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Wang J, Xiang Y, Fan M, Fang S, Hua Q. The Ubiquitin-Proteasome System in Tumor Metabolism. Cancers (Basel) 2023; 15:cancers15082385. [PMID: 37190313 DOI: 10.3390/cancers15082385] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/16/2023] [Accepted: 04/17/2023] [Indexed: 05/17/2023] Open
Abstract
Metabolic reprogramming, which is considered a hallmark of cancer, can maintain the homeostasis of the tumor environment and promote the proliferation, survival, and metastasis of cancer cells. For instance, increased glucose uptake and high glucose consumption, known as the "Warburg effect," play an essential part in tumor metabolic reprogramming. In addition, fatty acids are harnessed to satisfy the increased requirement for the phospholipid components of biological membranes and energy. Moreover, the anabolism/catabolism of amino acids, such as glutamine, cystine, and serine, provides nitrogen donors for biosynthesis processes, development of the tumor inflammatory environment, and signal transduction. The ubiquitin-proteasome system (UPS) has been widely reported to be involved in various cellular biological activities. A potential role of UPS in the metabolic regulation of tumor cells has also been reported, but the specific regulatory mechanism has not been elucidated. Here, we review the role of ubiquitination and deubiquitination modification on major metabolic enzymes and important signaling pathways in tumor metabolism to inspire new strategies for the clinical treatment of cancer.
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Affiliation(s)
- Jie Wang
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Yuandi Xiang
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Mengqi Fan
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Shizhen Fang
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Qingquan Hua
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
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Wang X, Yu G, Yan Z, Wan L, Wang W, Cui L. Lung Cancer Subtype Diagnosis by Fusing Image-Genomics Data and Hybrid Deep Networks. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:512-523. [PMID: 34855599 DOI: 10.1109/tcbb.2021.3132292] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Accurate diagnosis of cancer subtypes is crucial for precise treatment, because different cancer subtypes are involved with different pathology and require different therapies. Although deep learning techniques have made great success in computer vision and other fields, they do not work well on Lung cancer subtype diagnosis, due to the distinction of slide images between different cancer subtypes is ambiguous. Furthermore, they often over-fit to high-dimensional genomics data with limited samples, and do not fuse the image and genomics data in a sensible way. In this paper, we propose a hybrid deep network based approach LungDIG for Lung cancer subtype Diagnosis by fusing Image-Genomics data. LungDIG first tiles the tissue slide image into small patches and extracts the patch-level features by fine-tuning an Inception-V3 model. Since the patches may contain some false positives in non-diagnostic regions, it further designs a patch-level feature combination strategy to integrate the extracted patch features and maintain the diversity between different cancer subtypes. At the same time, it extracts the genomics features from Copy Number Variation data by an attention based nonlinear extractor. Next, it fuses the image and genomics features by an attention based multilayer perceptron (MLP) to diagnose cancer subtype. Experiments on TCGA lung cancer data show that LungDIG can not only achieve higher accuracy for cancer subtype diagnosis than state-of-the-art methods, but also have a high authenticity and good interpretability.
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Significance of a PTEN Mutational Status-Associated Gene Signature in the Progression and Prognosis of Endometrial Carcinoma. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:5130648. [PMID: 35251475 PMCID: PMC8890874 DOI: 10.1155/2022/5130648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/10/2021] [Accepted: 01/11/2022] [Indexed: 11/29/2022]
Abstract
Background PTEN mutations have been reported to be involved in the development and prognosis of endometrial carcinoma (EC). However, a prognostic gene signature associated with PTEN mutational status has not yet been developed. In this study, we generated a PTEN mutation-associated prognostic gene signature for EC. Methods We obtained the single-nucleotide variation and transcriptomic profiling data from The Cancer Genome Atlas database as training data and implemented the least absolute shrinkage and selection operator (LASSO) Cox regression algorithm to establish a PTEN mutation-associated prognostic gene signature. The overall survival rates of the high-risk and low-risk groups were determined with the Kaplan-Meier (K-M) method, and the accuracy of risk score prediction was tested by using the receiver operating characteristic (ROC) curve. Results The K-M curves revealed that the EC patients with PTEN mutations augured favorable survival outcomes. Differential expression analysis between the EC patients with PTEN mutation and wild-type PTEN identified 224 differentially expressed genes (DEGs). Eighty-four DEGs that manifested prognostic value were fitted into the LASSO-Cox analysis, and a PTEN gene signature with seven mutation-associated prognostic genes that showed robust prognostic ability was constructed; this signature was then successfully validated in the other two datasets from the cBioPortal database as well as with 60 clinical specimens. Furthermore, the PTEN mutation-associated prognostic gene signature proved to be an independent prognostic predictor of EC. Remarkably, the EC patients in the high-risk group were characterized by higher tumor stages and grades as well as lower tumor mutation burden with respect to EC, with a poor survival outcome. Collectively, the PTEN mutation-associated prognostic gene signature that we developed could now be used as a favorable prognostic biomarker for EC. Conclusion In summary, we developed and validated a prognostic predictor for EC associated with PTEN mutational status that may be used as a favorable prognostic biomarker and therapeutic target for EC.
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Pradhan RK, Ramakrishna W. Transposons: Unexpected players in cancer. Gene 2022; 808:145975. [PMID: 34592349 DOI: 10.1016/j.gene.2021.145975] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/19/2021] [Accepted: 09/24/2021] [Indexed: 12/21/2022]
Abstract
Transposons are repetitive DNA sequences encompassing about half of the human genome. They play a vital role in genome stability maintenance and contribute to genomic diversity and evolution. Their activity is regulated by various mechanisms considering the deleterious effects of these mobile elements. Various genetic risk factors and environmental stress conditions affect the regulatory pathways causing alteration of transposon expression. Our knowledge of the biological role of transposons is limited especially in various types of cancers. Retrotransposons of different types (LTR-retrotransposons, LINEs and SINEs) regulate a plethora of genes that have a role in cell reprogramming, tumor suppression, cell cycle, apoptosis, cell adhesion and migration, and DNA repair. The regulatory mechanisms of transposons, their deregulation and different mechanisms underlying transposon-mediated carcinogenesis in humans focusing on the three most prevalent types, lung, breast and colorectal cancers, were reviewed. The modes of regulation employed include alternative splicing, deletion, insertion, duplication in genes and promoters resulting in upregulation, downregulation or silencing of genes.
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Zhao M, Quan Y, Zeng J, Lyu X, Wang H, Lei JH, Feng Y, Xu J, Chen Q, Sun H, Xu X, Lu L, Deng CX. Cullin3 deficiency shapes tumor microenvironment and promotes cholangiocarcinoma in liver-specific Smad4/Pten mutant mice. Int J Biol Sci 2021; 17:4176-4191. [PMID: 34803491 PMCID: PMC8579464 DOI: 10.7150/ijbs.67379] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 09/26/2021] [Indexed: 11/24/2022] Open
Abstract
Cholangiocarcinoma (CC), the most lethal type of liver cancer, remains very difficult to treat due to an incomplete understanding of the cancer initiation and progression mechanisms and no effective therapeutic drugs. Thus, identification of genomic drivers and delineation of the underlying mechanisms are urgently needed. Here, we conducted a genome-wide CRISPR-Cas9 screening in liver-specific Smad4/Pten knockout mice (Smad4co/co;Ptenco/co;Alb-Cre, abbreviated as SPC), and identified 15 putative tumor suppressor genes, including Cullin3 (Cul3), whose deficiency increases protein levels of Nrf2 and Cyclin D1 that accelerate cholangiocytes expansion leading to the initiation of CC. Meanwhile, Cul3 deficiency also increases the secretion of Cxcl9 in stromal cells to attract T cells infiltration, and increases the production of Amphiregulin (Areg) mediated by Nrf2, which paracrinely induces inflammation in the liver, and promotes accumulation of exhausted PD1high CD8 T cells at the expenses of their cytotoxic activity, allowing CC progression. We demonstrate that the anti-PD1/PD-L1 blockade inhibits CC growth, and the effect is enhanced by combining with sorafenib selected from organoid mediated drug sensitive test. This model makes it possible to further identify more liver cancer suppressors, study molecular mechanisms, and develop effective therapeutic strategies.
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Affiliation(s)
- Ming Zhao
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau SAR, China
- Centre for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau SAR, China
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Yingyao Quan
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau SAR, China
- Centre for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau SAR, China
- Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University
| | - Jianming Zeng
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Xueying Lyu
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Haitao Wang
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Josh Haipeng Lei
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Yangyang Feng
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Jun Xu
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Qiang Chen
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau SAR, China
- MOE Frontieers Science Center for Precision Oncogene, University of Macau, Macau SAR, China
| | - Heng Sun
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau SAR, China
- MOE Frontieers Science Center for Precision Oncogene, University of Macau, Macau SAR, China
| | - Xiaoling Xu
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau SAR, China
- MOE Frontieers Science Center for Precision Oncogene, University of Macau, Macau SAR, China
| | - Ligong Lu
- Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University
| | - Chu-Xia Deng
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau SAR, China
- Centre for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau SAR, China
- MOE Frontieers Science Center for Precision Oncogene, University of Macau, Macau SAR, China
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Aiderus A, Contreras-Sandoval AM, Meshey AL, Newberg JY, Ward JM, Swing DA, Copeland NG, Jenkins NA, Mann KM, Mann MB. Promoterless Transposon Mutagenesis Drives Solid Cancers via Tumor Suppressor Inactivation. Cancers (Basel) 2021; 13:E225. [PMID: 33435458 PMCID: PMC7827284 DOI: 10.3390/cancers13020225] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 12/30/2020] [Accepted: 12/31/2020] [Indexed: 12/19/2022] Open
Abstract
A central challenge in cancer genomics is the systematic identification of single and cooperating tumor suppressor gene mutations driving cellular transformation and tumor progression in the absence of oncogenic driver mutation(s). Multiple in vitro and in vivo gene inactivation screens have enhanced our understanding of the tumor suppressor gene landscape in various cancers. However, these studies are limited to single or combination gene effects, specific organs, or require sensitizing mutations. In this study, we developed and utilized a Sleeping Beauty transposon mutagenesis system that functions only as a gene trap to exclusively inactivate tumor suppressor genes. Using whole body transposon mobilization in wild type mice, we observed that cumulative gene inactivation can drive tumorigenesis of solid cancers. We provide a quantitative landscape of the tumor suppressor genes inactivated in these cancers and show that, despite the absence of oncogenic drivers, these genes converge on key biological pathways and processes associated with cancer hallmarks.
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Affiliation(s)
- Aziz Aiderus
- Department of Molecular Oncology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA; (A.A.); (A.M.C.-S.); (A.L.M.); (J.Y.N.)
| | - Ana M. Contreras-Sandoval
- Department of Molecular Oncology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA; (A.A.); (A.M.C.-S.); (A.L.M.); (J.Y.N.)
| | - Amanda L. Meshey
- Department of Molecular Oncology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA; (A.A.); (A.M.C.-S.); (A.L.M.); (J.Y.N.)
| | - Justin Y. Newberg
- Department of Molecular Oncology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA; (A.A.); (A.M.C.-S.); (A.L.M.); (J.Y.N.)
- Cancer Research Program, Houston Methodist Research Institute, Houston, TX 77030, USA; (N.G.C.); (N.A.J.)
| | - Jerrold M. Ward
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore;
| | - Deborah A. Swing
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA;
| | - Neal G. Copeland
- Cancer Research Program, Houston Methodist Research Institute, Houston, TX 77030, USA; (N.G.C.); (N.A.J.)
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore;
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA;
| | - Nancy A. Jenkins
- Cancer Research Program, Houston Methodist Research Institute, Houston, TX 77030, USA; (N.G.C.); (N.A.J.)
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore;
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA;
| | - Karen M. Mann
- Department of Molecular Oncology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA; (A.A.); (A.M.C.-S.); (A.L.M.); (J.Y.N.)
- Cancer Research Program, Houston Methodist Research Institute, Houston, TX 77030, USA; (N.G.C.); (N.A.J.)
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore;
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA;
- Departments of Gastrointestinal Oncology & Malignant Hematology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
- Cancer Biology and Evolution Program, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
- Department of Oncologic Sciences, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Michael B. Mann
- Department of Molecular Oncology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA; (A.A.); (A.M.C.-S.); (A.L.M.); (J.Y.N.)
- Cancer Research Program, Houston Methodist Research Institute, Houston, TX 77030, USA; (N.G.C.); (N.A.J.)
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore;
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA;
- Cancer Biology and Evolution Program, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
- Department of Oncologic Sciences, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Donald A. Adam Melanoma and Skin Cancer Research Center of Excellence, Moffitt Cancer Center, Tampa, FL 33612, USA
- Department of Cutaneous Oncology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
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7
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Li C, Kasinski AL. InVivo Cancer-Based Functional Genomics. Trends Cancer 2020; 6:1002-1017. [PMID: 32828714 DOI: 10.1016/j.trecan.2020.07.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 07/13/2020] [Accepted: 07/20/2020] [Indexed: 12/18/2022]
Abstract
Pinpointing the underlying mechanisms that drive tumorigenesis in human patients is a prerequisite for identifying suitable therapeutic targets for precision medicine. In contrast to cell culture systems, mouse models are highly favored for evaluating tumor progression and therapeutic response in a more realistic in vivo context. The past decade has witnessed a dramatic increase in the number of functional genomic studies using diverse mouse models, including in vivo clustered regularly interspaced short palindromic repeats (CRISPR) and RNA interference (RNAi) screens, and these have provided a wealth of knowledge addressing multiple essential questions in translational cancer research. We compare the multiple mouse systems and genomic tools that are commonly used for in vivo screens to illustrate their strengths and limitations. Crucial components of screen design and data analysis are also discussed.
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Affiliation(s)
- Chennan Li
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; Bindley Biosciences Center, Purdue University, West Lafayette, IN 47907, USA
| | - Andrea L Kasinski
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; Bindley Biosciences Center, Purdue University, West Lafayette, IN 47907, USA; Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA.
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8
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Weber J, Braun CJ, Saur D, Rad R. In vivo functional screening for systems-level integrative cancer genomics. Nat Rev Cancer 2020; 20:573-593. [PMID: 32636489 DOI: 10.1038/s41568-020-0275-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/19/2020] [Indexed: 02/06/2023]
Abstract
With the genetic portraits of all major human malignancies now available, we next face the challenge of characterizing the function of mutated genes, their downstream targets, interactions and molecular networks. Moreover, poorly understood at the functional level are also non-mutated but dysregulated genomes, epigenomes or transcriptomes. Breakthroughs in manipulative mouse genetics offer new opportunities to probe the interplay of molecules, cells and systemic signals underlying disease pathogenesis in higher organisms. Herein, we review functional screening strategies in mice using genetic perturbation and chemical mutagenesis. We outline the spectrum of genetic tools that exist, such as transposons, CRISPR and RNAi and describe discoveries emerging from their use. Genome-wide or targeted screens are being used to uncover genomic and regulatory landscapes in oncogenesis, metastasis or drug resistance. Versatile screening systems support experimentation in diverse genetic and spatio-temporal settings to integrate molecular, cellular or environmental context-dependencies. We also review the combination of in vivo screening and barcoding strategies to study genetic interactions and quantitative cancer dynamics during tumour evolution. These scalable functional genomics approaches are transforming our ability to interrogate complex biological systems.
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Affiliation(s)
- Julia Weber
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technische Universität München, Munich, Germany
| | - Christian J Braun
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technische Universität München, Munich, Germany
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dieter Saur
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technische Universität München, Munich, Germany
- Institute of Translational Cancer Research and Experimental Cancer Therapy, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technische Universität München, Munich, Germany.
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technische Universität München, Munich, Germany.
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
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Ma GL, Qiao ZL, He D, Wang J, Kong YY, Xin XY, Wen FQ, Bao SJ, Ma ZR, Wang FS, Xie J, Hu YH. Establishment of a low-tumorigenic MDCK cell line and study of differential molecular networks. Biologicals 2020; 68:112-121. [PMID: 32928630 DOI: 10.1016/j.biologicals.2020.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 07/11/2020] [Accepted: 07/14/2020] [Indexed: 12/18/2022] Open
Abstract
Influenza is an acute respiratory infection caused by the influenza virus, and vaccination against influenza is considered the best way to prevent the onset and spread. MDCK (Madin-Darby canine kidney) cells are typically used to isolate the influenza virus, however, their high tumorigenicity is the main controversy in the production of influenza vaccines. Here, MDCK-C09 and MDCK-C35 monoclonal cell lines were established, which were proven to be low in tumorigenicity. RNA-seq of MDCK-C09, MDCK-C35, and MDCK-W73 cells was performed to investigate the putative tumorigenicity mechanisms. Tumor-related molecular interaction analysis of the differentially expressed genes indicates that hub genes, such as CUL3 and EGFR, may play essential roles in tumorigenicity differences between MDCK-C (MDCK-C09 and MDCK-C35) and MDCK-W (MDCK-W73) cells. Moreover, the analysis of cell proliferation regulation-associated molecular interaction shows that downregulated JUN and MYC, for instance, mediate increased proliferation of these cells. The present study provides a new low-tumorigenic MDCK cell line and describes the potential molecular mechanism for the low tumorigenicity and high proliferation rate.
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Affiliation(s)
- Gui-Lan Ma
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730030, PR China; Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou, 730030, PR China.
| | - Zi-Lin Qiao
- Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou, 730030, PR China.
| | - Dan He
- Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou, 730030, PR China.
| | - Jiao Wang
- Laboratory of Molecular Neural Biology, School of Life Sciences, Shanghai University, Shanghai, China.
| | - Yan-Yan Kong
- Huashan Hospital Affiliated to Fudan University, Shanghai, China.
| | - Xiao-Yong Xin
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730030, PR China.
| | - Feng-Qin Wen
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730030, PR China.
| | - Shi-Jun Bao
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730030, PR China.
| | - Zhong-Ren Ma
- Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou, 730030, PR China.
| | - Fu-Shuai Wang
- Laboratory of Molecular Neural Biology, School of Life Sciences, Shanghai University, Shanghai, China.
| | - Jiang Xie
- School of Computer Engineering and Science, Shanghai University, Shanghai, China.
| | - Yong-Hao Hu
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730030, PR China.
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10
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Wei R, Li P, He F, Wei G, Zhou Z, Su Z, Ni T. Comprehensive analysis reveals distinct mutational signature and its mechanistic insights of alcohol consumption in human cancers. Brief Bioinform 2020; 22:5841903. [PMID: 32480415 DOI: 10.1093/bib/bbaa066] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/24/2020] [Accepted: 03/31/2020] [Indexed: 12/20/2022] Open
Abstract
Alcohol consumption is a critical risk factor for multiple types of cancer. A genome can be attacked and acquire numerous somatic mutations in the environment of alcohol exposure. Mutational signature has the capacity illustrating the complex somatic mutation patterns in cancer genome. Recent studies have discovered distinct mutational signatures associating with alcohol consumption in liver and esophageal cancers. However, their prevalence among diverse cancers, impact of genetic background and origin of alcohol-induced mutational signatures remain unclear. By a comprehensive bioinformatics analysis on somatic mutations from patients of four cancer types with drinking information, we identified nine mutational signatures (signatures B-J), among which signature J (similar to COSMIC signature 16) was distinctive to alcohol drinking. Signature J was associated with HNSC, ESCA and LIHC but not PAAD. Interestingly, patients with mutated allele rs1229984 in ADH1B had lower level of signature J while mutated allele rs671 in ALDH2 exhibited higher signature J abundance, suggesting acetaldehyde is one cause of signature J. Intriguingly, somatic mutations of three potential cancer driver genes (TP53, CUL3 and NSD1) were found the critical contributors for increased mutational load of signature J in alcohol consumption patients. Furthermore, signature J was enriched with early accumulated clonal mutations compared to mutations derived from late tumor growth. This study systematically characterized alcohol-related mutational signature and indicated mechanistic insights into the prevalence, origin and gene-environment interaction regarding the risk oncogenic mutations associated with alcohol intake.
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Abstract
Covering: up to 2020The transcription factor NRF2 is one of the body's major defense mechanisms, driving transcription of >300 antioxidant response element (ARE)-regulated genes that are involved in many critical cellular processes including redox regulation, proteostasis, xenobiotic detoxification, and primary metabolism. The transcription factor NRF2 and natural products have an intimately entwined history, as the discovery of NRF2 and much of its rich biology were revealed using natural products both intentionally and unintentionally. In addition, in the last decade a more sinister aspect of NRF2 biology has been revealed. NRF2 is normally present at very low cellular levels and only activated when needed, however, it has been recently revealed that chronic, high levels of NRF2 can lead to diseases such as diabetes and cancer, and may play a role in other diseases. Again, this "dark side" of NRF2 was revealed and studied largely using a natural product, the quassinoid, brusatol. In the present review, we provide an overview of NRF2 structure and function to orient the general reader, we will discuss the history of NRF2 and NRF2-activating compounds and the biology these have revealed, and we will delve into the dark side of NRF2 and contemporary issues related to the dark side biology and the role of natural products in dissecting this biology.
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Affiliation(s)
- Donna D Zhang
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ 85721, USA.
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12
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Vanneste M, Feddersen CR, Varzavand A, Zhu EY, Foley T, Zhao L, Holt KH, Milhem M, Piper R, Stipp CS, Dupuy AJ, Henry MD. Functional Genomic Screening Independently Identifies CUL3 as a Mediator of Vemurafenib Resistance via Src-Rac1 Signaling Axis. Front Oncol 2020; 10:442. [PMID: 32346533 PMCID: PMC7169429 DOI: 10.3389/fonc.2020.00442] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/12/2020] [Indexed: 12/19/2022] Open
Abstract
Patients with malignant melanoma have a 5-year survival rate of only 15-20% once the tumor has metastasized to distant tissues. While MAP kinase pathway inhibitors (MAPKi) are initially effective for the majority of patients with melanoma harboring BRAFV600E mutation, over 90% of patients relapse within 2 years. Thus, there is a critical need for understanding MAPKi resistance mechanisms. In this manuscript, we performed a forward genetic screen using a whole genome shRNA library to identify negative regulators of vemurafenib resistance. We identified loss of NF1 and CUL3 as drivers of vemurafenib resistance. NF1 is a known driver of vemurafenib resistance in melanoma through its action as a negative regulator of RAS. However, the mechanism by which CUL3, a key protein in E3 ubiquitin ligase complexes, is involved in vemurafenib resistance was unknown. We found that loss of CUL3 was associated with an increase in RAC1 activity and MEKS298 phosphorylation. However, the addition of the Src family inhibitor saracatinib prevented resistance to vemurafenib in CUL3KD cells and reversed RAC1 activation. This finding suggests that inhibition of the Src family suppresses MAPKi resistance in CUL3KD cells by inactivation of RAC1. Our results also indicated that the loss of CUL3 does not promote the activation of RAC1 through stabilization, suggesting that CUL3 is involved in the stability of upstream regulators of RAC1. Collectively, our study identifies the loss of CUL3 as a driver of MAPKi resistance through activation of RAC1 and demonstrates that inhibition of the Src family can suppress the MAPKi resistance phenotype in CUL3KD cells by inactivating RAC1 protein.
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Affiliation(s)
- Marion Vanneste
- Department of Molecular Physiology and Biophysics, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, IA, United States
| | - Charlotte R. Feddersen
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Afshin Varzavand
- Department of Biology, College of Liberal Arts and Sciences, University of Iowa, Iowa City, IA, United States
| | - Elliot Y. Zhu
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Tyler Foley
- Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Lei Zhao
- Department of Molecular Physiology and Biophysics, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, IA, United States
| | - Kathleen H. Holt
- Viral Vector Core Facility, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Mohammed Milhem
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, United States
| | - Robert Piper
- Department of Molecular Physiology and Biophysics, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, IA, United States
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, United States
| | - Christopher S. Stipp
- Department of Biology, College of Liberal Arts and Sciences, University of Iowa, Iowa City, IA, United States
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, United States
| | - Adam J. Dupuy
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, United States
| | - Michael D. Henry
- Department of Molecular Physiology and Biophysics, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, IA, United States
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, United States
- Department of Radiation Oncology, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, IA, United States
- Department of Pathology, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, IA, United States
- Department of Urology, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, IA, United States
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13
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Transposon Insertion Mutagenesis in Mice for Modeling Human Cancers: Critical Insights Gained and New Opportunities. Int J Mol Sci 2020; 21:ijms21031172. [PMID: 32050713 PMCID: PMC7036786 DOI: 10.3390/ijms21031172] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 01/30/2020] [Accepted: 02/03/2020] [Indexed: 02/07/2023] Open
Abstract
Transposon mutagenesis has been used to model many types of human cancer in mice, leading to the discovery of novel cancer genes and insights into the mechanism of tumorigenesis. For this review, we identified over twenty types of human cancer that have been modeled in the mouse using Sleeping Beauty and piggyBac transposon insertion mutagenesis. We examine several specific biological insights that have been gained and describe opportunities for continued research. Specifically, we review studies with a focus on understanding metastasis, therapy resistance, and tumor cell of origin. Additionally, we propose further uses of transposon-based models to identify rarely mutated driver genes across many cancers, understand additional mechanisms of drug resistance and metastasis, and define personalized therapies for cancer patients with obesity as a comorbidity.
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Chiu HS, Martínez MR, Komissarova EV, Llobet-Navas D, Bansal M, Paull EO, Silva J, Yang X, Sumazin P, Califano A. The number of titrated microRNA species dictates ceRNA regulation. Nucleic Acids Res 2019; 46:4354-4369. [PMID: 29684207 PMCID: PMC5961349 DOI: 10.1093/nar/gky286] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 04/04/2018] [Indexed: 12/14/2022] Open
Abstract
microRNAs (miRNAs) play key roles in cancer, but their propensity to couple their targets as competing endogenous RNAs (ceRNAs) has only recently emerged. Multiple models have studied ceRNA regulation, but these models did not account for the effects of co-regulation by miRNAs with many targets. We modeled ceRNA and simulated its effects using established parameters for miRNA/mRNA interaction kinetics while accounting for co-regulation by multiple miRNAs with many targets. Our simulations suggested that co-regulation by many miRNA species is more likely to produce physiologically relevant context-independent couplings. To test this, we studied the overlap of inferred ceRNA networks from four tumor contexts-our proposed pan-cancer ceRNA interactome (PCI). PCI was composed of interactions between genes that were co-regulated by nearly three-times as many miRNAs as other inferred ceRNA interactions. Evidence from expression-profiling datasets suggested that PCI interactions are predictive of gene expression in 12 independent tumor- and non-tumor contexts. Biochemical assays confirmed ceRNA couplings for two PCI subnetworks, including oncogenes CCND1, HIF1A and HMGA2, and tumor suppressors PTEN, RB1 and TP53. Our results suggest that PCI is enriched for context-independent interactions that are coupled by many miRNA species and are more likely to be context independent.
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Affiliation(s)
- Hua-Sheng Chiu
- Texas Children's Cancer Center and Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | | | - Elena V Komissarova
- Department of Systems Biology, Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Center for Computational Biology and Bioinformatics, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA.,Department of Pathology and Cell Biology, Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Center for Computational Biology and Bioinformatics, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - David Llobet-Navas
- Bellvitge Biomedical Research Institute (IDIBELL), Gran via de l'Hospitalet, 199, L'Hospitalet de Llobregat 08908, Spain
| | - Mukesh Bansal
- Department of Systems Biology, Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Center for Computational Biology and Bioinformatics, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - Evan O Paull
- Department of Systems Biology, Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Center for Computational Biology and Bioinformatics, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - José Silva
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xuerui Yang
- MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Pavel Sumazin
- Texas Children's Cancer Center and Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Andrea Califano
- Department of Systems Biology, Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Center for Computational Biology and Bioinformatics, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA.,Department of Biomedical Informatics, and Department of Biochemistry and Molecular Biophysics, and Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Center for Computational Biology and Bioinformatics, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
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15
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Koyama T, Rhrissorrakrai K, Parida L. Analysis on GENIE reveals novel recurrent variants that affect molecular diagnosis of sizable number of cancer patients. BMC Cancer 2019; 19:114. [PMID: 30709382 PMCID: PMC6359859 DOI: 10.1186/s12885-019-5313-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 01/22/2019] [Indexed: 12/18/2022] Open
Abstract
Background Significant numbers of variants detected in cancer patients are often left labeled only as variants of unknown significance (VUS). In order to expand precision medicine to a wider population, we need to extend our knowledge of pathogenicity and drug response in the context of VUS’s. Methods In this study, we analyzed variants from AACR Project GENIE Consortium APG (Cancer Discov 7:818-831, 2017) and compared them to the COSMIC database Forbes et al. (Nucleic Acids Res 43:D805-811, 2015) to identify recurrent variants that would merit further study. We filtered out known hotspot variants, inactivating variants in tumor suppressors, and likely benign variants by comparing with COSMIC and ExAC Lee et al. (Science 337:967-971, 2012). Results We have identified 45,933 novel variants with unknown significance unique to GENIE. In our analysis, we found on average six variants per patient where two could be considered as pathogenic or likely pathogenic and the majority are VUS’s. More importantly, we have discovered 730 recurrent variants that appear more than 3 times in GENIE but less than 3 in COSMIC. If we combine the recurrences of GENIE and COSMIC for all variants, 2586 are newly identified as occurring more than 3 times than when using COSMIC alone. Conclusions Although it would be inappropriate to blindly accept these recurrent variants as pathogenic, they may warrant higher priority than other observed VUS’s. These newly identified recurrent variants might affect the molecular profiles of approximately 1 in 6 patients. Further analysis and characterization of these variants in both research and clinical contexts will improve patient treatments and the development of new therapeutics. Electronic supplementary material The online version of this article (10.1186/s12885-019-5313-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Takahiko Koyama
- IBM TJ Watson Research Center, Yorktown Heights, NY, 10598, USA.
| | | | - Laxmi Parida
- IBM TJ Watson Research Center, Yorktown Heights, NY, 10598, USA
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Abstract
Cancer is a complex disease that originates from genetic changes leading to multiple phenotypic manifestations that ultimately result in suffering and death from cancer. Attempts have been made to define the phenotypic and genetic "hallmarks" of cancer, but many of these "hallmarks" remain descriptive, while the underlying mechanisms responsible for these hallmarks remain elusive. For decades, cancer researchers have been methodically identifying the molecular mechanisms that result in tumor initiation, growth, metastases, and resistance to therapy. Great strides forward have been made and we are entering an era of "precision medicine" with the goal of treating each cancer based on its unique etiology. Increasingly, the decision to use targeted therapies and immunotherapies in the clinic is based on the genotype of the cancer being treated. For example, specific tyrosine kinase inhibitors are only prescribed to patients that express the tyrosine kinase protein on their cancer cells. Likewise, a genetically unstable cancer is predictive for successful immunotherapy. Knowledge of the specific genetic changes that result in overproduction of oncogenes and reduced production of tumor suppressors is crucial for advancing therapeutic options for cancer. The first chapter of this book presents a brief history of cancer gene discovery. In the remaining chapters of this book, we present protocols using in silico, in vitro, and in vivo techniques for identifying genetic drivers of cancer, in the hope that these protocols will be used to increase our knowledge of the molecular mechanisms driving cancer.
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17
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Guimaraes-Young A, Feddersen CR, Dupuy AJ. Sleeping Beauty Mouse Models of Cancer: Microenvironmental Influences on Cancer Genetics. Front Oncol 2019; 9:611. [PMID: 31338332 PMCID: PMC6629774 DOI: 10.3389/fonc.2019.00611] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 06/21/2019] [Indexed: 12/13/2022] Open
Abstract
The Sleeping Beauty (SB) transposon insertional mutagenesis system offers a streamlined approach to identify genetic drivers of cancer. With a relatively random insertion profile, SB is uniquely positioned for conducting unbiased forward genetic screens. Indeed, SB mouse models of cancer have revealed insights into the genetics of tumorigenesis. In this review, we highlight experiments that have exploited the SB system to interrogate the genetics of cancer in distinct biological contexts. We also propose experimental designs that could further our understanding of the relationship between tumor microenvironment and tumor progression.
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Affiliation(s)
- Amy Guimaraes-Young
- Department of Anatomy and Cell Biology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Charlotte R Feddersen
- Department of Anatomy and Cell Biology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Adam J Dupuy
- Department of Anatomy and Cell Biology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, United States
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18
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Hu JL, Hu XL, Lu CX, Chen XJ, Fu L, Han Q, Cang SD. Variants in the 3'-untranslated region of CUL3 is associated with risk of esophageal squamous cell carcinoma. J Cancer 2018; 9:3647-3650. [PMID: 30405832 PMCID: PMC6216002 DOI: 10.7150/jca.27052] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/18/2018] [Indexed: 12/30/2022] Open
Abstract
Background: Esophageal squamous cell carcinoma (ESCC) is one of the most lethal cancers in China. Recently, a study identified that cullin 3 (CUL3) was significantly mutated and deleted in ESCC. We then hypothesis that germline variants in CUL3 may also associated with the susceptibility of ESCC. Variants in the gene 3'-untranslated region (3'-UTR) may associate with gene expression by altering miRNAs binding. Material and Methods: We systematically searched for variants in the 3'-UTR of CUL3 using the Ensembl database. Taqman SNP Genotyping Assay was performed in 638 ESCC cases and 546 controls to examine the association between the rs2396092 and the risk of ESCC. The eQTL analysis for CUL3 were conducted by using the GTEx database. Results: We identified that the rs2396092 was significantly associated with the susceptibility of ESCC. Compared with the TT genotype carriers, the CT genotype and CC genotype carriers were correlated with risk of ESCC with odds ratio being 1.33 (95% CI: 1.04-1.70, P=0.0222) and 1.63 (95% CI: 1.07-2.50, P=0.0241), respectively. Different genotypes of rs2396092 was also shown to be correlated with altered CUL3 expression. Conclusion: The results emphasize the importance of CUL3 in the development of ESCC and may contribute to the personalized prevention of this cancer in the future.
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Affiliation(s)
- Jin-Long Hu
- Department of Oncology, People's Hospital of Zhengzhou University and Henan Provincial People's Hospital, Zhengzhou 450000, P. R. China
| | - Xin-Long Hu
- Department of Medical Imaging Technology, Henan University of Chinese Medicine, Zhengzhou 450000, P. R. China
| | - Chuang-Xin Lu
- Department of Oncology, People's Hospital of Zhengzhou University and Henan Provincial People's Hospital, Zhengzhou 450000, P. R. China
| | - Xue-Jiao Chen
- Department of Oncology, People's Hospital of Zhengzhou University and Henan Provincial People's Hospital, Zhengzhou 450000, P. R. China
| | - Lei Fu
- Department of Oncology, People's Hospital of Zhengzhou University and Henan Provincial People's Hospital, Zhengzhou 450000, P. R. China
| | - Qian Han
- Department of Radiotherapy, People's Hospital of Zhengzhou University and Henan Provincial People's Hospital, Zhengzhou 450000, P. R. China
| | - Shun-Dong Cang
- Department of Oncology, People's Hospital of Zhengzhou University and Henan Provincial People's Hospital, Zhengzhou 450000, P. R. China
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19
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O'Donnell KA. Advances in functional genetic screening with transposons and CRISPR/Cas9 to illuminate cancer biology. Curr Opin Genet Dev 2018; 49:85-94. [PMID: 29587177 PMCID: PMC6312197 DOI: 10.1016/j.gde.2018.03.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 02/27/2018] [Accepted: 03/08/2018] [Indexed: 12/18/2022]
Abstract
Large-scale genome sequencing studies have identified a wealth of mutations in human tumors and have dramatically advanced the field of cancer genetics. However, the functional consequences of an altered gene in tumor progression cannot always be inferred from mutation status alone. This underscores the critical need for complementary methods to assign functional significance to mutated genes in cancer. Transposons are mobile genetic elements that serve as powerful tools for insertional mutagenesis. Over the last decade, investigators have employed mouse models with ondemand transposon-mediated mutagenesis to perform unbiased genetic screens to identify clinically relevant genes that participate in the pathogenesis of human cancer. Two distinct DNA transposon mutagenesis systems, Sleeping Beauty (SB) and PiggyBac (PB), have been applied extensively in vivo and more recently, in ex vivo settings. These studies have informed our understanding of the genes and pathways that drive cancer initiation, progression, and metastasis. This review highlights the latest progress on cancer gene identification for specific cancer subtypes, as well as new technological advances and incorporation of the CRISPR/Cas9 toolbox into transposon-mediated functional genetic studies.
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Affiliation(s)
- Kathryn A O'Donnell
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390-9148, United States; Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX 75390-9148, United States; Hamon Center for Regenerative Science and Medicine, UT Southwestern Medical Center, Dallas, TX 75390-9148, United States.
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20
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Dolcino M, Pelosi A, Fiore PF, Patuzzo G, Tinazzi E, Lunardi C, Puccetti A. Gene Profiling in Patients with Systemic Sclerosis Reveals the Presence of Oncogenic Gene Signatures. Front Immunol 2018; 9:449. [PMID: 29559981 PMCID: PMC5845728 DOI: 10.3389/fimmu.2018.00449] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 02/20/2018] [Indexed: 12/11/2022] Open
Abstract
Systemic sclerosis (SSc) is a rare connective tissue disease characterized by three pathogenetic hallmarks: vasculopathy, dysregulation of the immune system, and fibrosis. A particular feature of SSc is the increased frequency of some types of malignancies, namely breast, lung, and hematological malignancies. Moreover, SSc may also be a paraneoplastic disease, again indicating a strong link between cancer and scleroderma. The reason of this association is still unknown; therefore, we aimed at investigating whether particular genetic or epigenetic factors may play a role in promoting cancer development in patients with SSc and whether some features are shared by the two conditions. We therefore performed a gene expression profiling of peripheral blood mononuclear cells (PBMCs) derived from patients with limited and diffuse SSc, showing that the various classes of genes potentially linked to the pathogenesis of SSc (such as apoptosis, endothelial cell activation, extracellular matrix remodeling, immune response, and inflammation) include genes that directly participate in the development of malignancies or that are involved in pathways known to be associated with carcinogenesis. The transcriptional analysis was then complemented by a complex network analysis of modulated genes which further confirmed the presence of signaling pathways associated with carcinogenesis. Since epigenetic mechanisms, such as microRNAs (miRNAs), are believed to play a central role in the pathogenesis of SSc, we also evaluated whether specific cancer-related miRNAs could be deregulated in the serum of SSc patients. We focused our attention on miRNAs already found upregulated in SSc such as miR-21-5p, miR-92a-3p, and on miR-155-5p, miR 126-3p and miR-16-5p known to be deregulated in malignancies associated to SSc, i.e., breast, lung, and hematological malignancies. miR-21-5p, miR-92a-3p, miR-155-5p, and miR-16-5p expression was significantly higher in SSc sera compared to healthy controls. Our findings indicate the presence of modulated genes and miRNAs that can play a predisposing role in the development of malignancies in SSc and are important for a better risk stratification of patients and for the identification of a better individualized precision medicine strategy.
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Affiliation(s)
- Marzia Dolcino
- Department of Medicine, University of Verona, Verona, Italy
| | - Andrea Pelosi
- Immunology Area, Pediatric Hospital Bambino Gesù, Rome, Italy
| | | | | | - Elisa Tinazzi
- Department of Medicine, University of Verona, Verona, Italy
| | | | - Antonio Puccetti
- Immunology Area, Pediatric Hospital Bambino Gesù, Rome, Italy.,Department of Experimental Medicine - Section of Histology, University of Genova, Genova, Italy
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Rontauroli S, Norfo R, Pennucci V, Zini R, Ruberti S, Bianchi E, Salati S, Prudente Z, Rossi C, Rosti V, Guglielmelli P, Barosi G, Vannucchi A, Tagliafico E, Manfredini R. miR-494-3p overexpression promotes megakaryocytopoiesis in primary myelofibrosis hematopoietic stem/progenitor cells by targeting SOCS6. Oncotarget 2017; 8:21380-21397. [PMID: 28423484 PMCID: PMC5400591 DOI: 10.18632/oncotarget.15226] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 01/23/2017] [Indexed: 11/25/2022] Open
Abstract
Primary myelofibrosis (PMF) is a chronic Philadelphia-negative myeloproliferative neoplasm characterized by hematopoietic stem cell-derived clonal myeloproliferation, involving especially the megakaryocyte lineage. To better characterize how the altered expression of microRNAs might contribute to PMF pathogenesis, we have previously performed the integrative analysis of gene and microRNA expression profiles of PMF hematopoietic stem/progenitor cells (HSPCs), which allowed us to identify miR-494-3p as the upregulated microRNA predicted to target the highest number of downregulated mRNAs.To elucidate the role of miR-494-3p in hematopoietic differentiation, in the present study we demonstrated that miR-494-3p enforced expression in normal HSPCs promotes megakaryocytopoiesis. Gene expression profiling upon miR-494-3p overexpression allowed the identification of genes commonly downregulated both after microRNA overexpression and in PMF CD34+ cells. Among them, suppressor of cytokine signaling 6 (SOCS6) was confirmed to be a miR-494-3p target by luciferase assay. Western blot analysis showed reduced level of SOCS6 protein as well as STAT3 activation in miR-494-3p overexpressing cells. Furthermore, transient inhibition of SOCS6 expression in HSPCs demonstrated that SOCS6 silencing stimulates megakaryocytopoiesis, mimicking the phenotypic effects observed upon miR-494-3p overexpression. Finally, to disclose the contribution of miR-494-3p upregulation to PMF pathogenesis, we performed inhibition experiments in PMF HSPCs, which showed that miR-494-3p silencing led to SOCS6 upregulation and impaired megakaryocyte differentiation.Taken together, our results describe for the first time the role of miR-494-3p during normal HSPC differentiation and suggest that its increased expression, and the subsequent downregulation of its target SOCS6, might contribute to the megakaryocyte hyperplasia commonly observed in PMF patients.
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Affiliation(s)
- Sebastiano Rontauroli
- Centre for Regenerative Medicine, Life Sciences Department, University of Modena and Reggio Emilia, Modena, Italy
| | - Ruggiero Norfo
- Centre for Regenerative Medicine, Life Sciences Department, University of Modena and Reggio Emilia, Modena, Italy
| | - Valentina Pennucci
- Centre for Regenerative Medicine, Life Sciences Department, University of Modena and Reggio Emilia, Modena, Italy
| | - Roberta Zini
- Centre for Regenerative Medicine, Life Sciences Department, University of Modena and Reggio Emilia, Modena, Italy
| | - Samantha Ruberti
- Centre for Regenerative Medicine, Life Sciences Department, University of Modena and Reggio Emilia, Modena, Italy
| | - Elisa Bianchi
- Centre for Regenerative Medicine, Life Sciences Department, University of Modena and Reggio Emilia, Modena, Italy
| | - Simona Salati
- Centre for Regenerative Medicine, Life Sciences Department, University of Modena and Reggio Emilia, Modena, Italy
| | - Zelia Prudente
- Centre for Regenerative Medicine, Life Sciences Department, University of Modena and Reggio Emilia, Modena, Italy
| | - Chiara Rossi
- Centre for Regenerative Medicine, Life Sciences Department, University of Modena and Reggio Emilia, Modena, Italy
| | - Vittorio Rosti
- Center for The Study of Myelofibrosis, Biotechnology Research Area, IRCCS Policlinico S. Matteo Foundation, Pavia, Italy
| | - Paola Guglielmelli
- CRIMM-Center for Research and Innovation for Myeloproliferative Neoplasms, AOU Careggi, and Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Giovanni Barosi
- Center for The Study of Myelofibrosis, Biotechnology Research Area, IRCCS Policlinico S. Matteo Foundation, Pavia, Italy
| | - Alessandro Vannucchi
- CRIMM-Center for Research and Innovation for Myeloproliferative Neoplasms, AOU Careggi, and Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Enrico Tagliafico
- Center for Genome Research, University of Modena and Reggio Emilia, Modena, Italy
| | - Rossella Manfredini
- Centre for Regenerative Medicine, Life Sciences Department, University of Modena and Reggio Emilia, Modena, Italy
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Dong B, Dai G, Xu L, Shi D. Detection of RACK1 and CTNNBL1‑induced activation of mouse splenocytes using an immunoprecipitation‑based technique. Mol Med Rep 2017; 16:7056-7063. [PMID: 28901482 DOI: 10.3892/mmr.2017.7485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 07/04/2017] [Indexed: 11/06/2022] Open
Abstract
Tumor cell lysates (TCLs) have been reported to induce antitumor immunity; however, it remains unclear which elements serve a role in this process. The present study identified 768 proteins that were upregulated in TCL prepared from Lewis lung cancer cells compared with the lysate from type II alveolar epithelial cells. Among the proteins that were upregulated in TCL, receptor for activated C kinase 1 (RACK1) and catenin β‑like 1 (CTNNBL1) are closely associated with cell proliferation and the inhibition of apoptosis. To determine the role of these proteins in TCL, a protein extraction method was designed, which was based on immunoprecipitation. Using this method, RACK1 and CTNNBL1 were extracted, whereas the other proteins within the TCL were not affected. The modified TCL exhibited a stronger ability to induce splenocyte apoptosis, whereas the ability to promote cell activation was reduced. These findings suggested that the TCL depends on RACK1 and CTNNBL1 to activate mouse immunocytes, including monocytes and B lymphocytes, and inhibit apoptosis. Therefore, the present study may provide information regarding the composition of TCLs and their positive regulatory effect on immunocytes.
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Affiliation(s)
- Bohan Dong
- Department of Biochemistry, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
| | - Guangli Dai
- Department of Gynecology and Obstetrics, Traditional Chinese Medical Hospital of Wuhu, Wuhu, Anhui 241000, P.R. China
| | - Lei Xu
- Department of Biochemistry, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
| | - Damin Shi
- Department of Biochemistry, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
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Dorr CR, Remmel RP, Muthusamy A, Fisher J, Moriarity BS, Yasuda K, Wu B, Guan W, Schuetz EG, Oetting WS, Jacobson PA, Israni AK. CRISPR/Cas9 Genetic Modification of CYP3A5 *3 in HuH-7 Human Hepatocyte Cell Line Leads to Cell Lines with Increased Midazolam and Tacrolimus Metabolism. Drug Metab Dispos 2017; 45:957-965. [PMID: 28533324 PMCID: PMC5518718 DOI: 10.1124/dmd.117.076307] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 05/18/2017] [Indexed: 02/06/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 engineering of the CYP3A5 *3 locus (rs776746) in human liver cell line HuH-7 (CYP3A5 *3/*3) has led to three CYP3A5 *1 cell lines by deletion of the exon 3B splice junction or point mutation. Cell lines CYP3A5 *1/*3 sd (single deletion), CYP3A5 *1/*1 dd (double deletion), or CYP3A5 *1/*3 pm (point mutation) expressed the CYP3A5 *1 mRNA and had elevated CYP3A5 mRNA (P < 0.0005 for all engineered cell lines) and protein expression compared with HuH-7. In metabolism assays, HuH-7 had less tacrolimus (all P < 0.05) or midazolam (MDZ) (all P < 0.005) disappearance than all engineered cell lines. HuH-7 had less 1-OH MDZ (all P < 0.0005) or 4-OH (all P < 0.005) production in metabolism assays than all bioengineered cell lines. We confirmed CYP3A5 metabolic activity with the CYP3A4 selective inhibitor CYP3CIDE. This is the first report of genomic CYP3A5 bioengineering in human cell lines with drug metabolism analysis.
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Affiliation(s)
- Casey R Dorr
- Molecular Epidemiology Laboratory, Minneapolis Medical Research Foundation, Minneapolis, Minnesota
| | - Rory P Remmel
- Molecular Epidemiology Laboratory, Minneapolis Medical Research Foundation, Minneapolis, Minnesota
| | - Amutha Muthusamy
- Molecular Epidemiology Laboratory, Minneapolis Medical Research Foundation, Minneapolis, Minnesota
| | - James Fisher
- Molecular Epidemiology Laboratory, Minneapolis Medical Research Foundation, Minneapolis, Minnesota
| | - Branden S Moriarity
- Molecular Epidemiology Laboratory, Minneapolis Medical Research Foundation, Minneapolis, Minnesota
| | - Kazuto Yasuda
- Molecular Epidemiology Laboratory, Minneapolis Medical Research Foundation, Minneapolis, Minnesota
| | - Baolin Wu
- Molecular Epidemiology Laboratory, Minneapolis Medical Research Foundation, Minneapolis, Minnesota
| | - Weihua Guan
- Molecular Epidemiology Laboratory, Minneapolis Medical Research Foundation, Minneapolis, Minnesota
| | - Erin G Schuetz
- Molecular Epidemiology Laboratory, Minneapolis Medical Research Foundation, Minneapolis, Minnesota
| | - William S Oetting
- Molecular Epidemiology Laboratory, Minneapolis Medical Research Foundation, Minneapolis, Minnesota
| | - Pamala A Jacobson
- Molecular Epidemiology Laboratory, Minneapolis Medical Research Foundation, Minneapolis, Minnesota
| | - Ajay K Israni
- Molecular Epidemiology Laboratory, Minneapolis Medical Research Foundation, Minneapolis, Minnesota
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24
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Rangel R, Guzman-Rojas L, Kodama T, Kodama M, Newberg JY, Copeland NG, Jenkins NA. Identification of New Tumor Suppressor Genes in Triple-Negative Breast Cancer. Cancer Res 2017; 77:4089-4101. [DOI: 10.1158/0008-5472.can-17-0785] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 04/28/2017] [Accepted: 06/05/2017] [Indexed: 11/16/2022]
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25
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Zhang C, Liu J, Huang G, Zhao Y, Yue X, Wu H, Li J, Zhu J, Shen Z, Haffty BG, Hu W, Feng Z. Cullin3-KLHL25 ubiquitin ligase targets ACLY for degradation to inhibit lipid synthesis and tumor progression. Genes Dev 2017; 30:1956-70. [PMID: 27664236 PMCID: PMC5066239 DOI: 10.1101/gad.283283.116] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 08/16/2016] [Indexed: 12/27/2022]
Abstract
ATP-citrate lyase (ACLY), a key enzyme for lipid synthesis, is frequently overexpressed or activated in cancer to promote lipid synthesis and tumor progression. Zhang et al. show that Cullin3 (CUL3), a core protein of the CUL3–RING ubiquitin ligase complex, interacts with ACLY through its adaptor protein, KLHL25, to ubiquitinate and degrade ACLY in cells. Through negative regulation of ACLY, CUL3 inhibits lipid synthesis, cell proliferation, and tumor growth in lung cancer cells. Increased lipid synthesis is a key characteristic of many cancers that is critical for cancer progression. ATP-citrate lyase (ACLY), a key enzyme for lipid synthesis, is frequently overexpressed or activated in cancer to promote lipid synthesis and tumor progression. Cullin3 (CUL3), a core protein for the CUL3–RING ubiquitin ligase complex, has been reported to be a tumor suppressor and frequently down-regulated in lung cancer. Here, we found that CUL3 interacts with ACLY through its adaptor protein, KLHL25 (Kelch-like family member 25), to ubiquitinate and degrade ACLY in cells. Through negative regulation of ACLY, CUL3 inhibits lipid synthesis, cell proliferation, and xenograft tumor growth of lung cancer cells. Furthermore, ACLY inhibitor SB-204990 greatly abolishes the promoting effect of CUL3 down-regulation on lipid synthesis, cell proliferation, and tumor growth. Importantly, low CUL3 expression is associated with high ACLY expression and poor prognosis in human lung cancer. In summary, our results identify CUL3–KLHL25 ubiquitin ligase as a novel negative regulator for ACLY and lipid synthesis and demonstrate that decreased CUL3 expression is an important mechanism for increased ACLY expression and lipid synthesis in lung cancer. These results also reveal that negative regulation of ACLY and lipid synthesis is a novel and critical mechanism for CUL3 in tumor suppression.
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Affiliation(s)
- Cen Zhang
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers University, The State University of New Jersey, New Brunswick, New Jersey 08903, USA
| | - Juan Liu
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers University, The State University of New Jersey, New Brunswick, New Jersey 08903, USA
| | - Grace Huang
- Nelson Institute of Environmental Medicine, New York University School of Medicine, New York University, Tuxedo, New Jersey 10987, USA
| | - Yuhan Zhao
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers University, The State University of New Jersey, New Brunswick, New Jersey 08903, USA
| | - Xuetian Yue
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers University, The State University of New Jersey, New Brunswick, New Jersey 08903, USA
| | - Hao Wu
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers University, The State University of New Jersey, New Brunswick, New Jersey 08903, USA
| | - Jun Li
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers University, The State University of New Jersey, New Brunswick, New Jersey 08903, USA
| | - Junlan Zhu
- Nelson Institute of Environmental Medicine, New York University School of Medicine, New York University, Tuxedo, New Jersey 10987, USA
| | - Zhiyuan Shen
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers University, The State University of New Jersey, New Brunswick, New Jersey 08903, USA
| | - Bruce G Haffty
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers University, The State University of New Jersey, New Brunswick, New Jersey 08903, USA
| | - Wenwei Hu
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers University, The State University of New Jersey, New Brunswick, New Jersey 08903, USA
| | - Zhaohui Feng
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers University, The State University of New Jersey, New Brunswick, New Jersey 08903, USA; Department of Pharmacology, Rutgers University, The State University of New Jersey, Piscataway, New Jersey 08854, USA
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26
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Genomic analysis of oesophageal squamous-cell carcinoma identifies alcohol drinking-related mutation signature and genomic alterations. Nat Commun 2017; 8:15290. [PMID: 28548104 PMCID: PMC5477513 DOI: 10.1038/ncomms15290] [Citation(s) in RCA: 156] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 03/16/2017] [Indexed: 12/21/2022] Open
Abstract
Approximately half of the world's 500,000 new oesophageal squamous-cell carcinoma (ESCC) cases each year occur in China. Here, we show whole-genome sequencing of DNA and RNA in 94 Chinese individuals with ESCC. We identify six mutational signatures (E1-E6), and Signature E4 is unique in ESCC linked to alcohol intake and genetic variants in alcohol-metabolizing enzymes. We discover significantly recurrent mutations in 20 protein-coding genes, 4 long non-coding RNAs and 10 untranslational regions. Functional analyses show six genes that have recurrent copy-number variants in three squamous-cell carcinomas (oesophageal, head and neck and lung) significantly promote cancer cell proliferation, migration and invasion. The most frequently affected genes by structural variation are LRP1B and TTC28. The aberrant cell cycle and PI3K-AKT pathways seem critical in ESCC. These results establish a comprehensive genomic landscape of ESCC and provide potential targets for precision treatment and prevention of the cancer.
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27
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Anwar SL, Wulaningsih W, Lehmann U. Transposable Elements in Human Cancer: Causes and Consequences of Deregulation. Int J Mol Sci 2017; 18:E974. [PMID: 28471386 PMCID: PMC5454887 DOI: 10.3390/ijms18050974] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 04/26/2017] [Accepted: 04/29/2017] [Indexed: 01/04/2023] Open
Abstract
Transposable elements (TEs) comprise nearly half of the human genome and play an essential role in the maintenance of genomic stability, chromosomal architecture, and transcriptional regulation. TEs are repetitive sequences consisting of RNA transposons, DNA transposons, and endogenous retroviruses that can invade the human genome with a substantial contribution in human evolution and genomic diversity. TEs are therefore firmly regulated from early embryonic development and during the entire course of human life by epigenetic mechanisms, in particular DNA methylation and histone modifications. The deregulation of TEs has been reported in some developmental diseases, as well as for different types of human cancers. To date, the role of TEs, the mechanisms underlying TE reactivation, and the interplay with DNA methylation in human cancers remain largely unexplained. We reviewed the loss of epigenetic regulation and subsequent genomic instability, chromosomal aberrations, transcriptional deregulation, oncogenic activation, and aberrations of non-coding RNAs as the potential mechanisms underlying TE deregulation in human cancers.
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Affiliation(s)
- Sumadi Lukman Anwar
- Division of Surgical Oncology, Department of Surgery Faculty of Medicine, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia.
- Institute of Pathology, Medizinische Hochschule Hannover, Hannover 30625, Germany.
- PILAR (Philippine and Indonesian Scholar) Research and Education, 20 Station Road, Cambridge CB1 2JD, UK.
| | - Wahyu Wulaningsih
- PILAR (Philippine and Indonesian Scholar) Research and Education, 20 Station Road, Cambridge CB1 2JD, UK.
- MRC (Medical Research Council) Unit for Lifelong Health and Ageing, University College London, London WC1B 5JU, UK.
- Division of Haematology/Oncology, Faculty of Medicine Universitas Gadjah Mada, Yogyakarta 55281, Indonesia.
| | - Ulrich Lehmann
- Institute of Pathology, Medizinische Hochschule Hannover, Hannover 30625, Germany.
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28
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Zeng R, Tan G, Li W, Ma Y. Increased Expression of Cullin 3 in Nasopharyngeal Carcinoma and Knockdown Inhibits Proliferation and Invasion. Oncol Res 2017; 26:111-122. [PMID: 28429677 PMCID: PMC7844559 DOI: 10.3727/096504017x14924753593574] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
This study aimed to investigate the clinical significance of cullin 3 expression in nasopharyngeal carcinoma (NPC), as well as to explore the regulatory mechanism of cullin 3 underlying the growth and metastasis of NPC cells. Our findings showed that the expression levels of cullin 3 were significantly increased in both NPC tissues and cell lines. A strong positive correlation was found between cullin 3 expression and the Ki-67-based proliferation index in NPC tissues. Moreover, cullin 3 overexpression was correlated with local relapse and distant metastasis in NPC patients. In vitro experiments showed that knockdown of cullin 3 caused a significant reduction in the proliferation of NPC cells, probably by inducing cell cycle arrest. In addition, downregulation of cullin 3 inhibited colony formation and the migratory and invasive capacities of NPC cells. The expression levels of PCNA and epithelial-to-mesenchymal transition (EMT)-related proteins were also meditated by cullin 3 in NPC cells. Based on these findings, we demonstrated that cullin 3 plays a promoting role in the malignant progression of NPC and suggest that the cullin 3-based ubiquitin proteasome pathway may be used as a promising therapeutic target for NPC.
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Affiliation(s)
- Ruifang Zeng
- Department of Otolaryngology/Head and Neck Surgery, Third Xiangya Hospital, Central South University, Changsha, Hunan, P.R. China
| | - Guolin Tan
- Department of Otolaryngology/Head and Neck Surgery, Third Xiangya Hospital, Central South University, Changsha, Hunan, P.R. China
| | - Wei Li
- Department of Otolaryngology/Head and Neck Surgery, Third Xiangya Hospital, Central South University, Changsha, Hunan, P.R. China
| | - Yanhong Ma
- Department of Otolaryngology/Head and Neck Surgery, Third Xiangya Hospital, Central South University, Changsha, Hunan, P.R. China
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29
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de la Rosa J, Weber J, Friedrich MJ, Li Y, Rad L, Ponstingl H, Liang Q, de Quirós SB, Noorani I, Metzakopian E, Strong A, Li MA, Astudillo A, Fernández-García MT, Fernández-García MS, Hoffman GJ, Fuente R, Vassiliou GS, Rad R, López-Otín C, Bradley A, Cadiñanos J. A single-copy Sleeping Beauty transposon mutagenesis screen identifies new PTEN-cooperating tumor suppressor genes. Nat Genet 2017; 49:730-741. [PMID: 28319090 PMCID: PMC5409503 DOI: 10.1038/ng.3817] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 02/24/2017] [Indexed: 12/11/2022]
Abstract
The overwhelming number of genetic alterations identified through cancer genome sequencing requires complementary approaches to interpret their significance and interactions. Here we developed a novel whole-body insertional mutagenesis screen in mice, which was designed for the discovery of Pten-cooperating tumor suppressors. Toward this aim, we coupled mobilization of a single-copy inactivating Sleeping Beauty transposon to Pten disruption within the same genome. The analysis of 278 transposition-induced prostate, breast and skin tumors detected tissue-specific and shared data sets of known and candidate genes involved in cancer. We validated ZBTB20, CELF2, PARD3, AKAP13 and WAC, which were identified by our screens in multiple cancer types, as new tumor suppressor genes in prostate cancer. We demonstrated their synergy with PTEN in preventing invasion in vitro and confirmed their clinical relevance. Further characterization of Wac in vivo showed obligate haploinsufficiency for this gene (which encodes an autophagy-regulating factor) in a Pten-deficient context. Our study identified complex PTEN-cooperating tumor suppressor networks in different cancer types, with potential clinical implications.
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Affiliation(s)
- Jorge de la Rosa
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.,Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA), Oviedo, Spain.,Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain
| | - Julia Weber
- Department of Internal Medicine II, Klinikum rechts der Isar, Technische Universität München, München, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Yilong Li
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Lena Rad
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Hannes Ponstingl
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Qi Liang
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | | | - Imran Noorani
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | | | - Alexander Strong
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Meng Amy Li
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Aurora Astudillo
- Servicio de Anatomía Patológica, Hospital Universitario Central de Asturias, Oviedo, Spain
| | | | | | - Gary J Hoffman
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.,School of Medicine, University of Western Australia, Crawley, Western Australia, Australia
| | - Rocío Fuente
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - George S Vassiliou
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Roland Rad
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.,Department of Internal Medicine II, Klinikum rechts der Isar, Technische Universität München, München, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carlos López-Otín
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain.,Centro de Investigación Biomédica en Red de Cáncer, Spain
| | - Allan Bradley
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Juan Cadiñanos
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.,Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA), Oviedo, Spain
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30
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Friedrich MJ, Rad L, Bronner IF, Strong A, Wang W, Weber J, Mayho M, Ponstingl H, Engleitner T, Grove C, Pfaus A, Saur D, Cadiñanos J, Quail MA, Vassiliou GS, Liu P, Bradley A, Rad R. Genome-wide transposon screening and quantitative insertion site sequencing for cancer gene discovery in mice. Nat Protoc 2017; 12:289-309. [PMID: 28079877 DOI: 10.1038/nprot.2016.164] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Transposon-mediated forward genetics screening in mice has emerged as a powerful tool for cancer gene discovery. It pinpoints cancer drivers that are difficult to find with other approaches, thus complementing the sequencing-based census of human cancer genes. We describe here a large series of mouse lines for insertional mutagenesis that are compatible with two transposon systems, PiggyBac and Sleeping Beauty, and give guidance on the use of different engineered transposon variants for constitutive or tissue-specific cancer gene discovery screening. We also describe a method for semiquantitative transposon insertion site sequencing (QiSeq). The QiSeq library preparation protocol exploits acoustic DNA fragmentation to reduce bias inherent to widely used restriction-digestion-based approaches for ligation-mediated insertion site amplification. Extensive multiplexing in combination with next-generation sequencing allows affordable ultra-deep transposon insertion site recovery in high-throughput formats within 1 week. Finally, we describe principles of data analysis and interpretation for obtaining insights into cancer gene function and genetic tumor evolution.
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Affiliation(s)
| | - Lena Rad
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Iraad F Bronner
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - Alexander Strong
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - Wei Wang
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - Julia Weber
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, &German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Matthew Mayho
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - Hannes Ponstingl
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - Thomas Engleitner
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, &German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Carolyn Grove
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - Anja Pfaus
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, &German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Dieter Saur
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, &German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Juan Cadiñanos
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK.,Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA), Oviedo, Spain
| | - Michael A Quail
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - George S Vassiliou
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - Pentao Liu
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - Allan Bradley
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton/Cambridge, UK
| | - Roland Rad
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, &German Cancer Consortium (DKTK), Heidelberg, Germany
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31
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Rangel R, Lee SC, Hon-Kim Ban K, Guzman-Rojas L, Mann MB, Newberg JY, Kodama T, McNoe LA, Selvanesan L, Ward JM, Rust AG, Chin KY, Black MA, Jenkins NA, Copeland NG. Transposon mutagenesis identifies genes that cooperate with mutant Pten in breast cancer progression. Proc Natl Acad Sci U S A 2016; 113:E7749-E7758. [PMID: 27849608 PMCID: PMC5137755 DOI: 10.1073/pnas.1613859113] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Triple-negative breast cancer (TNBC) has the worst prognosis of any breast cancer subtype. To better understand the genetic forces driving TNBC, we performed a transposon mutagenesis screen in a phosphatase and tensin homolog (Pten) mutant mice and identified 12 candidate trunk drivers and a much larger number of progression genes. Validation studies identified eight TNBC tumor suppressor genes, including the GATA-like transcriptional repressor TRPS1 Down-regulation of TRPS1 in TNBC cells promoted epithelial-to-mesenchymal transition (EMT) by deregulating multiple EMT pathway genes, in addition to increasing the expression of SERPINE1 and SERPINB2 and the subsequent migration, invasion, and metastasis of tumor cells. Transposon mutagenesis has thus provided a better understanding of the genetic forces driving TNBC and discovered genes with potential clinical importance in TNBC.
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Affiliation(s)
- Roberto Rangel
- Cancer Research Program, Houston Methodist Research Institute, Houston, TX 77030
| | - Song-Choon Lee
- Division of Genomics and Genetics, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Biopolis, Singapore 138673
| | - Kenneth Hon-Kim Ban
- Division of Genomics and Genetics, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Biopolis, Singapore 138673
- Deparment of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 138673
| | - Liliana Guzman-Rojas
- Cancer Research Program, Houston Methodist Research Institute, Houston, TX 77030
| | - Michael B Mann
- Cancer Research Program, Houston Methodist Research Institute, Houston, TX 77030
| | - Justin Y Newberg
- Cancer Research Program, Houston Methodist Research Institute, Houston, TX 77030
| | - Takahiro Kodama
- Cancer Research Program, Houston Methodist Research Institute, Houston, TX 77030
| | - Leslie A McNoe
- Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand
| | | | - Jerrold M Ward
- Division of Genomics and Genetics, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Biopolis, Singapore 138673
| | - Alistair G Rust
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, United Kingdom
| | - Kuan-Yew Chin
- Division of Genomics and Genetics, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Biopolis, Singapore 138673
| | - Michael A Black
- Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand
| | - Nancy A Jenkins
- Cancer Research Program, Houston Methodist Research Institute, Houston, TX 77030
- Division of Genomics and Genetics, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Biopolis, Singapore 138673
| | - Neal G Copeland
- Cancer Research Program, Houston Methodist Research Institute, Houston, TX 77030;
- Division of Genomics and Genetics, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Biopolis, Singapore 138673
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32
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Zhou L, Jiang F, Chen X, Liu Z, Ouyang Y, Zhao W, Yu D. Downregulation of miR-221/222 by a microRNA sponge promotes apoptosis in oral squamous cell carcinoma cells through upregulation of PTEN. Oncol Lett 2016; 12:4419-4426. [PMID: 28101204 PMCID: PMC5228168 DOI: 10.3892/ol.2016.5250] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 09/02/2016] [Indexed: 12/18/2022] Open
Abstract
MicroRNA-221 and microRNA-222 (miR-221/222) have been identified as oncogenes and confirmed to be overexpressed in various types of cancer. However, the regulation mechanism of miR-221/222 in oral squamous cell carcinoma (OSCC) remains to be fully elucidated. Previously, an miR-221/222 sponge was successfully constructed and its effect on the downregulation of miR-221/222 expression was investigated. In the present study, the dual luciferase reporter assay revealed a phosphatase and tensin homolog (PTEN) deletion on chromosome 10 to be a target gene of miR-221/222. It was also demonstrated that miR-221/222 suppression by transfection with an miR-221/222 sponge in vitro resulted in upregulation of PTEN. Notably, the proliferation and invasiveness of the miR-221/222 sponge-transfected cells was significantly inhibited, while apoptosis was promoted, when determined by Cell Counting Kit-8, Transwell assays and flow cytometry. The results of the present study prove that miR-221/222 may downregulate the expression of PTEN in OSCC cells and function as oncogenes, providing a novel insight into the underlying mechanism of OSCC tumorigenesis. The present study suggests that upregulating the expression of PTEN by downregulation of miR-221/222 may be a potential treatment for OSCC.
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Affiliation(s)
- Lijie Zhou
- Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong 510055, P.R. China; Department of Stomatology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, P.R. China
| | - Fangfang Jiang
- Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong 510055, P.R. China
| | - Xijuan Chen
- Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong 510055, P.R. China
| | - Zifeng Liu
- Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong 510055, P.R. China
| | - Ying Ouyang
- Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong 510055, P.R. China
| | - Wei Zhao
- Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong 510055, P.R. China
| | - Dongsheng Yu
- Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong 510055, P.R. China
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Narayanavari SA, Chilkunda SS, Ivics Z, Izsvák Z. Sleeping Beauty transposition: from biology to applications. Crit Rev Biochem Mol Biol 2016; 52:18-44. [PMID: 27696897 DOI: 10.1080/10409238.2016.1237935] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Sleeping Beauty (SB) is the first synthetic DNA transposon that was shown to be active in a wide variety of species. Here, we review studies from the last two decades addressing both basic biology and applications of this transposon. We discuss how host-transposon interaction modulates transposition at different steps of the transposition reaction. We also discuss how the transposon was translated for gene delivery and gene discovery purposes. We critically review the system in clinical, pre-clinical and non-clinical settings as a non-viral gene delivery tool in comparison with viral technologies. We also discuss emerging SB-based hybrid vectors aimed at combining the attractive safety features of the transposon with effective viral delivery. The success of the SB-based technology can be fundamentally attributed to being able to insert fairly randomly into genomic regions that allow stable long-term expression of the delivered transgene cassette. SB has emerged as an efficient and economical toolkit for safe and efficient gene delivery for medical applications.
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Affiliation(s)
- Suneel A Narayanavari
- a Mobile DNA , Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) , Berlin , Germany
| | - Shreevathsa S Chilkunda
- a Mobile DNA , Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) , Berlin , Germany
| | - Zoltán Ivics
- b Division of Medical Biotechnology , Paul Ehrlich Institute , Langen , Germany
| | - Zsuzsanna Izsvák
- a Mobile DNA , Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) , Berlin , Germany
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34
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Huo X, Li S, Shi T, Suo A, Ruan Z, Guo H, Yao Y. Cullin3 promotes breast cancer cells metastasis and epithelial-mesenchymal transition by targeting BRMS1 for degradation. Oncotarget 2016; 6:41959-75. [PMID: 26544623 PMCID: PMC4747201 DOI: 10.18632/oncotarget.5999] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 10/03/2015] [Indexed: 11/25/2022] Open
Abstract
Metastasis is the leading cause of death in breast cancer (BC) patients. However, until now, the mechanisms of BC metastasis remain elusive. Cullin3 is a highly conserved Cullin family member present in the genomes of all eukaryotes, which has been proposed as an oncogene in many types of tumors; however, its role and underlying mechanisms in BC remain unclear. Here we show that Cullin3 is elevated in BC and its expression level is positively correlated with metastasis. Overexpression of Cullin3 in BC cells increased proliferation, epithelial-mesenchymal transition, migration and invasion in vitro, and enhanced tumorigenic and metastatic capacities in vivo. In contrast, silencing Cullin3 in aggressive and invasive BC cells inhibited these processes. Mechanistically, we found Cullin3 exerts its function through promoting BRMS1 protein degradation, which was associated with EMT, migration and invasion. BRMS1 overexpression blocked Cullin3-driven EMT, and metastasis. Our results, for the first time, portray a pivotal role of Cullin3 in stimulating metastatic behaviors of BC cells. Targeting Cullin3 may thus be a useful strategy to impede BC cell invasion and metastasis.
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Affiliation(s)
- Xiongwei Huo
- Department of General Surgery, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Suoni Li
- Department of Oncology, Shaanxi Province Tumor Hospital, Xi'an, Shaanxi, 710061, China
| | - Tingting Shi
- Department of Oncology, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Aili Suo
- Department of Oncology, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Zhiping Ruan
- Department of Oncology, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Hui Guo
- Department of Oncology, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Yu Yao
- Department of Oncology, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
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35
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Um SW, Joung JG, Lee H, Kim H, Kim KT, Park J, Hayes DN, Park WY. Molecular Evolution Patterns in Metastatic Lymph Nodes Reflect the Differential Treatment Response of Advanced Primary Lung Cancer. Cancer Res 2016; 76:6568-6576. [PMID: 27634761 DOI: 10.1158/0008-5472.can-16-0873] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 08/03/2016] [Accepted: 08/17/2016] [Indexed: 11/16/2022]
Abstract
Tumor heterogeneity influences the clinical outcome of patients with cancer, and the diagnostic method to measure the tumor heterogeneity needs to be developed. We analyzed genomic features on pairs of primary and multiple metastatic lymph nodes from six patients with lung cancer using whole-exome sequencing and RNA sequencing. Although somatic single-nucleotide variants were shared in primary lung cancer and metastases, tumor evolution predicted by the pattern of genomic alterations was matched to anatomic location of the tumors. Four of six cases exhibited a branched clonal evolution pattern. Lymph nodes with acquired somatic variants demonstrated resistance to the cancer treatment. In this study, we demonstrated that multiple biopsies and sequencing strategies for different tumor regions are required for a comprehensive understanding of the landscape of genetic alteration and for guiding targeted therapy in advanced primary lung cancer. Cancer Res; 76(22); 6568-76. ©2016 AACR.
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Affiliation(s)
- Sang-Won Um
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
| | - Je-Gun Joung
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
| | - Hyun Lee
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hojoong Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Kyu-Tae Kim
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
| | - Jinha Park
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - D Neil Hayes
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea. .,Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Seoul, Korea
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36
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Wang J, Zhu ZH, Yang HB, Zhang Y, Zhao XN, Zhang M, Liu YB, Xu YY, Lei QY. Cullin 3 targets methionine adenosyltransferase IIα for ubiquitylation-mediated degradation and regulates colorectal cancer cell proliferation. FEBS J 2016; 283:2390-402. [PMID: 27213918 DOI: 10.1111/febs.13759] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 04/29/2016] [Accepted: 05/16/2016] [Indexed: 12/24/2022]
Abstract
Cullin 3 (CUL3) serves as a scaffold protein and assembles a large number of ubiquitin ligase complexes. It is involved in multiple cellular processes and plays a potential role in tumor development and progression. In this study, we demonstrate that CUL3 targets methionine adenosyltransferase IIα (MAT IIα) and promotes its proteasomal degradation through the ubiquitylation-mediated pathway. MAT IIα is a key enzyme in methionine metabolism and is associated with uncontrolled cell proliferation in cancer. We presently found that CUL3 down-regulation could rescue folate deprivation-induced MAT IIα exhaustion and growth arrest in colorectal cancer (CRC) cells. Further results from human CRC samples display an inverse correlation between CUL3 and MAT IIα protein levels. Our observations reveal a novel role of CUL3 in regulating cell proliferation by controlling the stability of MAT IIα.
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Affiliation(s)
- Jian Wang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, and Cancer Metabolism Lab, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Zi-Hua Zhu
- Department of Gastroenterology, Minhang Hospital, Fudan University, Shanghai, China
| | - Hong-Bin Yang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, and Cancer Metabolism Lab, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Ye Zhang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, and Cancer Metabolism Lab, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Xiang-Ning Zhao
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, and Cancer Metabolism Lab, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Min Zhang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, and Cancer Metabolism Lab, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Ying-Bin Liu
- Institute of Biliary Tract Disease, Xinhua Hospital, Affiliated to Shanghai Jiao Tong University, School of Medicine, China
| | - Ying-Ying Xu
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, and Cancer Metabolism Lab, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Qun-Ying Lei
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, and Cancer Metabolism Lab, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
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37
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DeNicola GM, Karreth FA, Adams DJ, Wong CC. The utility of transposon mutagenesis for cancer studies in the era of genome editing. Genome Biol 2015; 16:229. [PMID: 26481584 PMCID: PMC4612416 DOI: 10.1186/s13059-015-0794-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The use of transposons as insertional mutagens to identify cancer genes in mice has generated a wealth of information over the past decade. Here, we discuss recent major advances in transposon-mediated insertional mutagenesis screens and compare this technology with other screening strategies.
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Affiliation(s)
- Gina M DeNicola
- Meyer Cancer Center, Weill Cornell Medical College, New York, NY, 10021, USA
| | - Florian A Karreth
- Meyer Cancer Center, Weill Cornell Medical College, New York, NY, 10021, USA.
| | - David J Adams
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1HH, UK
| | - Chi C Wong
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1HH, UK. .,Department of Haematology, University of Cambridge, Hills Road, Cambridge, CB2 0XY, UK.
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