryogenesis, hematopoiesis and spermatogenesis. CUL4 genes are also clinically relevant as dysregulation can contribute to the onset of cancer and CRL4 complexes are often hijacked by certain viruses to promote viral replication and survival. Also, mutations in CUL4B have been implicated in a subset of patients suffering from syndromic X-linked intellectual disability (AKA mental retardation). Interestingly, the antitumor effects of immunomodulatory drugs are caused by their binding to the CRL4CRBN complex and re-directing the E3 ligase towards the Ikaros transcription factors IKZF1 and IKZF3. Because of their influence over key cellular functions and relevance to human disease, CRL4s are considered promising targets for therapeutic intervention.
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Affiliation(s)
- Jeffrey Hannah
- Department of Pathology, Weill Cornell Medical College, 1300 York Ave. NY, NY 10065, United States.
| | - Pengbo Zhou
- Department of Pathology, Weill Cornell Medical College, 1300 York Ave. NY, NY 10065, United States.
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Song J, Zhang J, Shao J. Knockdown of CUL4A inhibits invasion and induces apoptosis in osteosarcoma cells. Int J Immunopathol Pharmacol 2015; 28:263-9. [PMID: 26055549 DOI: 10.1177/0394632015586656] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 04/20/2015] [Indexed: 11/17/2022] Open
Abstract
Cullin4A (CUL4A) is implicated in many cellular events including cell survival and growth. However, the specific function and underlying mechanisms of CUL4A in cancer invasion have not yet been elucidated. In this work, we were focused on investigating the role of CUL4A in human osteosarcoma (OS). The expression level of CUL4A was evaluated by immunohistochemical (IHC) assay in human OS tissues. Lentivirus-mediated CUL4A shRNA (Lv-shCUL4A) constructed by us was transfected into OS cells for assessing its effects on cell proliferation and invasive potential, respectively detected by MTT and Transwell assays. It was demonstrated that the expression of CUL4A protein was markedly increased in OS tissues compared with the adjacent non-cancerous tissues (ANCT) (57.8% vs. 25.6%, P = 0.019), and was associated with the distant metastases in OS patients (P = 0.016). In vitro, silencing of CUL4A gene inhibited OS cell proliferation and invasion, and induced cell apoptosis, followed by increased expression of p27 and p53 and decreased expression of MMP-2. Therefore, these findings indicate that elevated expression of CUL4A is positively correlated with distant metastases in OS patients, and knockdown of CUL4A suppresses invasion and induces apoptosis in OS cells, suggesting that CUL4A may serve as a potential target for the treatment of OS.
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Affiliation(s)
- Jia Song
- Department of Orthopedic Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, PR China
| | - Jing Zhang
- Department of Orthopedic Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, PR China
| | - Jiang Shao
- Department of Orthopedic Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, PR China
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Liu C, Louhimo R, Laakso M, Lehtonen R, Hautaniemi S. Identification of sample-specific regulations using integrative network level analysis. BMC Cancer 2015; 15:319. [PMID: 25928379 PMCID: PMC4424448 DOI: 10.1186/s12885-015-1265-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Accepted: 03/25/2015] [Indexed: 11/10/2022] Open
Abstract
Background Histologically similar tumors even from the same anatomical position may still show high variability at molecular level hindering analysis of genome-wide data. Leveling the analysis to a gene regulatory network instead of focusing on single genes has been suggested to overcome the heterogeneity issue although the majority of the network methods require large datasets. Network methods that are able to function at a single sample level are needed to overcome the heterogeneity and sample size issues. Methods We present a novel network method, Differentially Expressed Regulation Analysis (DERA) that integrates expression data to biological network information at a single sample level. The sample-specific networks are subsequently used to discover samples with similar molecular functions by identification of regulations that are shared between samples or are specific for a subgroup. Results We applied DERA to identify key regulations in triple negative breast cancer (TNBC), which is characterized by lack of estrogen receptor, progesterone receptor and HER2 expression and has poorer prognosis than the other breast cancer subtypes. DERA identified 110 core regulations consisting of 28 disconnected subnetworks for TNBC. These subnetworks are related to oncogenic activity, proliferation, cancer survival, invasiveness and metastasis. Our analysis further revealed 31 regulations specific for TNBC as compared to the other breast cancer subtypes and thus form a basis for understanding TNBC. We also applied DERA to high-grade serous ovarian cancer (HGS-OvCa) data and identified several common regulations between HGS-OvCa and TNBC. The performance of DERA was compared to two pathway analysis methods GSEA and SPIA and our results shows better reproducibility and higher sensitivity in a small sample set. Conclusions We present a novel method called DERA to identify subnetworks that are similarly active for a group of samples. DERA was applied to breast cancer and ovarian cancer data showing our method is able to identify reliable and potentially important regulations with high reproducibility. R package is available at http://csbi.ltdk.helsinki.fi/pub/czliu/DERA/. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1265-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chengyu Liu
- Research Programs Unit, Genome-Scale Biology Research Program and Institute of Biomedicine, University of Helsinki, Haartmaninkatu 8, Helsinki, FI-00014, Finland.
| | - Riku Louhimo
- Research Programs Unit, Genome-Scale Biology Research Program and Institute of Biomedicine, University of Helsinki, Haartmaninkatu 8, Helsinki, FI-00014, Finland.
| | - Marko Laakso
- Research Programs Unit, Genome-Scale Biology Research Program and Institute of Biomedicine, University of Helsinki, Haartmaninkatu 8, Helsinki, FI-00014, Finland.
| | - Rainer Lehtonen
- Research Programs Unit, Genome-Scale Biology Research Program and Institute of Biomedicine, University of Helsinki, Haartmaninkatu 8, Helsinki, FI-00014, Finland.
| | - Sampsa Hautaniemi
- Research Programs Unit, Genome-Scale Biology Research Program and Institute of Biomedicine, University of Helsinki, Haartmaninkatu 8, Helsinki, FI-00014, Finland.
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Brown JS, Jackson SP. Ubiquitylation, neddylation and the DNA damage response. Open Biol 2015; 5:150018. [PMID: 25833379 PMCID: PMC4422126 DOI: 10.1098/rsob.150018] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 03/09/2015] [Indexed: 12/19/2022] Open
Abstract
Failure of accurate DNA damage sensing and repair mechanisms manifests as a variety of human diseases, including neurodegenerative disorders, immunodeficiency, infertility and cancer. The accuracy and efficiency of DNA damage detection and repair, collectively termed the DNA damage response (DDR), requires the recruitment and subsequent post-translational modification (PTM) of a complex network of proteins. Ubiquitin and the ubiquitin-like protein (UBL) SUMO have established roles in regulating the cellular response to DNA double-strand breaks (DSBs). A role for other UBLs, such as NEDD8, is also now emerging. This article provides an overview of the DDR, discusses our current understanding of the process and function of PTM by ubiquitin and NEDD8, and reviews the literature surrounding the role of ubiquitylation and neddylation in DNA repair processes, focusing particularly on DNA DSB repair.
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Affiliation(s)
- Jessica S Brown
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
| | - Stephen P Jackson
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
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Abstract
NEDD8 (neural precursor cell expressed developmentally downregulated protein 8) is a ubiquitin-like protein that activates the largest ubiquitin E3 ligase family, the cullin-RING ligases. Many non-cullin neddylation targets have been proposed in recent years. However, overexpression of exogenous NEDD8 can trigger NEDD8 conjugation through the ubiquitylation machinery, which makes validating potential NEDD8 targets challenging. Here, we re-evaluate studies of non-cullin targets of NEDD8 in light of the current understanding of the neddylation pathway, and suggest criteria for identifying genuine neddylation substrates under homeostatic conditions. We describe the biological processes that might be regulated by non-cullin neddylation, and the utility of neddylation inhibitors for research and as potential therapies. Understanding the biological significance of non-cullin neddylation is an exciting research prospect primed to reveal fundamental insights.
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Saucedo-Cuevas LP, Ruppen I, Ximénez-Embún P, Domingo S, Gayarre J, Muñoz J, Silva JM, García MJ, Benítez J. CUL4A contributes to the biology of basal-like breast tumors through modulation of cell growth and antitumor immune response. Oncotarget 2015; 5:2330-43. [PMID: 24870930 PMCID: PMC4039166 DOI: 10.18632/oncotarget.1915] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The CUL4A E3 ubiquitin ligase is involved in the regulation of many cellular processes and its amplification and/or overexpression has been observed in breast cancer. The 13q34 amplification, which is associated with the basal-like breast cancer subtype, has been proposed as one of the mechanism behind CUL4A up-regulation. However, the specific contribution of CUL4A to the biology of basal-like breast tumors has not yet been elucidated. In this work, by using cellular models of basal phenotype, we show the inhibitory effect of CUL4A silencing in the proliferation and growth of breast cancer cells both, in vitro and in vivo. We also demonstrate the transforming capacity of CUL4A exogenous overexpression in the 184B5 human mammary epithelial cells in vitro. Our results suggest a synergistic effect between CUL4A high levels and the activation of the RAS pathway in the tumorigenesis of basal-like breast cancer tumors. In addition, by using a proteomics approach we have defined novel candidate proteins and pathways that might mediate the oncogenic effect of CUL4A. In particular, we report a putative role of CUL4A in bypassing the immune system in breast cancer through the down-regulation of several molecules involved in the immune surveillance. These findings provide insight into the oncogenic properties of CUL4A in basal-like breast cancer and highlight the therapeutic opportunities to target CUL4A.
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Affiliation(s)
- Laura P Saucedo-Cuevas
- Group of Human Genetics, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Spain
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Wang Y, Zhang P, Liu Z, Wang Q, Wen M, Wang Y, Yuan H, Mao JH, Wei G. CUL4A overexpression enhances lung tumor growth and sensitizes lung cancer cells to erlotinib via transcriptional regulation of EGFR. Mol Cancer 2014; 13:252. [PMID: 25413624 PMCID: PMC4246448 DOI: 10.1186/1476-4598-13-252] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 11/10/2014] [Indexed: 12/21/2022] Open
Abstract
Background CUL4A has been proposed as oncogene in several types of human cancer, but its clinical significance and functional role in human non-small cell lung cancer (NSCLC) remain unclear. Methods Expression level of CUL4A was examined by RT-PCR and Western blot. Forced expression of CUL4A was mediated by retroviruses, and CUL4A silencing by shRNAs expressing lentiviruses. Growth capacity of lung cancer cells was measured by MTT in vitro and tumorigenesis in vivo, respectively. Results We found that CUL4A was highly expressed in human lung cancer tissues and lung cancer cell lines, and this elevated expression positively correlated with disease progression and prognosis. Overexpression of CUL4A in human lung cancer cell lines increased cell proliferation, inhibited apoptosis, and subsequently conferred resistance to chemotherapy. On other hand, silencing CUL4A expression in NSCLC cells reduced proliferation, promoted apoptosis and resulted in tumor growth inhibition in cancer xenograft model. Mechanistically, we revealed CUL4A regulated EGFR transcriptional expression and activation, and subsequently activated AKT. Targeted inhibition of EGFR activity blocked these CUL4A induced oncogenic activities. Conclusions Our results highlight the significance of CUL4A in NSCLC and suggest that CUL4A could be a promising therapy target and a potential biomarker for prognosis and EGFR target therapy in NSCLC patients. Electronic supplementary material The online version of this article (doi:10.1186/1476-4598-13-252) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Guangwei Wei
- Department of Anatomy and Key Laboratory of Experimental Teratology, Ministry of Education, Shandong University School of Medicine, 44 Wenhua Xi Road, Jinan, Shandong 250012, P,R, China.
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Zhao X, Jiang B, Hu H, Mao F, Mi J, Li Z, Liu Q, Shao C, Gong Y. Zebrafish cul4a, but not cul4b, modulates cardiac and forelimb development by upregulating tbx5a expression. Hum Mol Genet 2014; 24:853-64. [PMID: 25274780 DOI: 10.1093/hmg/ddu503] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
CUL4A and CUL4B are closely related cullin family members and can each assemble a Cullin-RING E3 ligase complex (CRL) and participate in a variety of biological processes. While the CRLs formed by the two cullin members may have common targets, the two appeared to have very different consequences when mutated or disrupted in mammals. We here investigated the roles of cul4a and cul4b during zebrafish embryogenesis by using the morpholino knockdown approach. We found that cul4a is essential for cardiac development as well as for pectoral fin development. Whereas cul4a morphants appeared to be unperturbed in chamber specification, they failed to undergo heart looping. The failures in heart looping and pectoral fin formation in cul4a morphants were accompanied by greatly reduced proliferation of cardiac cells and pectoral fin-forming cells. We demonstrated that tbx5a, a transcription factor essential for heart and limb development, is transcriptionally upregulated by cul4a and mediates the function of cul4a in cardiac and pectoral fin development. In contrast to the critical importance of cul4a, cul4b appeared to be dispensable for zebrafish development and was incapable of compensating for the loss of cul4a. This work provides the first demonstration of an essential role of cul4a, but not cul4b, in cardiac development and in the regulation of tbx5a in zebrafish. These findings justify exploring the functional role of CUL4A in human cardiac development.
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Affiliation(s)
- Xiaohan Zhao
- The Key Laboratory of Experimental Teratology, Ministry of Education and Institute of Molecular Medicine and Genetics, Shandong University School of Medicine, Jinan, Shandong 250012, China
| | - Baichun Jiang
- The Key Laboratory of Experimental Teratology, Ministry of Education and Institute of Molecular Medicine and Genetics, Shandong University School of Medicine, Jinan, Shandong 250012, China
| | - Huili Hu
- The Key Laboratory of Experimental Teratology, Ministry of Education and Institute of Molecular Medicine and Genetics, Shandong University School of Medicine, Jinan, Shandong 250012, China
| | - Fei Mao
- The Key Laboratory of Experimental Teratology, Ministry of Education and Institute of Molecular Medicine and Genetics, Shandong University School of Medicine, Jinan, Shandong 250012, China
| | - Jun Mi
- The Key Laboratory of Experimental Teratology, Ministry of Education and Institute of Molecular Medicine and Genetics, Shandong University School of Medicine, Jinan, Shandong 250012, China
| | - Zhaohui Li
- The Key Laboratory of Experimental Teratology, Ministry of Education and Institute of Molecular Medicine and Genetics, Shandong University School of Medicine, Jinan, Shandong 250012, China
| | - Qiji Liu
- The Key Laboratory of Experimental Teratology, Ministry of Education and Institute of Molecular Medicine and Genetics, Shandong University School of Medicine, Jinan, Shandong 250012, China
| | - Changshun Shao
- The Key Laboratory of Experimental Teratology, Ministry of Education and Institute of Molecular Medicine and Genetics, Shandong University School of Medicine, Jinan, Shandong 250012, China
| | - Yaoqin Gong
- The Key Laboratory of Experimental Teratology, Ministry of Education and Institute of Molecular Medicine and Genetics, Shandong University School of Medicine, Jinan, Shandong 250012, China
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Ding X, Zhu L, Ji T, Zhang X, Wang F, Gan S, Zhao M, Yang H. Long intergenic non-coding RNAs (LincRNAs) identified by RNA-seq in breast cancer. PLoS One 2014; 9:e103270. [PMID: 25084155 PMCID: PMC4118859 DOI: 10.1371/journal.pone.0103270] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 06/29/2014] [Indexed: 12/27/2022] Open
Abstract
In an attempt to find the correlation of aberrant expression of long intergenic noncoding RNAs (lincRNAs) with cancer, twenty-five samples of breast cancer tissue and respective adjacent normal tissue were studied for the expression of lincRNAs by RNA-seq. Among the 538 lincRNAs studied, 124 lincRNAs were exclusively expressed in cancer adjacent tissues and 62 lincRNAs were exclusively expressed in the cancer tissues. Furthermore, the expression of 134 lincRNAs was higher while 272 lower in breast cancer tissue compared with adjacent tissue. The expression of four selected lincRNAs (BC2, BC4, BC5, and BC8) was validated by semi-quantitative and real-time PCR. It was revealed that expression of lincRNA-BC5 was positively correlated with patients' age, pathological stage, and progesterone receptor concentration, while lincRNA-BC8 was negatively correlated with progesterone receptor expression. Higher expression of lincRNA-BC4 was seen in advanced breast cancer grade. LincRNA-BC2 showed no specific changes in the pathological features studied. Interactions between selected lincRNAs and breast cancer associated proteins were highly suggested by RPIseq based on the specific secondary structure. The results demonstrated that this group of lincRNAs was aberrantly expressed in breast cancer. They might play important roles in the function of oncogenes or tumor suppressors affecting the development and progression of breast cancer.
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Affiliation(s)
- Xianfeng Ding
- Institute of Bioengineering, College of Life Science, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, P.R. China
| | - Limin Zhu
- Institute of Bioengineering, College of Life Science, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, P.R. China
| | - Ting Ji
- Institute of Bioengineering, College of Life Science, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, P.R. China
| | - Xiping Zhang
- Zhejiang Cancer Research Institute, Department of Breast Tumor Surgery, Zhejiang Cancer Hospital, Banshan Bridge, Hangzhou, Zhejiang, P.R. China
| | - Fengmei Wang
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, P.R. China
| | - Shaoju Gan
- Institute of Bioengineering, College of Life Science, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, P.R. China
| | - Ming Zhao
- Institute of Bioengineering, College of Life Science, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, P.R. China
| | - Hongjian Yang
- Zhejiang Cancer Research Institute, Department of Breast Tumor Surgery, Zhejiang Cancer Hospital, Banshan Bridge, Hangzhou, Zhejiang, P.R. China
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Yang YL, Hung MS, Wang Y, Ni J, Mao JH, Hsieh D, Au A, Kumar A, Quigley D, Fang LT, Yeh CC, Xu Z, Jablons DM, You L. Lung tumourigenesis in a conditional Cul4A transgenic mouse model. J Pathol 2014; 233:113-23. [PMID: 24648314 DOI: 10.1002/path.4352] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 02/15/2014] [Accepted: 03/10/2014] [Indexed: 12/29/2022]
Abstract
Cullin4A (Cul4A) is a scaffold protein that assembles cullin-RING ubiquitin ligase (E3) complexes and regulates many cellular events, including cell survival, development, growth and cell cycle control. Our previous study suggested that Cul4A is oncogenic in vitro, but its oncogenic role in vivo has not been studied. Here, we used a Cul4A transgenic mouse model to study the potential oncogenic role of Cul4A in lung tumour development. After Cul4A over-expression was induced in the lungs for 32 weeks, atypical epithelial cells were observed. After 40 weeks, lung tumours were visible and were characterized as grade I or II adenocarcinomas. Immunohistochemistry (IHC) revealed decreased levels of Cul4A-associated proteins p21(CIP1) and tumour suppressor p19(ARF) in the lung tumours, suggesting that Cul4A regulated their expression in these tumours. Increased levels of p27(KIP1) and p16(INK4a) were also detected in these tumours. Moreover, the protein level of DNA replication licensing factor CDT1 was decreased. Genomic instability in the lung tumours was further analysed by the results from pericentrin protein expression and array comparative genomic hybridization analysis. Furthermore, knocking down Cul4A expression in lung cancer H2170 cells increased their sensitivity to the chemotherapy drug cisplatin in vitro, suggesting that Cul4A over-expression is associated with cisplatin resistance in the cancer cells. Our findings indicate that Cul4A is oncogenic in vivo, and this Cul4A mouse model is a tool in understanding the mechanisms of Cul4A in human cancers and for testing experimental therapies targeting Cul4A.
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Affiliation(s)
- Yi-Lin Yang
- Department of Surgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
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From chromosomal abnormalities to the identification of target genes in mouse models of breast cancer. Cancer Genet 2014; 207:233-46. [DOI: 10.1016/j.cancergen.2014.06.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 05/16/2014] [Accepted: 06/20/2014] [Indexed: 12/30/2022]
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Wang Y, Wen M, Kwon Y, Xu Y, Liu Y, Zhang P, He X, Wang Q, Huang Y, Jen KY, LaBarge MA, You L, Kogan SC, Gray JW, Mao JH, Wei G. CUL4A induces epithelial-mesenchymal transition and promotes cancer metastasis by regulating ZEB1 expression. Cancer Res 2013; 74:520-31. [PMID: 24305877 DOI: 10.1158/0008-5472.can-13-2182] [Citation(s) in RCA: 158] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The ubiquitin ligase CUL4A has been implicated in tumorigenesis, but its contributions to progression and metastasis have not been evaluated. Here, we show that CUL4A is elevated in breast cancer as well as in ovarian, gastric, and colorectal tumors in which its expression level correlates positively with distant metastasis. CUL4A overexpression in normal or malignant human mammary epithelial cells increased their neoplastic properties in vitro and in vivo, markedly increasing epithelial-mesenchymal transition (EMT) and the metastatic capacity of malignant cells. In contrast, silencing CUL4A in aggressive breast cancer cells inhibited these processes. Mechanistically, we found that CUL4A modulated histone H3K4me3 at the promoter of the EMT regulatory gene ZEB1 in a manner associated with its transcription. ZEB1 silencing blocked CUL4A-driven proliferation, EMT, tumorigenesis, and metastasis. Furthermore, in human breast cancers, ZEB1 expression correlated positively with CUL4A expression and distant metastasis. Taken together, our findings reveal a pivotal role of CUL4A in regulating the metastatic behavior of breast cancer cells.
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Affiliation(s)
- Yunshan Wang
- Authors' Affiliations: Department of Human Anatomy and Key Laboratory of Experimental Teratology, Ministry of Education; Department of Biochemistry and Molecular Biology, Shandong University School of Medicine; Department of Respiratory Medicine, Qilu Hospital, Shandong University, Jinan; International Biotechnology R&D Center, Shandong University School of Ocean, Weihai, Shandong, China; Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley; Department of Pathology; Thoracic Oncology Laboratory, Department of Surgery; Helen Diller Family Comprehensive Cancer Center and Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California; and Department of Biomedical Engineering, Oregon Health and Science University, Portland, Oregon
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Bommeljé CC, Weeda VB, Huang G, Shah K, Bains S, Buss E, Shaha M, Gönen M, Ghossein R, Ramanathan SY, Singh B. Oncogenic function of SCCRO5/DCUN1D5 requires its Neddylation E3 activity and nuclear localization. Clin Cancer Res 2013; 20:372-81. [PMID: 24192928 DOI: 10.1158/1078-0432.ccr-13-1252] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
PURPOSE To determine mechanisms by which SCCRO5 (aka DCUN1D5) promotes oncogenesis. EXPERIMENTAL DESIGN SCCRO5 mRNA and protein expression were assessed in 203 randomly selected primary cancer tissue samples, matched histologically normal tissues, and cell lines by use of real-time PCR and Western blot analysis. SCCRO5 overexpression was correlated with survival. The effect of SCCRO5 knockdown on viability was assessed in selected cancer cell lines. Structure-function studies were performed to determine the SCCRO5 residues required for binding to the neddylation components, for neddylation-promoting activity, and for transformation. RESULTS In oral and lung squamous cell carcinomas, SCCRO5 mRNA levels corresponded with protein levels and overexpression correlated with decreased disease-specific survival. Knockdown of SCCRO5 by RNAi resulted in a selective decrease in the viability of cancer cells with high endogenous levels, suggesting the presence of oncogene addiction. SCCRO5 promoted cullin neddylation while maintaining conserved reaction processivity paradigms involved in ubiquitin and ubiquitin-like protein conjugation, establishing it as a component of the neddylation E3. Neddylation activities in vitro required the potentiating of neddylation (PONY) domain but not the nuclear localization sequence (NLS) domain. In contrast, both the NLS domain and the PONY domain were required for transformation of NIH-3T3 cells. CONCLUSIONS Our data suggest that SCCRO5 has oncogenic potential that requires its function as a component of the neddylation E3. Neddylation activity and nuclear localization of SCCRO5 are important for its in vivo function.
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Affiliation(s)
- Claire C Bommeljé
- Authors' Affiliations: Department of Surgery, Laboratory of Epithelial Cancer Biology and Departments of Epidemiology and Biostatistics and Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
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Moscovich M, LeDoux MS, Xiao J, Rampon GL, Vemula SR, Rodriguez RL, Foote KD, Okun MS. Dystonia, facial dysmorphism, intellectual disability and breast cancer associated with a chromosome 13q34 duplication and overexpression of TFDP1: case report. BMC MEDICAL GENETICS 2013; 14:70. [PMID: 23849371 PMCID: PMC3722009 DOI: 10.1186/1471-2350-14-70] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 07/03/2013] [Indexed: 12/02/2022]
Abstract
Background Dystonia is a movement disorder characterized by involuntary sustained muscle contractions causing twisting and repetitive movements or abnormal postures. Some cases of primary and neurodegenerative dystonia have been associated with mutations in individual genes critical to the G1-S checkpoint pathway (THAP1, ATM, CIZ1 and TAF1). Secondary dystonia is also a relatively common clinical sign in many neurogenetic disorders. However, the contribution of structural variation in the genome to the etiopathogenesis of dystonia remains largely unexplored. Case presentation Cytogenetic analyses with the Affymetrix Genome-Wide Human SNP Array 6.0 identified a chromosome 13q34 duplication in a 36 year-old female with global developmental delay, facial dysmorphism, tall stature, breast cancer and dystonia, and her neurologically-normal father. Dystonia improved with bilateral globus pallidus interna (GPi) deep brain stimulation (DBS). Genomic breakpoint analysis, quantitative PCR (qPCR) and leukocyte gene expression were used to characterize the structural variant. The 218,345 bp duplication was found to include ADPRHL1, DCUN1D2, and TMCO3, and a 69 bp fragment from a long terminal repeat (LTR) located within Intron 3 of TFDP1. The 3' breakpoint was located within Exon 1 of a TFDP1 long non-coding RNA (NR_026580.1). In the affected subject and her father, gene expression was higher for all three genes located within the duplication. However, in comparison to her father, mother and neurologically-normal controls, the affected subject also showed marked overexpression (2×) of the transcription factor TFDP1 (NM_007111.4). Whole-exome sequencing identified an SGCE variant (c.1295G > A, p.Ser432His) that could possibly have contributed to the development of dystonia in the proband. No pathogenic mutations were identified in BRCA1 or BRCA2. Conclusion Overexpression of TFDP1 has been associated with breast cancer and may also be linked to the tall stature, dysmorphism and dystonia seen in our patient.
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