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Xie D, Pan Y, Chen J, Mao C, Li Z, Qiu F, Yang L, Deng Y, Lu J. Association of genetic variants in soy isoflavones metabolism-related genes with decreased lung cancer risk. Gene 2024; 927:148732. [PMID: 38945312 DOI: 10.1016/j.gene.2024.148732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 06/02/2024] [Accepted: 06/25/2024] [Indexed: 07/02/2024]
Abstract
BACKGROUND Soy isoflavones have been reported to exhibit anti-tumor effects. We hypothesize that genetic variants in soy isoflavone metabolism-related genes are associated with the risk of lung cancer. METHODS A two-stage case-control study design was conducted in this study. The discovery stage included 300 lung cancer cases and 600 healthy controls to evaluate the association of candidate genetic variants with lung cancer risk. The validation stage involved 1200 cases and 1200 controls to validate the associations found. Furthermore, qPCR was performed to assess the mRNA expression levels of different genotypes of the SNP. ELISA was used to explore the association between genotype and soy isoflavone levels, as well as the association between soy isoflavone levels and lung cancer risk. RESULTS A nonlinear association was observed between plasma soy isoflavone levels and lung cancer risk, with higher soy isoflavone levels associated with lower lung cancer risk (P < 0.001). The two-stage case-control study identified that UGT1A1 rs3755319 A > C was associated with decreased lung cancer risk (Recessive model: adjusted OR = 0.69, 95 %CI = 0.57-0.84, P < 0.001). Moreover, eQTL analysis showed that the expression level of UGT1A1 in the rs3755319 CC genotype was lower than in the AA + AC genotype (P < 0.05). The plasma concentration of soy isoflavones in the rs3755319 CC genotype was higher than in the AA + AC genotype (P = 0.008). CONCLUSIONS We identified a potentially functional SNP, UGT1A1 rs3755319 A > C, as being associated with decreased lung cancer risk. Further experiments will be needed to explore the mechanisms underlying the observed associations.
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Affiliation(s)
- Dongming Xie
- The Key Laboratory of Advanced Interdisciplinary Studies, The First Affiliated Hospital, The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, PR China
| | - Yujie Pan
- The Key Laboratory of Advanced Interdisciplinary Studies, The First Affiliated Hospital, The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, PR China
| | - Jinbin Chen
- Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, PR China
| | - Chun Mao
- The Key Laboratory of Advanced Interdisciplinary Studies, The First Affiliated Hospital, The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, PR China
| | - Zhi Li
- The Key Laboratory of Advanced Interdisciplinary Studies, The First Affiliated Hospital, The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, PR China
| | - Fuman Qiu
- The Key Laboratory of Advanced Interdisciplinary Studies, The First Affiliated Hospital, The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, PR China
| | - Lei Yang
- The Key Laboratory of Advanced Interdisciplinary Studies, The First Affiliated Hospital, The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, PR China
| | - Yibin Deng
- Centre for Medical Laboratory Science, the Affiliated Hospital of Youjiang Medical University for Nationalities, No. 18 Zhongshaner Rd., Youjiang District, Baise 533000, PR China; Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, No. 18 Zhongshaner Rd., Youjiang District, Baise 533000, PR China.
| | - Jiachun Lu
- The Key Laboratory of Advanced Interdisciplinary Studies, The First Affiliated Hospital, The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, PR China.
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2
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Guo L, Zhang W, Zhang X, Wang J, Nie J, Jin X, Ma Y, Wang S, Zhou X, Zhang Y, Xu Y, Tanaka Y, Yuan J, Liao XH, Gong Y, Su L. A novel transcription factor SIPA1: identification and verification in triple-negative breast cancer. Oncogene 2023; 42:2641-2654. [PMID: 37500797 PMCID: PMC10457189 DOI: 10.1038/s41388-023-02787-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 07/11/2023] [Accepted: 07/14/2023] [Indexed: 07/29/2023]
Abstract
Transcription factors (TFs) regulate the expression of genes responsible for cell growth, differentiation, and responses to environmental factors. In this study, we demonstrated that signal-induced proliferation-associated 1 (SIPA1), known as a Rap-GTPase-activating protein, bound DNA and served as a TF. Importin β1 was found to interact with SIPA1 upon fibronectin treatment. A TGAGTCAB motif was recognized and bound by DNA-binding region (DBR) of SIPA1, which was confirmed by electrophoretic mobility shift assay. SIPA1 regulated the transcription of multiple genes responsible for signal transduction, DNA synthesis, cell adhesion, cell migration, and so on. Transcription of fibronectin 1, which is crucial for cell junction and migration of triple-negative breast cancer (TNBC) cells, was regulated by SIPA1 in a DBR-dependent manner both in vivo and in vitro. Furthermore, single-cell transcriptome sequencing analysis of specimens from a metastatic TNBC patient revealed that SIPA1 was highly expressed in metastatic TNBC. Hence, this study demonstrated that SIPA1 served as a TF, promoting TNBC migration, invasion, and metastasis.
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Affiliation(s)
- Lijuan Guo
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Wanjun Zhang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Xue Zhang
- Department of Breast Surgery, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, 430060, China
| | - Jun Wang
- Institute of Biology and Medicine, College of Life Sciences and Health, Wuhan University of Science and Technology, Hubei, 430081, P. R. China
| | - Jiaqi Nie
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Xiaomeng Jin
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Ying Ma
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Shi Wang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Xinhong Zhou
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Yilei Zhang
- The Institute of Molecular and Translational Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, China
| | - Yan Xu
- Department of Immunology and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Yoshimasa Tanaka
- Center for Medical Innovation, Nagasaki University, 1-7-1, Sakamoto, Nagasaki, 852-8588, Japan
| | - Jingping Yuan
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xing-Hua Liao
- Institute of Biology and Medicine, College of Life Sciences and Health, Wuhan University of Science and Technology, Hubei, 430081, P. R. China.
| | - Yiping Gong
- Department of Breast Surgery, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, 430060, China.
| | - Li Su
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
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3
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Liu Y, Chudgar N, Mastrogiacomo B, He D, Lankadasari MB, Bapat S, Jones GD, Sanchez-Vega F, Tan KS, Schultz N, Mukherjee S, Offit K, Bao Y, Bott MJ, Rekhtman N, Adusumilli PS, Li BT, Mayo MW, Jones DR. A germline SNP in BRMS1 predisposes patients with lung adenocarcinoma to metastasis and can be ameliorated by targeting c-fos. Sci Transl Med 2022; 14:eabo1050. [PMID: 36197962 PMCID: PMC9926934 DOI: 10.1126/scitranslmed.abo1050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
About 50% of patients with early-stage, surgically resected lung cancer will develop distant metastasis. There remains an unmet need to identify patients likely to develop recurrence and to design innovative therapies to decrease this risk. Two primary isoforms of BRMS1, v1 and v2, are present in humans. Using next-generation sequencing of BRMS1 on matched human noncancerous lung tissue and non-small cell lung cancer (NSCLC) specimens, we identified single-nucleotide polymorphism (SNP) rs1052566 that results in an A273V mutation of BRMS1v2. This SNP is homozygous (BRMS1v2A273V/A273V) in 8% of the population and correlates with aggressive biology in lung adenocarcinoma (LUAD). Mechanistically, we show that BRMS1v2 A273V abolishes the metastasis suppressor function of BRMS1v2 and promotes robust cell invasion and metastases by activation of c-fos-mediated gene-specific transcriptional regulation. BRMS1v2 A273V increases cell invasion in vitro and increases metastases in both tail-vein injection xenografts and LUAD patient-derived organoid (PDO) intracardiac injection metastasis in vivo models. Moreover, we show that BRMS1v2 A273V fails to interact with nuclear Src, thereby activating intratumoral c-fos in vitro. Higher c-fos results in up-regulation of CEACAM6, which drives metastases in vitro and in vivo. Using both xenograft and PDO metastasis models, we repurposed T5224 for treatment, a c-fos pharmacologic inhibitor investigated in clinical trials for arthritis, and observed suppression of metastases in BRMS1v2A273V/A273V LUAD in mice. Collectively, we elucidate the mechanism of BRMS1v2A273V/A273V-induced metastases and offer a putative therapeutic strategy for patients with LUAD who have this germline alteration.
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Affiliation(s)
- Yuan Liu
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA,Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Neel Chudgar
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Brooke Mastrogiacomo
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA,Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center; New York, NY USA
| | - Di He
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Manendra B. Lankadasari
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Samhita Bapat
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Gregory D. Jones
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | | | - Kay See Tan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Nikolaus Schultz
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center; New York, NY USA
| | - Semanti Mukherjee
- Department of Medicine, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Yongde Bao
- Department of Microbiology, University of Virginia; Charlottesville, VA 22908, USA
| | - Matthew J. Bott
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA,Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center; New York, NY USA
| | - Natasha Rekhtman
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA,Department of Pathology, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Prasad S. Adusumilli
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA,Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Bob T. Li
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA,Department of Medicine, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Marty W. Mayo
- Department of Biochemistry & Molecular Genetics, University of Virginia; Charlottesville, VA 22908, USA
| | - David R. Jones
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA,Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA,Corresponding Author: David R. Jones, MD, Professor & Chief, Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 7, New York, NY 10065 USA Phone: 212-639-6428; Fax: 232-639-6686;
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4
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Xiang Y, Feng L, Liu H, Liu Y, Li J, Su L, Liao X. SIPA1 Regulates LINC01615 to Promote Metastasis in Triple-Negative Breast Cancer. Cancers (Basel) 2022; 14:cancers14194815. [PMID: 36230738 PMCID: PMC9562673 DOI: 10.3390/cancers14194815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/25/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Breast cancer is a malignant tumor that often endangers women. After undergoing surgery and supplementary chemotherapy, however, tumor recurrence has not been well researched. The primary cause is high metastatic rates. Hence, bioinformatic and functional analyses were performed to indicate the effect of LINC01615 on breast cancer. We revealed that LINC01615 is regulated by the transcription factor SIPA1 in promoting breast cancer cell malignancy. Abstract Long non-coding RNAs (lncRNAs) are reported to play an important regulatory effect in carcinogenesis and malignancy. We found by high-throughput sequencing that LINC01615 is upregulated in breast cancer patients and reduces patients’ overall survival. In vivo and in vitro experiments, we clarified that overexpression of LINC01615 can promote breast cancer cell metastasis ability. The expression of LINC01615 is regulated by the transcriptional activator SIPA1, thereby promoting carcinogenesis in breast cancer cells. Our research clarified that LINC01615 can act as an oncogenic factor in promoting the development of breast cancer.
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Affiliation(s)
- Yuan Xiang
- Department of Medical Laboratory, Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, China
| | - Lingyun Feng
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430081, China
| | - Hui Liu
- Institute of Biology and Medicine, College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan 430081, China
| | - Yuhuan Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430081, China
| | - Jiapeng Li
- Institute of Biology and Medicine, College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan 430081, China
| | - Li Su
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430081, China
- Correspondence: (L.S.); (X.L.); Tel.: +86-027-8779-2072 (L.S.); +86-027-6889-3590 (X.L.); Fax: +86-027-6889-3590 (X.L.)
| | - Xinghua Liao
- Institute of Biology and Medicine, College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan 430081, China
- Correspondence: (L.S.); (X.L.); Tel.: +86-027-8779-2072 (L.S.); +86-027-6889-3590 (X.L.); Fax: +86-027-6889-3590 (X.L.)
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5
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Liu C, Jiang W, Zhang L, Hargest R, Martin TA. SIPA1 Is a Modulator of HGF/MET Induced Tumour Metastasis via the Regulation of Tight Junction-Based Cell to Cell Barrier Function. Cancers (Basel) 2021; 13:1747. [PMID: 33917539 PMCID: PMC8038768 DOI: 10.3390/cancers13071747] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/26/2021] [Accepted: 04/01/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Lung cancer is the leading cause of cancer death. SIPA1 is a mitogen induced GTPase activating protein (GAP) and may hamper cell cycle progression. SIPA1 has been shown to be involved in MET signaling and may contribute to tight junction (TJ) function and cancer metastasis. METHODS Human lung tumour cohorts were analyzed. In vitro cell function assays were performed after knock down of SIPA1 in lung cancer cells with/without treatment. Quantitative polymerase chain reaction (qPCR) and western blotting were performed to analyze expression of HGF (hepatocyte growth factor), MET, and their downstream markers. Immunohistochemistry (IHC) and immunofluorescence (IFC) staining were performed. RESULTS Higher expression of SIPA1 in lung tumours was associated with a poorer prognosis. Knockdown of SIPA1 decreased invasiveness and proliferation of in vitro cell lines, and the SIPA1 knockdown cells demonstrated leaky barriers. Knockdown of SIPA1 decreased tight junction-based barrier function by downregulating MET at the protein but not the transcript level, through silencing of Grb2, SOCS, and PKCμ (Protein kinase Cµ), reducing the internalization and recycling of MET. Elevated levels of SIPA1 protein are correlated with receptor tyrosine kinases (RTKs), especially HGF/MET and TJs. The regulation of HGF on barrier function and invasion required the presence of SIPA1. CONCLUSIONS SIPA1 plays an essential role in lung tumourigenesis and metastasis. SIPA1 may be a diagnostic and prognostic predictive biomarker. SIPA1 may also be a potential therapeutic target for non-small cell lung cancer (NSCLC) patients with aberrant MET expression and drug resistance.
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Affiliation(s)
- Chang Liu
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK; (C.L.); (W.J.)
| | - Wenguo Jiang
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK; (C.L.); (W.J.)
| | - Lijian Zhang
- Peking University School of Oncology and Peking University Cancer Hospital, Fucheng Road, Beijing 100142, China;
| | - Rachel Hargest
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK; (C.L.); (W.J.)
| | - Tracey A. Martin
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK; (C.L.); (W.J.)
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6
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Liu C, Jiang WG, Hargest R, Martin TA. The role of SIPA1 in the development of cancer and metastases (Review). Mol Clin Oncol 2020; 13:32. [PMID: 32789016 DOI: 10.3892/mco.2020.2102] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 06/16/2020] [Indexed: 01/13/2023] Open
Abstract
Cancer is a leading cause of mortality and the majority of deaths are due to metastases. Many molecules have been implicated in the development of metastases. Signal induced proliferation associated protein 1 (SIPA1), a mitogen-inducible gene, has been demonstrated to be involved in the metastasis of various solid tumours and may indicate a poor prognosis. Polymorphisms of SIPA1 can be associated with several different types of cancer and interactions between SIPA1 and binding molecules integrate a series of cellular functions, which may promote the development and metastasis of cancer. The mechanisms by which SIPA1 promotes the development and metastasis of cancer varies among tumour types. The present review describes the structure, function and regulation of SIPA1 and focuses on its role in cancer metastasis. Possibilities for future research and the clinical application of SIPA1 are also discussed.
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Affiliation(s)
- Chang Liu
- Cardiff China Medical Research Collaborative, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Wen Guo Jiang
- Cardiff China Medical Research Collaborative, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Rachel Hargest
- Cardiff China Medical Research Collaborative, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Tracey Amanda Martin
- Cardiff China Medical Research Collaborative, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
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Abstract
Tumour heterogeneity poses a substantial problem for the clinical management of cancer. Somatic evolution of the cancer genome results in genetically distinct subclones in the primary tumour with different biological properties and therapeutic sensitivities. The problem of heterogeneity is compounded in metastatic disease owing to the complexity of the metastatic process and the multiple biological hurdles that the tumour cell must overcome to establish a clinically overt metastatic lesion. New advances in sequencing technology and clinical sample acquisition are providing insights into the phylogenetic relationship of metastases and primary tumours at the level of somatic tumour genetics while also illuminating fundamental mechanisms of the metastatic process. In addition to somatically acquired genetic heterogeneity in the tumour cells, inherited population-based genetic heterogeneity can profoundly modify metastatic biology and further complicate the development of effective, broadly applicable antimetastatic therapies. Here, we examine how genetic heterogeneity impacts metastatic disease and the implications of current knowledge for future research endeavours and therapeutic interventions.
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8
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Zhang L, Hao C, Li J, Qu Y, Bao L, Li Y, Yue Z, Zhang M, Yu X, Chen H, Zhang J, Wang D, Yao W. Bioinformatics methods for identifying differentially expressed genes and signaling pathways in nano-silica stimulated macrophages. Tumour Biol 2017; 39:1010428317709284. [PMID: 28653889 DOI: 10.1177/1010428317709284] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The incidence of disease relating to nanoparticle exposure has been rising rapidly in recent years, for which there is no effective treatment. Macrophage is suggested to play a crucial role in the development of pulmonary disease. To investigate the changes in macrophage after being stimulated by nanometer silica dust and to explore potential biomarkers and signaling pathways, the gene chip GSE13005 was downloaded from Gene Expression Omnibus database, which contained 21 samples: 3 samples per group and 7 groups in total. Macrophages in the control group were cultured in serum-free medium, while the experimental groups were treated with nanometer silica dust in different sizes and concentrations, respectively. To identify the differentially expressed genes and explore their potential functions, we adopted the gene ontology analysis and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis and also constructed protein-protein interaction network. As a result, 1972 differentially expressed genes were identified from 22,690 microarray data in the gene chip, 1069 genes were upregulated and 903 genes were downregulated. Results of the gene ontology analysis indicated that the differentially expressed genes were widely distributed in intracellular and extracellular regions, regulating macrophage apoptosis, inflammatory response, and cell differentiation. The Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that the majority of differentially expressed genes were enriched in cytokine-cytokine receptor interaction, cancer or phagosome transcriptional misregulation. The top 10 hub genes, S100a9, Nos3, Psmd14, Psmd4, Lck, Atp6v1h, Jun, Foxh1, Pex14, and Fadd were identified from protein-protein interaction network. In addition, Nos3, Psmd14, Atp6v1h, and Jun were clustered into module M2 (rc = 0.74, p < 0.01), which mainly regulates cell carcinogenesis and antivirus process. In conclusion, differentially expressed genes screened from this study may provide new insights into the exploration of mechanisms, biomarkers, and therapeutic targets for diseases relating to nanoparticle exposure.
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Affiliation(s)
- Lin Zhang
- 1 Department of Occupational and Environmental Health, College of Public Health, Zhengzhou University, Zhengzhou, China.,2 Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China.,3 Key Laboratory of Reproductive Endocrinology, Ministry of Education, Shandong University, Jinan, China.,4 National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, China
| | - Changfu Hao
- 1 Department of Occupational and Environmental Health, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Juan Li
- 1 Department of Occupational and Environmental Health, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Yaqian Qu
- 1 Department of Occupational and Environmental Health, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Lei Bao
- 1 Department of Occupational and Environmental Health, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Yiping Li
- 1 Department of Occupational and Environmental Health, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Zhongzheng Yue
- 1 Department of Occupational and Environmental Health, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Miao Zhang
- 1 Department of Occupational and Environmental Health, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Xinghao Yu
- 1 Department of Occupational and Environmental Health, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Huiting Chen
- 1 Department of Occupational and Environmental Health, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Jianhui Zhang
- 1 Department of Occupational and Environmental Health, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Di Wang
- 1 Department of Occupational and Environmental Health, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Wu Yao
- 1 Department of Occupational and Environmental Health, College of Public Health, Zhengzhou University, Zhengzhou, China
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9
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Li J, Lu J, He Y, Wu Y, Wu Y, Song X, Jiang Y, Tang M, Weng X, Yi W, Luo X, Sun L, Bode AM, Cao Y. A new functional IDH2 genetic variant is associated with the risk of lung cancer. Mol Carcinog 2016; 56:1082-1087. [PMID: 27649069 DOI: 10.1002/mc.22573] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 09/06/2016] [Accepted: 09/16/2016] [Indexed: 12/20/2022]
Abstract
Recently, mutations in isocitrate dehydrogenase 1/2 (IDH1/2) were discovered in 70% of low-grade glioma and secondary glioblastoma multiforme. The discovery of an oncogenic function and the identification of onco-metabolites of IDH1/2 support new roles for metabolism in cancer. For example, some evidence indicates that IDH2 might also exhibit oncogenic functions by promoting cellular metabolism and cancer cell growth. We examined the association between IDH2 rs11540478 and lung cancer risk in 262 lung cancer patient cases and 602 healthy control subjects and also investigated the biological function of rs11540478 in vivo. We found that a higher risk was observed in lung cancer patient carriers of rs11540478 TT and CT compared with CC carriers (OR = 1.44; 95%CI = 1.04-2.00; P = 0.03). The frequency of IDH2 rs11540478 TT and CT carriers was decreased in healthy individuals between the ages of 50-77 compared to those aged 30-49 (OR = 0.67; 95%CI = 0.47-0.96; P = 0.03). Functional analysis showed the effect of rs11540478 on IDH2 expression and lung cancer cell viability, with higher IDH2 expression and cell viability among T allele compared with C allele. IDH2 mRNA was higher in peripheral blood lymphocytes from lung cancer patients compared to healthy subjects. Herein, for the first time we identified IDH2 rs11540478 as a new susceptibility locus for lung cancer. The effect of rs11540478 on mRNA expression of IDH2 and lung cancer cell viability might provide new insight for the genetic basis of lung cancer. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Jiangjiang Li
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, China.,Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, Changsha, China
| | - Jingchen Lu
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, China.,Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, Changsha, China.,Department of Medical Oncology, Xiangya Hospital, Central South University, Changsha, China
| | - Ya He
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, China.,Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, Changsha, China
| | - Yong Wu
- Department of Medicine Clinical Laboratory, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Yuan Wu
- Department of Medicine Clinical Laboratory, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Xin Song
- Cancer Biotherapy Center, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, China
| | - Yuee Jiang
- Department of Clinical Laboratory, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Min Tang
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, China.,Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, Changsha, China
| | - Xinxian Weng
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, China.,Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, Changsha, China
| | - Wei Yi
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, China.,Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, Changsha, China
| | - Xiangjian Luo
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, China.,Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, Changsha, China
| | - Lunquan Sun
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, China.,Center for Molecular Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Ann M Bode
- The Hormel Institute, University of Minnesota, Austin, Minnesota
| | - Ya Cao
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, China.,Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, Changsha, China
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10
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Wang L, Cheng L, Li NN, Yu WJ, Sun XY, Peng R. Association of four new candidate genetic variants with Parkinson's disease in a Han Chinese population. Am J Med Genet B Neuropsychiatr Genet 2016; 171B:342-7. [PMID: 26678010 DOI: 10.1002/ajmg.b.32410] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 12/03/2015] [Indexed: 11/08/2022]
Abstract
Large-scale meta-analysis of genome-wide association data has identified six new risk loci (SIPA1L2, INPP5F, MIR4697, GCH1, VPS13C, and DDRGK1) for Parkinson's disease (PD). However, the characteristics of those loci in a Han Chinese population from mainland China are unknown. We examined genetic associations of VPS13C rs2414739, MIR4697 rs329648, GCH1 rs11158026, and SIPA1L2 rs10797576 with PD susceptibility in a Han Chinese population of 1028 sporadic PD patients and 1109 healthy controls. All subjects were genotyped for these loci using the Sequenom iPLEX Assay. We also conducted further stratified analysis according to age at onset and compared the clinical characteristics between minor allele carriers and non-carriers for each locus. However, we did not observe any significant difference in genotype distribution between PD patients and controls for the four loci, even after being stratified by age at onset. Besides, minor allele carriers cannot be distinguished from non-carriers based on their clinical features. Our findings first demonstrated that VPS13C rs2414739, MIR4697 rs329648, GCH1 rs11158026, and SIPA1L2 rs10797576 do not confer a significant risk for PD in Chinese population. Additional replication studies in other populations and functional studies are warranted to better validate the role of the four new loci in PD risk.
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Affiliation(s)
- Ling Wang
- Department of Neurology, West China Hospital, Sichuan University, Sichuan, P.R. China
| | - Lan Cheng
- Department of Neurology, West China Hospital, Sichuan University, Sichuan, P.R. China
| | - Nan-Nan Li
- Department of Neurology, West China Hospital, Sichuan University, Sichuan, P.R. China
| | - Wen-Juan Yu
- Department of Neurology, West China Hospital, Sichuan University, Sichuan, P.R. China
| | - Xiao-Yi Sun
- Department of Neurology, West China Hospital, Sichuan University, Sichuan, P.R. China
| | - Rong Peng
- Department of Neurology, West China Hospital, Sichuan University, Sichuan, P.R. China
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11
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Ugenskienė R, Myrzaliyeva D, Jankauskaitė R, Gedminaitė J, Jančiauskienė R, Šepetauskienė E, Juozaitytė E. The contribution of SIPA1 and RRP1B germline polymorphisms to breast cancer phenotype, lymph node status and survival in a group of Lithuanian young breast cancer patients. Biomarkers 2016; 21:363-70. [PMID: 26901824 DOI: 10.3109/1354750x.2016.1141989] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The germline polymorphisms in signal-inducing proliferation-associated protein 1 (SIPA1) and ribosomal RNR processing 1B (RRP1B) might be involved in breast cancer metastasis. The aim of this study was to analyze how SIPA1 and RRP1B polymorphisms contribute to breast cancer phenotype, lymph node status and survival. A group of 100 young, I-II stage breast cancer patients were analyzed for SIPA1 and RRP1B polymorphisms with PCR-RFLP assay. SIPA1 c.2760G > A, c.545C > T and RRP1B c.436T > C polymorphisms were associated with lymph node status, survival and tumor grade, respectively. Our results suggest that SIPA1 and RRP1B germline polymorphisms are important for breast cancer prognosis.
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Affiliation(s)
- Rasa Ugenskienė
- a Oncology Research Laboratory, Oncology Institute, Lithuanian University of Health Sciences , Kaunas , Lithuania
| | - Dana Myrzaliyeva
- b Oncology Institute, Lithuanian University of Health Sciences , Kaunas , Lithuania , and
| | - Roberta Jankauskaitė
- a Oncology Research Laboratory, Oncology Institute, Lithuanian University of Health Sciences , Kaunas , Lithuania
| | - Jurgita Gedminaitė
- b Oncology Institute, Lithuanian University of Health Sciences , Kaunas , Lithuania , and
| | - Rasa Jančiauskienė
- b Oncology Institute, Lithuanian University of Health Sciences , Kaunas , Lithuania , and
| | - Eglė Šepetauskienė
- c Center of Informatics Technologies, Lithuanian University of Health Sciences , Kaunas , Lithuania
| | - Elona Juozaitytė
- b Oncology Institute, Lithuanian University of Health Sciences , Kaunas , Lithuania , and
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12
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Hunter K. The role of individual inheritance in tumor progression and metastasis. J Mol Med (Berl) 2015; 93:719-25. [PMID: 26054921 DOI: 10.1007/s00109-015-1299-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 05/18/2015] [Accepted: 05/19/2015] [Indexed: 01/02/2023]
Abstract
Metastasis, the dissemination and growth of tumor cells at secondary sites, is the primary cause of patient mortality from solid tumors. Metastasis is an extremely complex, inefficient process requiring contributions of not only the tumor cell but also local and distant environmental factors, at both the cellular and molecular level. Variation in the function of any of the steps in the metastatic cascade may therefore have profound implications for the ultimate course of the disease. In addition to the somatic and cellular heterogeneity that can affect cancer outcome, an individual's specific ancestry or genetic background can also significantly influence metastatic progression. These inherited variants not only encoded for metastatic susceptibility but also provided a window to study critical factors that are not easily accessible with current technologies. Furthermore, investigations into inherited metastatic susceptibility enable identification of important molecular and cellular processes that are not subject to mutation and are consequently not detectable by standard cancer genome sequencing strategies. Incorporation of inherited variation into metastasis research therefore provides methods to more comprehensively investigate the etiology of the lethal consequences of tumor progression.
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Affiliation(s)
- Kent Hunter
- Laboratory of Cancer Biology and Genetics, CCR/NCI/NIH, Building 37 Room 5046C, 37 Convent Drive, Bethesda, MD, 20892-4264, USA,
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13
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The SIPA1 -313A>G polymorphism is associated with prognosis in inoperable non-small cell lung cancer. Tumour Biol 2014; 36:1273-8. [PMID: 25352027 DOI: 10.1007/s13277-014-2753-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 10/20/2014] [Indexed: 12/16/2022] Open
Abstract
Polymorphism in signal-induced proliferation-associated 1 (SIPA1) gene may contribute to the development of metastasis in human cancers. In this preliminary study, we examined the association of the SIPA1 -313A>G (rs931127) polymorphism with overall survival (OS) and progression-free survival (PFS) in 351 inoperable patients with non-small cell lung cancer (NSCLC) treated with radiotherapy or radiochemotherapy (curative or palliative). The GG homozygotes had significantly shorter PFS under codominant and recessive models in all patients (hazard ratio (HR) 1.47, p = 0.035, and HR 1.47, p = 0.022, respectively) and in advanced stage subgroup (HR 1.49, p = 0.037, and HR 1.48, p = 0.023, respectively). The GG genotype was also associated with reduced OS and PFS (codominant model: HR 2.41, p = 0.020, and HR 2.34, p = 0.020, respectively; recessive model: HR 2.16, p = 0.026, and HR 2.18, p = 0.022, respectively) in radiotherapy alone subgroup. Moreover, the SIPA1 -313GG was identified as an independent adverse prognostic factor for PFS in the cohort. Our results indicate, for the first time, that the SIPA1 -313A>G may have a prognostic role in unresected NSCLC making it a potential predictor of poor survival due to earlier progression.
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