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Hojo M, Maeno A, Sakamoto Y, Yamamoto Y, Taquahashi Y, Hirose A, Suzuki J, Inomata A, Nakae D. Time-Course of Transcriptomic Change in the Lungs of F344 Rats Repeatedly Exposed to a Multiwalled Carbon Nanotube in a 2-Year Test. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:2105. [PMID: 37513116 PMCID: PMC10383707 DOI: 10.3390/nano13142105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/13/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023]
Abstract
Despite intensive toxicological studies of carbon nanotubes (CNTs) over the last two decades, only a few studies have demonstrated their pulmonary carcinogenicities in chronic animal experiments, and the underlying molecular mechanisms are still unclear. To obtain molecular insights into CNT-induced lung carcinogenicity, we performed a transcriptomic analysis using a set of lung tissues collected from rats in a 2-year study, in which lung tumors were induced by repeated intratracheal instillations of a multiwalled carbon nanotube, MWNT-7. The RNA-seq-based transcriptome identified a large number of significantly differentially expressed genes at Year 0.5, Year 1, and Year 2. Ingenuity Pathway Analysis revealed that macrophage-elicited signaling pathways such as phagocytosis, acute phase response, and Toll-like receptor signaling were activated throughout the experimental period. At Year 2, cancer-related pathways including ERBB signaling and some axonal guidance signaling pathways such as EphB4 signaling were perturbed. qRT-PCR and immunohistochemistry indicated that several key molecules such as Osteopontin/Spp1, Hmox1, Mmp12, and ERBB2 were markedly altered and/or localized in the preneoplastic lesions, suggesting their participation in the induction of lung cancer. Our findings support a scenario of inflammation-induced carcinogenesis and contribute to a better understanding of the molecular mechanism of MWCNT carcinogenicity.
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Affiliation(s)
- Motoki Hojo
- Department of Pharmaceutical and Environmental Sciences, Tokyo Metropolitan Institute of Public Health, 3-24-1 Hyakunincho, Shinjuku-ku, Tokyo 169-0073, Japan
| | - Ai Maeno
- Department of Pharmaceutical and Environmental Sciences, Tokyo Metropolitan Institute of Public Health, 3-24-1 Hyakunincho, Shinjuku-ku, Tokyo 169-0073, Japan
| | - Yoshimitsu Sakamoto
- Department of Pharmaceutical and Environmental Sciences, Tokyo Metropolitan Institute of Public Health, 3-24-1 Hyakunincho, Shinjuku-ku, Tokyo 169-0073, Japan
| | - Yukio Yamamoto
- Department of Pharmaceutical and Environmental Sciences, Tokyo Metropolitan Institute of Public Health, 3-24-1 Hyakunincho, Shinjuku-ku, Tokyo 169-0073, Japan
| | - Yuhji Taquahashi
- Division of Cellular and Molecular Toxicology, Center for Biological Safety and Research, National Institute of Health Sciences, 3-25-26 Tono-machi, Kawasaki-ku, Kawasaki 210-9501, Kanagawa, Japan
| | - Akihiko Hirose
- Chemicals Assessment and Research Center, Chemicals Evaluation and Research Institute, Japan, 1-4-25 Koraku, Bunkyo-ku, Tokyo 112-0004, Japan
| | - Jin Suzuki
- Department of Pharmaceutical and Environmental Sciences, Tokyo Metropolitan Institute of Public Health, 3-24-1 Hyakunincho, Shinjuku-ku, Tokyo 169-0073, Japan
| | - Akiko Inomata
- Department of Pharmaceutical and Environmental Sciences, Tokyo Metropolitan Institute of Public Health, 3-24-1 Hyakunincho, Shinjuku-ku, Tokyo 169-0073, Japan
| | - Dai Nakae
- Department of Medical Sports, Faculty of Health Care and Medical Sports, Teikyo Heisei University, 4-1 Uruido-Minami, Ichihara 290-0193, Chiba, Japan
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2
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Lau A, Le N, Nguyen C, Kandpal RP. Signals transduced by Eph receptors and ephrin ligands converge on MAP kinase and AKT pathways in human cancers. Cell Signal 2023; 104:110579. [PMID: 36572189 DOI: 10.1016/j.cellsig.2022.110579] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022]
Abstract
Eph receptors, the largest known family of receptor tyrosine kinases, and ephrin ligands have been implicated in a variety of human cancers. The novel bidirectional signaling events initiated by binding of Eph receptors to their cognate ephrin ligands modulate many cellular processes such as proliferation, metastasis, angiogenesis, invasion, and apoptosis. The relationships between the abundance of a unique subset of Eph receptors and ephrin ligands with associated cellular processes indicate a key role of these molecules in tumorigenesis. The combinatorial expression of these molecules converges on MAP kinase and/or AKT/mTOR signaling pathways. The intracellular target proteins of the initial signal may, however, vary in some cancers. Furthermore, we have also described the commonality of up- and down-regulation of individual receptors and ligands in various cancers. The current state of research in Eph receptors illustrates MAP kinase and mTOR pathways as plausible targets for therapeutic interventions in various cancers.
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Affiliation(s)
- Andreas Lau
- Department of Basic Medical Sciences, Western University of Health Sciences, Pomona, CA 91766, United States of America
| | - Nghia Le
- Department of Basic Medical Sciences, Western University of Health Sciences, Pomona, CA 91766, United States of America
| | - Claudia Nguyen
- Department of Basic Medical Sciences, Western University of Health Sciences, Pomona, CA 91766, United States of America
| | - Raj P Kandpal
- Department of Basic Medical Sciences, Western University of Health Sciences, Pomona, CA 91766, United States of America.
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3
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Li D, Wang J, Fang Y, Hu Y, Xiao Y, Cui Q, Jiang C, Sun S, Chen H, Ye L, Sun Q. Impaired cell-cell communication and axon guidance because of pulmonary hypoperfusion during postnatal alveolar development. Respir Res 2023; 24:12. [PMID: 36631871 PMCID: PMC9833865 DOI: 10.1186/s12931-023-02319-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 01/06/2023] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Pulmonary hypoperfusion is common in children with congenital heart diseases (CHDs) or pulmonary hypertension (PH) and causes adult pulmonary dysplasia. Systematic reviews have shown that some children with CHDs or PH have mitigated clinical outcomes with COVID-19. Understanding the effects of pulmonary hypoperfusion on postnatal alveolar development may aid in the development of methods to improve the pulmonary function of children with CHDs or PH and improve their care during the COVID-19 pandemic, which is characterized by cytokine storm and persistent inflammation. METHODS AND RESULTS We created a neonatal pulmonary hypoperfusion model through pulmonary artery banding (PAB) surgery at postnatal day 1 (P1). Alveolar dysplasia was confirmed by gross and histological examination at P21. Transcriptomic analysis of pulmonary tissues at P7(alveolar stage 2) and P14(alveolar stage 4) revealed that the postnatal alveolar development track had been changed due to pulmonary hypoperfusion. Under the condition of pulmonary hypoperfusion, the cell-cell communication and axon guidance, which both determine the final number of alveoli, were lost; instead, there was hyperactive cell cycle activity. The transcriptomic results were further confirmed by the examination of axon guidance and cell cycle markers. Because axon guidance controls inflammation and immune cell activation, the loss of axon guidance may explain the lack of severe COVID-19 cases among children with CHDs or PH accompanied by pulmonary hypoperfusion. CONCLUSIONS This study suggested that promoting cell-cell communication or supplementation with guidance molecules may treat pulmonary hypoperfusion-induced alveolar dysplasia, and that COVID-19 is less likely to cause a cytokine storm in children with CHD or PH accompanied by pulmonary hypoperfusion.
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Affiliation(s)
- Debao Li
- grid.16821.3c0000 0004 0368 8293Department of Thoracic and Cardiovascular Surgery, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, 1678 Dongfang Road, Shanghai, 200127 China
| | - Jing Wang
- grid.16821.3c0000 0004 0368 8293Department of Infectious Diseases, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yuan Fang
- grid.412523.30000 0004 0386 9086Department of Plastic and Reconstructive Surgery, School of Medicine, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yuqing Hu
- grid.16821.3c0000 0004 0368 8293Department of Cardiology, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yingying Xiao
- grid.16821.3c0000 0004 0368 8293Department of Thoracic and Cardiovascular Surgery, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, 1678 Dongfang Road, Shanghai, 200127 China
| | - Qing Cui
- grid.16821.3c0000 0004 0368 8293Department of Cardiology, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Chuan Jiang
- grid.16821.3c0000 0004 0368 8293Department of Thoracic and Cardiovascular Surgery, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, 1678 Dongfang Road, Shanghai, 200127 China
| | - Sijuan Sun
- grid.16821.3c0000 0004 0368 8293Department of Pediatric Intensive Care Unit, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hao Chen
- grid.16821.3c0000 0004 0368 8293Department of Thoracic and Cardiovascular Surgery, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, 1678 Dongfang Road, Shanghai, 200127 China
| | - Lincai Ye
- grid.16821.3c0000 0004 0368 8293Department of Thoracic and Cardiovascular Surgery, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, 1678 Dongfang Road, Shanghai, 200127 China ,grid.16821.3c0000 0004 0368 8293Institute of Pediatric Translational Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China ,grid.16821.3c0000 0004 0368 8293Shanghai Institute for Pediatric Congenital Heart Disease, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, 1678 Dongfang Road, Shanghai, 200127 China
| | - Qi Sun
- grid.16821.3c0000 0004 0368 8293Department of Thoracic and Cardiovascular Surgery, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, 1678 Dongfang Road, Shanghai, 200127 China
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Sengupta D, Bhattacharya G, Ganguli S, Sengupta M. Structural insights and evaluation of the potential impact of missense variants on the interactions of SLIT2 with ROBO1/4 in cancer progression. Sci Rep 2020; 10:21909. [PMID: 33318575 PMCID: PMC7736846 DOI: 10.1038/s41598-020-78882-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/01/2020] [Indexed: 02/07/2023] Open
Abstract
The cognate interaction of ROBO1/4 with its ligand SLIT2 is known to be involved in lung cancer progression. However, the precise role of genetic variants, disrupting the molecular interactions is less understood. All cancer-associated missense variants of ROBO1/4 and SLIT2 from COSMIC were screened for their pathogenicity. Homology modelling was done in Modeller 9.17, followed by molecular simulation in GROMACS. Rigid docking was performed for the cognate partners in PatchDock with refinement in HADDOCK server. Post-docking alterations in conformational, stoichiometric, as well as structural parameters, were assessed. The disruptive variants were ranked using a weighted scoring scheme. In silico prioritisation of 825 variants revealed 379 to be potentially pathogenic out of which, about 12% of the variants, i.e. ROBO1 (14), ROBO4 (8), and SLIT2 (23) altered the cognate docking. Six variants of ROBO1 and 5 variants of ROBO4 were identified as "high disruptors" of interactions with SLIT2 wild type. Likewise, 17 and 13 variants of SLIT2 were found to be "high disruptors" of its interaction with ROBO1 and ROBO4, respectively. Our study is the first report on the impact of cancer-associated missense variants on ROBO1/4 and SLIT2 interactions that might be the drivers of lung cancer progression.
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Affiliation(s)
- Debmalya Sengupta
- Department of Genetics, University of Calcutta, University College of Science (UCSTA), 35, Ballygunge Circular Road, Kolkata, 700 019, India
| | - Gairika Bhattacharya
- Department of Genetics, University of Calcutta, University College of Science (UCSTA), 35, Ballygunge Circular Road, Kolkata, 700 019, India
- Cactus Communications, Mumbai, India
| | - Sayak Ganguli
- Department of Biotechnology, St. Xavier's College (Autonomous), 30, Mother Teresa Sarani, Kolkata, 700 016, India.
| | - Mainak Sengupta
- Department of Genetics, University of Calcutta, University College of Science (UCSTA), 35, Ballygunge Circular Road, Kolkata, 700 019, India.
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Zhang Y, Yang M, Ng DM, Haleem M, Yi T, Hu S, Zhu H, Zhao G, Liao Q. Multi-omics Data Analyses Construct TME and Identify the Immune-Related Prognosis Signatures in Human LUAD. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:860-873. [PMID: 32805489 PMCID: PMC7452010 DOI: 10.1016/j.omtn.2020.07.024] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/15/2020] [Accepted: 07/20/2020] [Indexed: 02/06/2023]
Abstract
Lung cancer has been the focus of attention for many researchers in recent years for the leading contribution to cancer-related death worldwide, in which lung adenocarcinoma (LUAD) is the most common histological type. However, the potential mechanism behind LUAD initiation and progression remains unclear. Aiming to dissect the tumor microenvironment of LUAD and to discover more informative prognosis signatures, we investigated the immune-related differences in three types of genetic or epigenetic characteristics (expression status, somatic mutation, and DNA methylation) and considered the potential roles that these alterations have in the immune response and both the immune-related metabolic and neural systems by analyzing the multi-omics data from The Cancer Genome Atlas (TCGA) portal. Additionally, a four-step strategy based on lasso regression and Cox regression was used to construct the prognostic prediction model. For the prognostic predictions on the independent test set, the performance of the trained models (average concordance index [C-index] = 0.839) is satisfied, with average 1-year, 3-year, and 5-year areas under the curve (AUCs) equal to 0.796, 0.786, and 0.777. Finally, the overall model was constructed based on all samples, which comprised 27 variables and achieved a high degree of accuracy on the 1-year (AUC = 0.861), 3-year (AUC = 0.850), and 5-year (AUC = 0.916) survival predictions.
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Affiliation(s)
- Yuwei Zhang
- Hwa Mei Hospital, University of Chinese Academy of Science, Ningbo, Zhejiang, China; Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathophysiology Technology, Medical School of Ningbo University, Ningbo, China; Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences
| | - Minglei Yang
- Hwa Mei Hospital, University of Chinese Academy of Science, Ningbo, Zhejiang, China; Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences
| | - Derry Minyao Ng
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathophysiology Technology, Medical School of Ningbo University, Ningbo, China
| | - Maria Haleem
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathophysiology Technology, Medical School of Ningbo University, Ningbo, China
| | - Tianfei Yi
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathophysiology Technology, Medical School of Ningbo University, Ningbo, China
| | - Shiyun Hu
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathophysiology Technology, Medical School of Ningbo University, Ningbo, China
| | - Huangkai Zhu
- Hwa Mei Hospital, University of Chinese Academy of Science, Ningbo, Zhejiang, China; Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences
| | - Guofang Zhao
- Hwa Mei Hospital, University of Chinese Academy of Science, Ningbo, Zhejiang, China; Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences.
| | - Qi Liao
- Hwa Mei Hospital, University of Chinese Academy of Science, Ningbo, Zhejiang, China; Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathophysiology Technology, Medical School of Ningbo University, Ningbo, China; Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences.
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6
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Shih JH, Chen HY, Lin SC, Yeh YC, Shen R, Lang YD, Wu DC, Chen CY, Chen RH, Chou TY, Jou YS. Integrative analyses of noncoding RNAs reveal the potential mechanisms augmenting tumor malignancy in lung adenocarcinoma. Nucleic Acids Res 2020; 48:1175-1191. [PMID: 31853539 PMCID: PMC7026595 DOI: 10.1093/nar/gkz1149] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 07/06/2019] [Accepted: 12/01/2019] [Indexed: 01/12/2023] Open
Abstract
Precise noncoding RNA (ncRNA)-based network prediction is necessary to reveal ncRNA functions and pathological mechanisms. Here, we established a systemic pipeline to identify prognostic ncRNAs, predict their functions and explore their pathological mechanisms in lung adenocarcinoma (LUAD). After in silico and experimental validation based on evaluations of prognostic value in multiple LUAD cohorts, we selected the PTTG3P pseudogene from among other prognostic ncRNAs (MIR497HG, HSP078, TBX5-AS1, LOC100506990 and C14orf64) for mechanistic studies. PTTG3P upregulation in LUAD cells shortens the metaphase to anaphase transition in mitosis, increases cell viability after cisplatin or paclitaxel treatment, facilitates tumor growth that leads to poor survival in orthotopic lung models, and is associated with a poor survival rate in LUAD patients in the TCGA cohort who received chemotherapy. Mechanistically, PTTG3P acts as an ncRNA that interacts with the transcription factor FOXM1 to regulate the transcriptional activation of the mitotic checkpoint kinase BUB1B, which augments tumor growth and chemoresistance and leads to poor outcomes for LUAD patients. Overall, we established a systematic strategy to uncover prognostic ncRNAs with functional prediction methods suitable for pan-cancer studies. Moreover, we revealed that PTTG3P, due to its upregulation of the PTTG3P/FOXM1/BUB1B axis, could be a therapeutic target for LUAD patients.
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Affiliation(s)
- Jou-Ho Shih
- Genome and Systems Biology Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan.,Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Hsin-Yi Chen
- Graduate Institute of Cancer Biology & Drug Discovery, College of Medical Science & Technology, Taipei Medical University, Taipei 11221, Taiwan
| | - Shin-Chih Lin
- Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei 11221, Taiwan.,Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan.,Division of Molecular Pathology, Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei 11221, Taiwan
| | - Yi-Chen Yeh
- Division of Molecular Pathology, Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei 11221, Taiwan
| | - Roger Shen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan.,Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei 11221, Taiwan
| | - Yaw-Dong Lang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Dung-Chi Wu
- Genome and Systems Biology Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan.,Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Chien-Yu Chen
- Genome and Systems Biology Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan.,Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Ruey-Hwa Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Teh-Ying Chou
- Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei 11221, Taiwan.,Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan.,Division of Molecular Pathology, Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei 11221, Taiwan.,Institute of Clinical Medicine, National Yang-Ming University, Taipei 11221, Taiwan
| | - Yuh-Shan Jou
- Genome and Systems Biology Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan.,Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan.,Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei 11221, Taiwan
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7
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Gene Expression and Epigenetic Changes in Mice Following Inhalation of Copper(II) Oxide Nanoparticles. NANOMATERIALS 2020; 10:nano10030550. [PMID: 32197515 PMCID: PMC7153614 DOI: 10.3390/nano10030550] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/12/2020] [Accepted: 03/17/2020] [Indexed: 12/13/2022]
Abstract
We investigated the transcriptomic response and epigenetic changes in the lungs of mice exposed to inhalation of copper(II) oxide nanoparticles (CuO NPs) (8 × 105 NPs/m3) for periods of 3 days, 2 weeks, 6 weeks, and 3 months. A whole genome transcriptome and miRNA analysis was performed using next generation sequencing. Global DNA methylation was assessed by ELISA. The inhalation resulted in the deregulation of mRNA transcripts: we detected 170, 590, 534, and 1551 differentially expressed transcripts after 3 days, 2 weeks, 6 weeks, and 3 months of inhalation, respectively. Biological processes and pathways affected by inhalation, differed between 3 days exposure (collagen formation) and longer treatments (immune response). Periods of two weeks exposure further induced apoptotic processes, 6 weeks of inhalation affected the cell cycle, and 3 months of treatment impacted the processes related to cell adhesion. The expression of miRNA was not affected by 3 days of inhalation. Prolonged exposure periods modified miRNA levels, although the numbers were relatively low (17, 18, and 38 miRNAs, for periods of 2 weeks, 6 weeks, and 3 months, respectively). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis based on miRNA–mRNA interactions, revealed the deregulation of processes implicated in the immune response and carcinogenesis. Global DNA methylation was not significantly affected in any of the exposure periods. In summary, the inhalation of CuO NPs impacted on both mRNA and miRNA expression. A significant transcriptomic response was already observed after 3 days of exposure. The affected biological processes and pathways indicated the negative impacts on the immune system and potential role in carcinogenesis.
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8
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Rynning I, Neca J, Vrbova K, Libalova H, Rossner P, Holme JA, Gützkow KB, Afanou AKJ, Arnoldussen YJ, Hruba E, Skare Ø, Haugen A, Topinka J, Machala M, Mollerup S. In Vitro Transformation of Human Bronchial Epithelial Cells by Diesel Exhaust Particles: Gene Expression Profiling and Early Toxic Responses. Toxicol Sci 2019; 166:51-64. [PMID: 30010986 PMCID: PMC6204768 DOI: 10.1093/toxsci/kfy183] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Occupational exposure to diesel exhaust may cause lung cancer in humans. Mechanisms include DNA-damage and inflammatory responses. Here, the potential of NIST SRM2975 diesel exhaust particles (DEP) to transform human bronchial epithelial cells (HBEC3) in vitro was investigated. Long-term exposure of HBEC3 to DEP led to increased colony growth in soft agar. Several DEP-transformed cell lines were established and based on the expression of epithelial-to-mesenchymal-transition (EMT) marker genes, one of them (T2-HBEC3) was further characterized. T2-HBEC3 showed a mesenchymal/fibroblast-like morphology, reduced expression of CDH1, and induction of CDH2 and VIM. T2-HBEC3 had reduced migration potential compared with HBEC3 and little invasion capacity. Gene expression profiling showed baseline differences between HBEC3 and T2-HBEC3 linked to lung carcinogenesis. Next, to assess differences in sensitivity to DEP between parental HBEC3 and T2-HBEC3, gene expression profiling was carried out after DEP short-term exposure. Results revealed changes in genes involved in metabolism of xenobiotics and lipids, as well as inflammation. HBEC3 displayed a higher steady state of IL1B gene expression and release of IL-1β compared with T2-HBEC3. HBEC3 and T2-HBEC3 showed similar susceptibility towards DEP-induced genotoxic effects. Liquid-chromatography-tandem-mass-spectrometry was used to measure secretion of eicosanoids. Generally, major prostaglandin species were released in higher concentrations from T2-HBEC3 than from HBEC3 and several analytes were altered after DEP-exposure. In conclusion, long-term exposure to DEP-transformed human bronchial epithelial cells in vitro. Differences between HBEC3 and T2-HBEC3 regarding baseline levels and DEP-induced changes of particularly CYP1A1, IL-1β, PGE2, and PGF2α may have implications for acute inflammation and carcinogenesis.
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Affiliation(s)
- Iselin Rynning
- Section for Toxicology and Biological Work Environment, Department of Chemical and Biological Work Environment, National Institute of Occupational Health, N-0304 Oslo, Norway
| | - Jiri Neca
- Department of Chemistry and Toxicology, Veterinary Research Institute, 621 00 Brno, Czech Republic
| | - Kristyna Vrbova
- Department of Genetic Toxicology and Nanotoxicology, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Helena Libalova
- Department of Genetic Toxicology and Nanotoxicology, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Pavel Rossner
- Department of Genetic Toxicology and Nanotoxicology, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Jørn A Holme
- Division of Infection Control, Environment and Health, Department of Air and Noise
| | - Kristine B Gützkow
- Division of Infection Control, Department of Molecular Biology, Norwegian Institute of Public Health, N-0304 Oslo, Norway
| | - Anani K Johnny Afanou
- Section for Toxicology and Biological Work Environment, Department of Chemical and Biological Work Environment, National Institute of Occupational Health, N-0304 Oslo, Norway
| | - Yke J Arnoldussen
- Section for Toxicology and Biological Work Environment, Department of Chemical and Biological Work Environment, National Institute of Occupational Health, N-0304 Oslo, Norway
| | - Eva Hruba
- Department of Chemistry and Toxicology, Veterinary Research Institute, 621 00 Brno, Czech Republic
| | - Øivind Skare
- Department of Occupational Medicine and Epidemiology, National Institute of Occupational Health, N-0304 Oslo, Norway
| | - Aage Haugen
- Section for Toxicology and Biological Work Environment, Department of Chemical and Biological Work Environment, National Institute of Occupational Health, N-0304 Oslo, Norway
| | - Jan Topinka
- Department of Genetic Toxicology and Nanotoxicology, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Miroslav Machala
- Department of Chemistry and Toxicology, Veterinary Research Institute, 621 00 Brno, Czech Republic
| | - Steen Mollerup
- Section for Toxicology and Biological Work Environment, Department of Chemical and Biological Work Environment, National Institute of Occupational Health, N-0304 Oslo, Norway
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9
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Characterization of Host Responses during Pseudomonas aeruginosa Acute Infection in the Lungs and Blood and after Treatment with the Synthetic Immunomodulatory Peptide IDR-1002. Infect Immun 2018; 87:IAI.00661-18. [PMID: 30323028 PMCID: PMC6300642 DOI: 10.1128/iai.00661-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 10/02/2018] [Indexed: 12/26/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that causes nosocomial pneumonia and infects patients with cystic fibrosis. P. aeruginosa lung infections are difficult to treat due to bacterial resistance to antibiotics, and strains with multidrug resistance are becoming more prevalent. Pseudomonas aeruginosa is an opportunistic pathogen that causes nosocomial pneumonia and infects patients with cystic fibrosis. P. aeruginosa lung infections are difficult to treat due to bacterial resistance to antibiotics, and strains with multidrug resistance are becoming more prevalent. Here, we examined the use of a small host defense peptide, innate defense regulator 1002 (IDR-1002), in an acute P. aeruginosa lung infection in vivo. IDR-1002 significantly reduced the bacterial burden in bronchoalveolar lavage fluid (BALF), as well as MCP-1 in BALF and serum, KC in serum, and interleukin 6 (IL-6) in BALF. Transcriptome sequencing (RNA-Seq) was conducted on lungs and whole blood, and the effects of P. aeruginosa, IDR-1002, and the combination of P. aeruginosa and IDR-1002 were evaluated. Differential gene expression analysis showed that P. aeruginosa increased multiple inflammatory and innate immune pathways, as well as affected hemostasis, matrix metalloproteinases, collagen biosynthesis, and various metabolism pathways in the lungs and/or blood. Infected mice treated with IDR-1002 had significant changes in gene expression compared to untreated infected mice, with fewer differentially expressed genes associated with the inflammatory and innate immune responses to microbial infection, and treatment also affected morphogenesis, certain metabolic pathways, and lymphocyte activation. Overall, these results showed that IDR-1002 was effective in treating P. aeruginosa acute lung infections and associated inflammation.
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10
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Meucci S, Keilholz U, Heim D, Klauschen F, Cacciatore S. Somatic genome alterations in relation to age in lung squamous cell carcinoma. Oncotarget 2018; 9:32161-32172. [PMID: 30181806 PMCID: PMC6114948 DOI: 10.18632/oncotarget.25848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 07/12/2018] [Indexed: 12/31/2022] Open
Abstract
Lung squamous cell carcinoma (LUSC) is the most common cause of global cancer-related mortality and the major risk factors is smoking consumption. By analyzing ∼500 LUSC samples from The Cancer Genome Atlas, we detected a higher mutational burden as well as a higher level of methylation changes in younger patients. The SNPs mutational profiling showed enrichments of smoking-related signature 4 and defective DNA mismatch repair (MMR)-related signature 6 in younger patients, while the defective DNA MMR signature 26 was enriched among older patients. Furthermore, gene set enrichment analysis was performed in order to explore functional effect of somatic alterations in relation to patient age. Extracellular Matrix-Receptor Interaction, Nucleotide Excision Repair and Axon Guidance seem crucial disrupted pathways in younger patients. We hypothesize that a higher sensitivity to smoking-related damages and the enrichment of defective DNA MMR related mutations may contribute to the higher mutational burden of younger patients. The two distinct age-related defective DNA MMR signatures 6 and 26 might be crucial mutational patterns in LUSC tumorigenesis which may develop distinct phenotypes. Our study provides indications of age-dependent differences in mutational backgrounds (SNPs and CNVs) as well as epigenetic patterns that might be relevant for age adjusted treatment approaches.
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Affiliation(s)
- Stefano Meucci
- Charité Comprehensive Cancer Center, Charité University Hospital, Berlin, Germany
| | - Ulrich Keilholz
- Charité Comprehensive Cancer Center, Charité University Hospital, Berlin, Germany
| | - Daniel Heim
- Institut für Pathologie, Charité University Hospital, Berlin, Germany
| | | | - Stefano Cacciatore
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, England, UK
- International Centre for Genetic Engineering and Biotechnology, Cancer Genomics Group, Cape Town, South Africa
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11
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Semaphorin 3C and Its Receptors in Cancer and Cancer Stem-Like Cells. Biomedicines 2018; 6:biomedicines6020042. [PMID: 29642487 PMCID: PMC6027460 DOI: 10.3390/biomedicines6020042] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Revised: 03/27/2018] [Accepted: 04/03/2018] [Indexed: 01/13/2023] Open
Abstract
Neurodevelopmental programs are frequently dysregulated in cancer. Semaphorins are a large family of guidance cues that direct neuronal network formation and are also implicated in cancer. Semaphorins have two kinds of receptors, neuropilins and plexins. Besides their role in development, semaphorin signaling may promote or suppress tumors depending on their context. Sema3C is a secreted semaphorin that plays an important role in the maintenance of cancer stem-like cells, promotes migration and invasion, and may facilitate angiogenesis. Therapeutic strategies that inhibit Sema3C signaling may improve cancer control. This review will summarize the current research on the Sema3C pathway and its potential as a therapeutic target.
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12
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Sato Y, Matsuo A, Kudoh S, Fang L, Hasegawa K, Shinmyo Y, Ito T. Expression of Draxin in Lung Carcinomas. Acta Histochem Cytochem 2018; 51:53-62. [PMID: 29622850 PMCID: PMC5880803 DOI: 10.1267/ahc.17035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 01/16/2018] [Indexed: 12/20/2022] Open
Abstract
Guidance molecules, such as Netrin-1, and their receptors have important roles in controlling axon pathfinding, modulate biological activities of various cancer cells, and may be a useful target for cancer therapy. Dorsal repulsive axon guidance protein (Draxin) is a novel guidance molecule that binds not only common guidance molecule receptors with Netrin-1, but also directly binds the EGF domain of Netrin-1 through a 22-amino-acid peptide (22aa). By immunostaining, Draxin was positively expressed in small cell carcinoma, adenocarcinoma (ADC), and squamous cell carcinoma of the lung. In addition, western blot analysis revealed that Draxin was expressed in all histological types of lung cancer cell lines examined. Knockdown of Draxin in an ADC cell line H358 resulted in altered expression of molecules associated with proliferation and apoptosis. The Ki-67 labeling index of Draxin-knockdown ADC cells was increased compared to that of control ADC cells. In H358 cells, treatment of 22aa induced phosphorylation of histone H3, but did not change apoptosis-associated enzymes. These data suggest that Draxin might be involved in cell proliferation and apoptosis in lung adenocarcinoma cells.
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Affiliation(s)
- Younosuke Sato
- Department of Pathology and Experimental Medicine, Graduate School of Medical Sciences, Kumamoto University
| | - Akira Matsuo
- Department of Pathology and Experimental Medicine, Graduate School of Medical Sciences, Kumamoto University
| | - Shinji Kudoh
- Department of Pathology and Experimental Medicine, Graduate School of Medical Sciences, Kumamoto University
| | - Liu Fang
- Department of Pathology and Experimental Medicine, Graduate School of Medical Sciences, Kumamoto University
- Department of Clinical Laboratory, Fourth Affiliated Hospital of Harbin Medical University
| | - Koki Hasegawa
- Center for Instrumental Analysis, Kyoto Pharmaceutical University
| | - Yohei Shinmyo
- Department of Biophysical Genetics, Graduate School of Medical Sciences, Kanazawa University
| | - Takaaki Ito
- Department of Pathology and Experimental Medicine, Graduate School of Medical Sciences, Kumamoto University
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13
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Tokar T, Pastrello C, Ramnarine VR, Zhu CQ, Craddock KJ, Pikor LA, Vucic EA, Vary S, Shepherd FA, Tsao MS, Lam WL, Jurisica I. Differentially expressed microRNAs in lung adenocarcinoma invert effects of copy number aberrations of prognostic genes. Oncotarget 2018; 9:9137-9155. [PMID: 29507679 PMCID: PMC5823624 DOI: 10.18632/oncotarget.24070] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 01/02/2018] [Indexed: 12/30/2022] Open
Abstract
In many cancers, significantly down- or upregulated genes are found within chromosomal regions with DNA copy number alteration opposite to the expression changes. Generally, this paradox has been overlooked as noise, but can potentially be a consequence of interference of epigenetic regulatory mechanisms, including microRNA-mediated control of mRNA levels. To explore potential associations between microRNAs and paradoxes in non-small-cell lung cancer (NSCLC) we curated and analyzed lung adenocarcinoma (LUAD) data, comprising gene expressions, copy number aberrations (CNAs) and microRNA expressions. We integrated data from 1,062 tumor samples and 241 normal lung samples, including newly-generated array comparative genomic hybridization (aCGH) data from 63 LUAD samples. We identified 85 “paradoxical” genes whose differential expression consistently contrasted with aberrations of their copy numbers. Paradoxical status of 70 out of 85 genes was validated on sample-wise basis using The Cancer Genome Atlas (TCGA) LUAD data. Of these, 41 genes are prognostic and form a clinically relevant signature, which we validated on three independent datasets. By meta-analysis of results from 9 LUAD microRNA expression studies we identified 24 consistently-deregulated microRNAs. Using TCGA-LUAD data we showed that deregulation of 19 of these microRNAs explains differential expression of the paradoxical genes. Our results show that deregulation of paradoxical genes is crucial in LUAD and their expression pattern is maintained epigenetically, defying gene copy number status.
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Affiliation(s)
- Tomas Tokar
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Chiara Pastrello
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Varune R Ramnarine
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada.,The Vancouver Prostate Centre, Vancouver General Hospital, Vancouver, Canada
| | - Chang-Qi Zhu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Kenneth J Craddock
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Larrisa A Pikor
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, Canada
| | - Emily A Vucic
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, Canada
| | - Simon Vary
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada.,Mathematical Institute, University of Oxford, Oxford, United Kingdom.,Faculty of Mathematics, Physics and Informatics, Comenius University, Bratislava, Slovakia
| | - Frances A Shepherd
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Ming-Sound Tsao
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Wan L Lam
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, Canada
| | - Igor Jurisica
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Canada.,Department of Computer Science, University of Toronto, Toronto, Canada.,Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
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14
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Evanno E, Godet J, Piccirilli N, Guilhot J, Milin S, Gombert JM, Fouchaq B, Roche J. Tri-methylation of H3K79 is decreased in TGF-β1-induced epithelial-to-mesenchymal transition in lung cancer. Clin Epigenetics 2017; 9:80. [PMID: 28804523 PMCID: PMC5549304 DOI: 10.1186/s13148-017-0380-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 07/31/2017] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The epithelial-to-mesenchymal transition (EMT) enables epithelial cancer cells to acquire mesenchymal features and contributes to metastasis and resistance to treatment. This process involves epigenetic reprogramming for gene expression. We explored global histone modifications during TGF-β1-induced EMT in two non-small cell lung cancer (NSCLC) cell lines and tested different epigenetic treatment to modulate or partially reverse EMT. RESULTS Loss of classical epithelial markers and gain of mesenchymal markers were verified in A549 and H358 cell lines during TGF-β1-induced EMT. In addition, we noticed increased expression of the axonal guidance protein semaphorin 3C (SEMA3C) and PD-L1 (programmed death-ligand 1) involved in the inhibition of the immune system, suggesting that both SEMA3C and PD-L1 could be the new markers of TGF-β1-induced EMT. H3K79me3 and H2BK120me1 were decreased in A549 and H358 cell lines after a 48-h TGF-β1 treatment, as well as H2BK120ac in A549 cells. However, decreased H3K79me3 was not associated with expression of the histone methyltransferase DOT1L. Furthermore, H3K79me3 was decreased in tumors compared in normal tissues and not associated with cell proliferation. Associations of histone deacetylase inhibitor (SAHA) with DOT1L inhibitors (EPZ5676 or SGC0946) or BET bromodomain inhibitor (PFI-1) were efficient to partially reverse TGF-β1 effects by decreasing expression of PD-L1, SEMA3C, and its receptor neuropilin-2 (NRP2) and by increasing epithelial markers such as E-cadherin. CONCLUSION Histone methylation was modified during EMT, and combination of epigenetic compounds with conventional or targeted chemotherapy might contribute to reduce metastasis and to enhance clinical responses.
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Affiliation(s)
- Emilie Evanno
- Eurofins Cerep SA, Le Bois l’Evêque, F-86600 Celle L’Evescault, France
- Université de Poitiers, Laboratoire LNEC, F-86022 Poitiers, France
| | - Julie Godet
- CHU de Poitiers, Service d’Anatomie et de Cytologie Pathologiques, F-86021 Poitiers, France
| | | | - Joëlle Guilhot
- INSERM CIC 0802, CHU de Poitiers, F-86021 Poitiers, France
| | - Serge Milin
- CHU de Poitiers, Service d’Anatomie et de Cytologie Pathologiques, F-86021 Poitiers, France
| | - Jean Marc Gombert
- INSERM U1082, CHU de Poitiers, F-86021 Poitiers, France
- Service Immunologie, CHU de Poitiers, F-86021 Poitiers, France
| | - Benoit Fouchaq
- Eurofins Cerep SA, Le Bois l’Evêque, F-86600 Celle L’Evescault, France
| | - Joëlle Roche
- Laboratoire Ecologie et Biologie des Interactions (EBI), Université de Poitiers, UMR-CNRS 7267, F-86073 Poitiers, France
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15
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Pancewicz-Wojtkiewicz J, Eljaszewicz A, Kowalczuk O, Niklinska W, Charkiewicz R, Kozłowski M, Miasko A, Moniuszko M. Prognostic significance of Notch ligands in patients with non-small cell lung cancer. Oncol Lett 2016; 13:506-510. [PMID: 28123589 DOI: 10.3892/ol.2016.5420] [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: 06/14/2016] [Accepted: 09/29/2016] [Indexed: 01/07/2023] Open
Abstract
The Notch signaling pathway is deregulated in numerous solid types of cancer including non-small cell lung cancer (NSCLC). However, the profile of Notch ligand expression remains unclear. Therefore, the present study aimed to determine the profile of Notch ligands in NSCLC patients and to investigate whether quantitative assessment of Notch ligand expression may have prognostic significance in NSCLC patients. The study was performed in 61 pairs of tumor and matched unaffected lung tissue specimens obtained from patients with various stages of NSCLC, which were analyzed by reverse transcription-polymerase chain reaction. The marked expression levels of certain analyzed genes were detected in NSCLC samples and in noncancerous lung samples. Of the five Notch ligands, jagged 1 (Jag1), jagged 2, delta-like protein 1 and delta-like protein 4 were expressed in the majority of tissues, but their expression levels were reduced in NSCLC when compared with noncancerous lung tissue (P<0.001). Delta-like protein 3 expression was consistently low and was observed only in 21/61 tumor tissue samples. Taken together, Notch ligands are expressed in NSCLC. However, the expression level is reduced when compared to noncancerous tissue. Furthermore, the present study revealed that quantitative assessment of Jag1 expression in NSCLC may improve prognostication of patient survival.
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Affiliation(s)
| | - Andrzej Eljaszewicz
- Department of Regenerative Medicine and Immune Regulation, Medical University of Bialystok, 15-269 Bialystok, Poland
| | - Oksana Kowalczuk
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland
| | - Wieslawa Niklinska
- Department of Histology and Embryology, Medical University of Bialystok, 15-269 Bialystok, Poland
| | - Radoslaw Charkiewicz
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland
| | - Miroslaw Kozłowski
- Department of Thoracic Surgery, Medical University of Bialystok, 15-269 Bialystok, Poland
| | - Agnieszka Miasko
- Department of Histology and Embryology, Medical University of Bialystok, 15-269 Bialystok, Poland
| | - Marcin Moniuszko
- Department of Regenerative Medicine and Immune Regulation, Medical University of Bialystok, 15-269 Bialystok, Poland
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16
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Greening DW, Ji H, Chen M, Robinson BWS, Dick IM, Creaney J, Simpson RJ. Secreted primary human malignant mesothelioma exosome signature reflects oncogenic cargo. Sci Rep 2016; 6:32643. [PMID: 27605433 PMCID: PMC5015102 DOI: 10.1038/srep32643] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 08/11/2016] [Indexed: 02/07/2023] Open
Abstract
Malignant mesothelioma (MM) is a highly-aggressive heterogeneous malignancy, typically diagnosed at advanced stage. An important area of mesothelioma biology and progression is understanding intercellular communication and the contribution of the secretome. Exosomes are secreted extracellular vesicles shown to shuttle cellular cargo and direct intercellular communication in the tumour microenvironment, facilitate immunoregulation and metastasis. In this study, quantitative proteomics was used to investigate MM-derived exosomes from distinct human models and identify select cargo protein networks associated with angiogenesis, metastasis, and immunoregulation. Utilising bioinformatics pathway/network analyses, and correlation with previous studies on tumour exosomes, we defined a select mesothelioma exosomal signature (mEXOS, 570 proteins) enriched in tumour antigens and various cancer-specific signalling (HPGD/ENO1/OSMR) and secreted modulators (FN1/ITLN1/MAMDC2/PDGFD/GBP1). Notably, such circulating cargo offers unique insights into mesothelioma progression and tumour microenvironment reprogramming. Functionally, we demonstrate that oncogenic exosomes facilitate the migratory capacity of fibroblast/endothelial cells, supporting the systematic model of MM progression associated with vascular remodelling and angiogenesis. We provide biophysical and proteomic characterisation of exosomes, define a unique oncogenic signature (mEXOS), and demonstrate the regulatory capacity of exosomes in cell migration/tube formation assays. These findings contribute to understanding tumour-stromal crosstalk in the context of MM, and potential new diagnostic and therapeutic extracellular targets.
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Affiliation(s)
- David W. Greening
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Hong Ji
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Maoshan Chen
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Bruce W. S. Robinson
- National Centre for Asbestos Related Diseases, School of Medicine and Pharmacology, University of Western Australia, 6009, Australia
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Perth, Western Australia, 6009, Australia
| | - Ian M. Dick
- National Centre for Asbestos Related Diseases, School of Medicine and Pharmacology, University of Western Australia, 6009, Australia
| | - Jenette Creaney
- National Centre for Asbestos Related Diseases, School of Medicine and Pharmacology, University of Western Australia, 6009, Australia
- Australian Mesothelioma Tissue Bank, Sir Charles Gairdner Hospital, Perth, Western Australia, 6009, Australia
| | - Richard J. Simpson
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
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17
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Gene-set Analysis with CGI Information for Differential DNA Methylation Profiling. Sci Rep 2016; 6:24666. [PMID: 27090937 PMCID: PMC4836301 DOI: 10.1038/srep24666] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 03/30/2016] [Indexed: 12/17/2022] Open
Abstract
DNA methylation is a well-established epigenetic biomarker for many diseases. Studying the relationships among a group of genes and their methylations may help to unravel the etiology of diseases. Since CpG-islands (CGIs) play a crucial role in the regulation of transcription during methylation, including them in the analysis may provide further information in understanding the pathogenesis of cancers. Such CGI information, however, has usually been overlooked in existing gene-set analyses. Here we aimed to include both pathway information and CGI status to rank competing gene-sets and identify among them the genes most likely contributing to DNA methylation changes. To accomplish this, we devised a Bayesian model for matched case-control studies with parameters for CGI status and pathway associations, while incorporating intra-gene-set information. Three cancer studies with candidate pathways were analyzed to illustrate this approach. The strength of association for each candidate pathway and the influence of each gene were evaluated. Results show that, based on probabilities, the importance of pathways and genes can be determined. The findings confirm that some of these genes are cancer-related and may hold the potential to be targeted in drug development.
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18
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Qian DC, Byun J, Han Y, Greene CS, Field JK, Hung RJ, Brhane Y, Mclaughlin JR, Fehringer G, Landi MT, Rosenberger A, Bickeböller H, Malhotra J, Risch A, Heinrich J, Hunter DJ, Henderson BE, Haiman CA, Schumacher FR, Eeles RA, Easton DF, Seminara D, Amos CI. Identification of shared and unique susceptibility pathways among cancers of the lung, breast, and prostate from genome-wide association studies and tissue-specific protein interactions. Hum Mol Genet 2015; 24:7406-20. [PMID: 26483192 PMCID: PMC4664175 DOI: 10.1093/hmg/ddv440] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 09/11/2015] [Accepted: 10/12/2015] [Indexed: 12/18/2022] Open
Abstract
Results from genome-wide association studies (GWAS) have indicated that strong single-gene effects are the exception, not the rule, for most diseases. We assessed the joint effects of germline genetic variations through a pathway-based approach that considers the tissue-specific contexts of GWAS findings. From GWAS meta-analyses of lung cancer (12 160 cases/16 838 controls), breast cancer (15 748 cases/18 084 controls) and prostate cancer (14 160 cases/12 724 controls) in individuals of European ancestry, we determined the tissue-specific interaction networks of proteins expressed from genes that are likely to be affected by disease-associated variants. Reactome pathways exhibiting enrichment of proteins from each network were compared across the cancers. Our results show that pathways associated with all three cancers tend to be broad cellular processes required for growth and survival. Significant examples include the nerve growth factor (P = 7.86 × 10(-33)), epidermal growth factor (P = 1.18 × 10(-31)) and fibroblast growth factor (P = 2.47 × 10(-31)) signaling pathways. However, within these shared pathways, the genes that influence risk largely differ by cancer. Pathways found to be unique for a single cancer focus on more specific cellular functions, such as interleukin signaling in lung cancer (P = 1.69 × 10(-15)), apoptosis initiation by Bad in breast cancer (P = 3.14 × 10(-9)) and cellular responses to hypoxia in prostate cancer (P = 2.14 × 10(-9)). We present the largest comparative cross-cancer pathway analysis of GWAS to date. Our approach can also be applied to the study of inherited mechanisms underlying risk across multiple diseases in general.
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Affiliation(s)
- David C Qian
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Jinyoung Byun
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Younghun Han
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Casey S Greene
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John K Field
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool Cancer Research Centre, Liverpool L69 3GA, UK
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Yonathan Brhane
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - John R Mclaughlin
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
| | - Gordon Fehringer
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Maria Teresa Landi
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Albert Rosenberger
- Department of Genetic Epidemiology, University Medical Centre Göttingen, 37099 Göttingen, Germany
| | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Centre Göttingen, 37099 Göttingen, Germany
| | - Jyoti Malhotra
- Division of Hematology and Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Angela Risch
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Joachim Heinrich
- Institute of Epidemiology I, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - David J Hunter
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Brian E Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Fredrick R Schumacher
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Rosalind A Eeles
- Department of Cancer Genetics, Institute of Cancer Research, London SW7 3RP, UK and
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Daniela Seminara
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christopher I Amos
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA,
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19
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Huang T, Kang W, Cheng ASL, Yu J, To KF. The emerging role of Slit-Robo pathway in gastric and other gastro intestinal cancers. BMC Cancer 2015; 15:950. [PMID: 26674478 PMCID: PMC4682238 DOI: 10.1186/s12885-015-1984-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 12/08/2015] [Indexed: 01/12/2023] Open
Abstract
Gastric cancer remains one of the most common cancers worldwide and one of the leading cause for cancer-related deaths. Due to the high frequency of metastasis, it is still one of the most lethal malignancies in which kinds of signaling pathways are involved in. The Roundabout (ROBO) receptors and their secreted SLIT glycoprotein ligands, which were originally identified as important axon guidance molecules, have implication in the regulation of neurons and glia, leukocytes, and endothelial cells migration. Recent researches also put high emphasis on the important roles of the Slit-Robo pathway in tumorigenesis, cancer progression and metastasis. Herein we provide a comprehensive review on the role of these molecules and their associated signaling pathway in gastric and other gastrointestinal cancers. Improved knowledge of the Slit-Robo signaling pathway in gastric carcinoma will be useful for deep understanding the mechanisms of tumor development and identifying ideal targets of anticancer therapy in gastric carcinoma.
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Affiliation(s)
- Tingting Huang
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Oncology in South China, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, SAR, PR China.
- Institute of Digestive Disease, Partner State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, SAR, PR China.
- Li Ka Shing Institute of Health Science, Sir Y.K. Pao Cancer Center, The Chinese University of Hong Kong, Hong Kong, SAR, PR China.
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, PR China.
| | - Wei Kang
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Oncology in South China, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, SAR, PR China.
- Institute of Digestive Disease, Partner State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, SAR, PR China.
- Li Ka Shing Institute of Health Science, Sir Y.K. Pao Cancer Center, The Chinese University of Hong Kong, Hong Kong, SAR, PR China.
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, PR China.
| | - Alfred S L Cheng
- Institute of Digestive Disease, Partner State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, SAR, PR China.
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, PR China.
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, PR China.
| | - Jun Yu
- Institute of Digestive Disease, Partner State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, SAR, PR China.
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, PR China.
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, PR China.
| | - Ka Fai To
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Oncology in South China, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, SAR, PR China.
- Institute of Digestive Disease, Partner State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, SAR, PR China.
- Li Ka Shing Institute of Health Science, Sir Y.K. Pao Cancer Center, The Chinese University of Hong Kong, Hong Kong, SAR, PR China.
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, PR China.
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20
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Barsotti AM, Ryskin M, Zhong W, Zhang WG, Giannakou A, Loreth C, Diesl V, Follettie M, Golas J, Lee M, Nichols T, Fan C, Li G, Dann S, Fantin VR, Arndt K, Verhelle D, Rollins RA. Epigenetic reprogramming by tumor-derived EZH2 gain-of-function mutations promotes aggressive 3D cell morphologies and enhances melanoma tumor growth. Oncotarget 2015; 6:2928-38. [PMID: 25671303 PMCID: PMC4413628 DOI: 10.18632/oncotarget.2758] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 11/16/2014] [Indexed: 12/20/2022] Open
Abstract
In addition to genetic alterations, cancer cells are characterized by myriad epigenetic changes. EZH2 is a histone methyltransferase that is over-expressed and mutated in cancer. The EZH2 gain-of-function (GOF) mutations first identified in lymphomas have recently been reported in melanoma (~2%) but remain uncharacterized. We expressed multiple EZH2 GOF mutations in the A375 metastatic skin melanoma cell line and observed both increased H3K27me3 and dramatic changes in 3D culture morphology. In these cells, prominent morphological changes were accompanied by a decrease in cell contractility and an increase in collective cell migration. At the molecular level, we observed significant alteration of the axonal guidance pathway, a pathway intricately involved in the regulation of cell shape and motility. Furthermore, the aggressive 3D morphology of EZH2 GOF-expressing melanoma cells (both endogenous and ectopic) was attenuated by EZH2 catalytic inhibition. Finally, A375 cells expressing exogenous EZH2 GOF mutants formed larger tumors than control cells in mouse xenograft studies. This study not only demonstrates the first functional characterization of EZH2 GOF mutants in non-hematopoietic cells, but also provides a rationale for EZH2 catalytic inhibition in melanoma.
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Affiliation(s)
- Anthony M Barsotti
- Oncology Research Unit, Pfizer Worldwide Research and Development, Pearl River, NY 10965, USA
| | - Michael Ryskin
- Oncology Research Unit, Pfizer Worldwide Research and Development, Pearl River, NY 10965, USA
| | - Wenyan Zhong
- Oncology Research Unit, Pfizer Worldwide Research and Development, Pearl River, NY 10965, USA
| | - Wei-Guo Zhang
- Oncology Research Unit, Pfizer Worldwide Research and Development, Pearl River, NY 10965, USA
| | - Andreas Giannakou
- Oncology Research Unit, Pfizer Worldwide Research and Development, Pearl River, NY 10965, USA
| | - Christine Loreth
- Oncology Research Unit, Pfizer Worldwide Research and Development, Cambridge, MA 02140, USA
| | - Veronica Diesl
- Oncology Research Unit, Pfizer Worldwide Research and Development, Cambridge, MA 02140, USA
| | - Maximillian Follettie
- Oncology Research Unit, Pfizer Worldwide Research and Development, Pearl River, NY 10965, USA.,Oncology Research Unit, Pfizer Worldwide Research and Development, Cambridge, MA 02140, USA
| | - Jonathon Golas
- Oncology Research Unit, Pfizer Worldwide Research and Development, Pearl River, NY 10965, USA
| | - Michelle Lee
- Drug Safety Research and Development, Pfizer Worldwide Research and Development, San Diego, CA 92121, USA
| | - Timothy Nichols
- Drug Safety Research and Development, Pfizer Worldwide Research and Development, San Diego, CA 92121, USA
| | - Conglin Fan
- Oncology Research Unit, Pfizer Worldwide Research and Development, San Diego, CA 92121, USA
| | - Gang Li
- Oncology Research Unit, Pfizer Worldwide Research and Development, San Diego, CA 92121, USA
| | - Stephen Dann
- Oncology Research Unit, Pfizer Worldwide Research and Development, San Diego, CA 92121, USA
| | - Valeria R Fantin
- Oncology Research Unit, Pfizer Worldwide Research and Development, San Diego, CA 92121, USA
| | - Kim Arndt
- Oncology Research Unit, Pfizer Worldwide Research and Development, Pearl River, NY 10965, USA
| | - Dominique Verhelle
- Oncology Research Unit, Pfizer Worldwide Research and Development, San Diego, CA 92121, USA
| | - Robert A Rollins
- Oncology Research Unit, Pfizer Worldwide Research and Development, Pearl River, NY 10965, USA
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21
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Kong R, Yi F, Wen P, Liu J, Chen X, Ren J, Li X, Shang Y, Nie Y, Wu K, Fan D, Zhu L, Feng W, Wu JY. Myo9b is a key player in SLIT/ROBO-mediated lung tumor suppression. J Clin Invest 2015; 125:4407-20. [PMID: 26529257 PMCID: PMC4665778 DOI: 10.1172/jci81673] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 09/21/2015] [Indexed: 11/17/2022] Open
Abstract
Emerging evidence indicates that the neuronal guidance molecule SLIT plays a role in tumor suppression, as SLIT-encoding genes are inactivated in several types of cancer, including lung cancer; however, it is not clear how SLIT functions in lung cancer. Here, our data show that SLIT inhibits cancer cell migration by activating RhoA and that myosin 9b (Myo9b) is a ROBO-interacting protein that suppresses RhoA activity in lung cancer cells. Structural analyses revealed that the RhoGAP domain of Myo9b contains a unique patch that specifically recognizes RhoA. We also determined that the ROBO intracellular domain interacts with the Myo9b RhoGAP domain and inhibits its activity; therefore, SLIT-dependent activation of RhoA is mediated by ROBO inhibition of Myo9b. In a murine model, compared with control lung cancer cells, SLIT-expressing cells had a decreased capacity for tumor formation and lung metastasis. Evaluation of human lung cancer and adjacent nontumor tissues revealed that Myo9b is upregulated in the cancer tissue. Moreover, elevated Myo9b expression was associated with lung cancer progression and poor prognosis. Together, our data identify Myo9b as a key player in lung cancer and as a ROBO-interacting protein in what is, to the best of our knowledge, a newly defined SLIT/ROBO/Myo9b/RhoA signaling pathway that restricts lung cancer progression and metastasis. Additionally, our work suggests that targeting the SLIT/ROBO/Myo9b/RhoA pathway has potential as a diagnostic and therapeutic strategy for lung cancer.
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Affiliation(s)
- Ruirui Kong
- State Key Laboratory of Brain and Cognitive Science and
| | - Fengshuang Yi
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Pushuai Wen
- State Key Laboratory of Brain and Cognitive Science and
| | - Jianghong Liu
- State Key Laboratory of Brain and Cognitive Science and
| | - Xiaoping Chen
- Department of Neurology, Center for Genetic Medicine, Lurie Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Jinqi Ren
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xiaofei Li
- Department of Thoracic Surgery, Tangdu Hospital, and
| | - Yulong Shang
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Shaanxi, China
| | - Yongzhan Nie
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Shaanxi, China
| | - Kaichun Wu
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Shaanxi, China
| | - Daiming Fan
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Shaanxi, China
| | - Li Zhu
- State Key Laboratory of Brain and Cognitive Science and
| | - Wei Feng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jane Y. Wu
- State Key Laboratory of Brain and Cognitive Science and
- Department of Neurology, Center for Genetic Medicine, Lurie Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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22
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Loukola A, Buchwald J, Gupta R, Palviainen T, Hällfors J, Tikkanen E, Korhonen T, Ollikainen M, Sarin AP, Ripatti S, Lehtimäki T, Raitakari O, Salomaa V, Rose RJ, Tyndale RF, Kaprio J. A Genome-Wide Association Study of a Biomarker of Nicotine Metabolism. PLoS Genet 2015; 11:e1005498. [PMID: 26407342 PMCID: PMC4583245 DOI: 10.1371/journal.pgen.1005498] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 08/14/2015] [Indexed: 11/25/2022] Open
Abstract
Individuals with fast nicotine metabolism typically smoke more and thus have a greater risk for smoking-induced diseases. Further, the efficacy of smoking cessation pharmacotherapy is dependent on the rate of nicotine metabolism. Our objective was to use nicotine metabolite ratio (NMR), an established biomarker of nicotine metabolism rate, in a genome-wide association study (GWAS) to identify novel genetic variants influencing nicotine metabolism. A heritability estimate of 0.81 (95% CI 0.70-0.88) was obtained for NMR using monozygotic and dizygotic twins of the FinnTwin cohort. We performed a GWAS in cotinine-verified current smokers of three Finnish cohorts (FinnTwin, Young Finns Study, FINRISK2007), followed by a meta-analysis of 1518 subjects, and annotated the genome-wide significant SNPs with methylation quantitative loci (meQTL) analyses. We detected association on 19q13 with 719 SNPs exceeding genome-wide significance within a 4.2 Mb region. The strongest evidence for association emerged for CYP2A6 (min p = 5.77E-86, in intron 4), the main metabolic enzyme for nicotine. Other interesting genes with genome-wide significant signals included CYP2B6, CYP2A7, EGLN2, and NUMBL. Conditional analyses revealed three independent signals on 19q13, all located within or in the immediate vicinity of CYP2A6. A genetic risk score constructed using the independent signals showed association with smoking quantity (p = 0.0019) in two independent Finnish samples. Our meQTL results showed that methylation values of 16 CpG sites within the region are affected by genotypes of the genome-wide significant SNPs, and according to causal inference test, for some of the SNPs the effect on NMR is mediated through methylation. To our knowledge, this is the first GWAS on NMR. Our results enclose three independent novel signals on 19q13.2. The detected CYP2A6 variants explain a strikingly large fraction of variance (up to 31%) in NMR in these study samples. Further, we provide evidence for plausible epigenetic mechanisms influencing NMR.
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Affiliation(s)
- Anu Loukola
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Jadwiga Buchwald
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Richa Gupta
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Teemu Palviainen
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Jenni Hällfors
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Institute for Molecular Medicine FIMM, University of Helsinki, Helsinki, Finland
| | - Emmi Tikkanen
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Institute for Molecular Medicine FIMM, University of Helsinki, Helsinki, Finland
| | - Tellervo Korhonen
- Department of Public Health, University of Helsinki, Helsinki, Finland
- National Institute for Health and Welfare, Helsinki, Finland
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Miina Ollikainen
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Antti-Pekka Sarin
- Institute for Molecular Medicine FIMM, University of Helsinki, Helsinki, Finland
- National Institute for Health and Welfare, Helsinki, Finland
| | - Samuli Ripatti
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Institute for Molecular Medicine FIMM, University of Helsinki, Helsinki, Finland
- Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Department of Clinical Chemistry, University of Tampere School of Medicine, Tampere, Finland
| | - Olli Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
| | - Veikko Salomaa
- National Institute for Health and Welfare, Helsinki, Finland
| | - Richard J. Rose
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, Indiana, United States of America
| | - Rachel F. Tyndale
- Campbell Family Mental Health Research Institute, CAMH, and Departments of Pharmacology & Toxicology and Psychiatry, University of Toronto, Toronto, Canada
| | - Jaakko Kaprio
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Institute for Molecular Medicine FIMM, University of Helsinki, Helsinki, Finland
- National Institute for Health and Welfare, Helsinki, Finland
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23
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Gara RK, Kumari S, Ganju A, Yallapu MM, Jaggi M, Chauhan SC. Slit/Robo pathway: a promising therapeutic target for cancer. Drug Discov Today 2015; 20:156-64. [PMID: 25245168 PMCID: PMC4445861 DOI: 10.1016/j.drudis.2014.09.008] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 08/19/2014] [Accepted: 09/12/2014] [Indexed: 12/19/2022]
Abstract
Axon guidance molecules, slit glycoprotein (Slit) and Roundabout receptor (Robo), have implications in the regulation of physiological processes. Recent studies indicate that Slit and Robo also have important roles in tumorigenesis, cancer progression and metastasis. The Slit/Robo pathway can be considered a master regulator for multiple oncogenic signaling pathways. Herein, we provide a comprehensive review on the role of these molecules and their associated signaling pathways in cancer progression and metastasis. Overall, the current available data suggest that the Slit/Robo pathway could be a promising target for development of anticancer drugs.
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Affiliation(s)
- Rishi K Gara
- Department of Pharmaceutical Sciences and Center for Cancer Research, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Sonam Kumari
- Department of Pharmaceutical Sciences and Center for Cancer Research, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Aditya Ganju
- Department of Pharmaceutical Sciences and Center for Cancer Research, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Murali M Yallapu
- Department of Pharmaceutical Sciences and Center for Cancer Research, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Meena Jaggi
- Department of Pharmaceutical Sciences and Center for Cancer Research, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
| | - Subhash C Chauhan
- Department of Pharmaceutical Sciences and Center for Cancer Research, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
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24
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Genome-wide DNA methylation profiles and their relationships with mRNA and the microRNA transcriptome in bovine muscle tissue (Bos taurine). Sci Rep 2014; 4:6546. [PMID: 25306978 PMCID: PMC4194443 DOI: 10.1038/srep06546] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 09/15/2014] [Indexed: 12/21/2022] Open
Abstract
DNA methylation is a key epigenetic modification in mammals and plays important roles in muscle development. We sampled longissimus dorsi muscle (LDM) from a well-known elite native breed of Chinese Qinchuan cattle living within the same environment but displaying distinct skeletal muscle at the fetal and adult stages. We generated and provided a genome-wide landscape of DNA methylomes and their relationship with mRNA and miRNA for fetal and adult muscle studies. Integration analysis revealed a total of 77 and 1,054 negatively correlated genes with methylation in the promoter and gene body regions, respectively, in both the fetal and adult bovine libraries. Furthermore, we identified expression patterns of high-read genes that exhibit a negative correlation between methylation and expression from nine different tissues at multiple developmental stages of bovine muscle-related tissue or organs. In addition, we validated the MeDIP-Seq results by bisulfite sequencing PCR (BSP) in some of the differentially methylated promoters. Together, these results provide valuable data for future biomedical research and genomic and epigenomic studies of bovine skeletal muscle that may help uncover the molecular basis underlying economically valuable traits in cattle. This comprehensive map also provides a solid basis for exploring the epigenetic mechanisms of muscle growth and development.
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25
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Li C, Liu VWS, Chiu PM, Yao KM, Ngan HYS, Chan DW. Reduced expression of AMPK-β1 during tumor progression enhances the oncogenic capacity of advanced ovarian cancer. Mol Cancer 2014; 13:49. [PMID: 24602453 PMCID: PMC4016028 DOI: 10.1186/1476-4598-13-49] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 02/21/2014] [Indexed: 12/25/2022] Open
Abstract
AMP-activated protein kinase (AMPK) is a key energy sensor that is involved in regulating cell metabolism. Our previous study revealed that the subunits of the heterotimeric AMPK enzyme are diversely expressed during ovarian cancer progression. However, the impact of the variable expression of these AMPK subunits in ovarian cancer oncogenesis remains obscure. Here, we provide evidence to show that reduced expression of the AMPK-β1 subunit during tumor progression is associated with the increased oncogenic capacity of advanced ovarian cancer cells. Immunohistochemical analysis revealed that AMPK-β1 levels were reduced in advanced-stage (P = 0.008), high-grade (P = 0.013) and metastatic ovarian cancers (P = 0.008). Intriguingly, down-regulation of AMPK-β1 was progressively reduced from tumor stages 1 to 3 of ovarian cancer. Functionally, enforced expression of AMPK-β1 inhibited ovarian-cancer-cell proliferation, anchorage-independent cell growth, cell migration and invasion. Conversely, depletion of AMPK-β1 by siRNA enhanced the oncogenic capacities of ovarian cancer cells, suggesting that the loss of AMPK-β1 favors the aggressiveness of ovarian cancer. Mechanistically, enforced expression of AMPK-β1 increased AMPK activity, which, in turn, induced cell-cycle arrest via inhibition of AKT/ERK signaling activity as well as impaired cell migration/invasion through the suppression of JNK signaling in ovarian cancer cells. Taken together, these findings suggest that the reduced expression of AMPK-β1 confers lower AMPK activity, which enhances the oncogenic capacity of advanced-stage ovarian cancer.
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Affiliation(s)
| | | | | | | | - Hextan Y S Ngan
- Department of Obstetrics & Gynecology, The University of Hong Kong, 6th Floor, Professorial Block, Queen Mary Hospital, Pokfulam, Hong Kong, SAR, People's Republic of China.
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26
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Al-Greene NT, Means AL, Lu P, Jiang A, Schmidt CR, Chakravarthy AB, Merchant NB, Washington MK, Zhang B, Shyr Y, Deane NG, Beauchamp RD. Four jointed box 1 promotes angiogenesis and is associated with poor patient survival in colorectal carcinoma. PLoS One 2013; 8:e69660. [PMID: 23922772 PMCID: PMC3726759 DOI: 10.1371/journal.pone.0069660] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 06/11/2013] [Indexed: 01/08/2023] Open
Abstract
Angiogenesis, the recruitment and re-configuration of pre-existing vasculature, is essential for tumor growth and metastasis. Increased tumor vascularization often correlates with poor patient outcomes in a broad spectrum of carcinomas. We identified four jointed box 1 (FJX1) as a candidate regulator of tumor angiogenesis in colorectal cancer. FJX1 mRNA and protein are upregulated in human colorectal tumor epithelium as compared with normal epithelium and colorectal adenomas, and high expression of FJX1 is associated with poor patient prognosis. FJX1 mRNA expression in colorectal cancer tissues is significantly correlated with changes in known angiogenesis genes. Augmented expression of FJX1 in colon cancer cells promotes growth of xenografts in athymic mice and is associated with increased tumor cell proliferation and vascularization. Furthermore, FJX1 null mice develop significantly fewer colonic polyps than wild-type littermates after combined dextran sodium sulfate (DSS) and azoxymethane (AOM) treatment. In vitro, conditioned media from FJX1 expressing cells promoted endothelial cell capillary tube formation in a HIF1-α dependent manner. Taken together our results support the conclusion that FJX1 is a novel regulator of tumor progression, due in part, to its effect on tumor vascularization.
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Affiliation(s)
- Nicole T. Al-Greene
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Anna L. Means
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Surgery, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Pengcheng Lu
- Department of Biostatistics, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Aixiang Jiang
- Department of Biostatistics, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Carl R. Schmidt
- Department of Surgery, Vanderbilt University, Nashville, Tennessee, United States of America
| | - A. Bapsi Chakravarthy
- Department of Radiation Oncology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Nipun B. Merchant
- Department of Surgery, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee, United States of America
| | - M. Kay Washington
- Department of Pathology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Microbiology and Immunology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Bing Zhang
- Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Yu Shyr
- Department of Biostatistics, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Natasha G. Deane
- Department of Surgery, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, Tennessee, United States of America
| | - R. Daniel Beauchamp
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Surgery, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Cancer Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- * E-mail:
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27
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Towards a functional proteomics approach to the comprehension of idiopathic pulmonary fibrosis, sarcoidosis, systemic sclerosis and pulmonary Langerhans cell histiocytosis. J Proteomics 2013; 83:60-75. [DOI: 10.1016/j.jprot.2013.03.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 02/22/2013] [Accepted: 03/09/2013] [Indexed: 01/02/2023]
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28
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Powell DR, Blasky AJ, Britt SG, Artinger KB. Riding the crest of the wave: parallels between the neural crest and cancer in epithelial-to-mesenchymal transition and migration. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2013; 5:511-22. [PMID: 23576382 PMCID: PMC3739939 DOI: 10.1002/wsbm.1224] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The neural crest (NC) is first induced as an epithelial population of cells at the neural plate border requiring complex signaling between bone morphogenetic protein, Wnt, and fibroblast growth factors to differentiate the neural and NC fate from the epidermis. Remarkably, following induction, these cells undergo an epithelial-to-mesenchymal transition (EMT), delaminate from the neural tube, and migrate through various tissue types and microenvironments before reaching their final destination where they undergo terminal differentiation. This process is mirrored in cancer metastasis, where a primary tumor will undergo an EMT before migrating and invading other cell populations to create a secondary tumor site. In recent years, as our understanding of NC EMT and migration has deepened, important new insights into tumorigenesis and metastasis have also been achieved. These discoveries have been driven by the observation that many cancers misregulate developmental genes to reacquire proliferative and migratory states. In this review, we examine how the NC provides an excellent model for studying EMT and migration. These data are discussed from the perspective of the gene regulatory networks that control both NC and cancer cell EMT and migration. Deciphering these processes in a comparative manner will expand our knowledge of the underlying etiology and pathogenesis of cancer and promote the development of novel targeted therapeutic strategies for cancer patients. © 2013 Wiley Periodicals, Inc.
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Affiliation(s)
- Davalyn R Powell
- Graduate Program in Cell Biology, Stem Cells and Development, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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29
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Son TW, Yun SP, Yong MS, Seo BN, Ryu JM, Youn HY, Oh YM, Han HJ. Netrin-1 protects hypoxia-induced mitochondrial apoptosis through HSP27 expression via DCC- and integrin α6β4-dependent Akt, GSK-3β, and HSF-1 in mesenchymal stem cells. Cell Death Dis 2013; 4:e563. [PMID: 23538444 PMCID: PMC3615739 DOI: 10.1038/cddis.2013.94] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Netrin (Ntn) has the potential to be successfully applied as an anti-apoptotic agent with a high affinity for tissue, for therapeutic strategies of umbilical cord blood-derived mesenchymal stem cells (UCB-MSC), although the mechanism by which Ntn-1 protects hypoxic injury has yet to be identified. Therefore, the present study examined the effect of Ntn-1 on hypoxia-induced UCB-MSC apoptosis, as well as the potential underlying mechanisms of its protective effect. Hypoxia (72 h) reduced cell viability (MTT reduction, and [3H]-thymidine incorporation) and cell number, and induced apoptosis (annexin and/or PI positive), which were reversed by Ntn-1 (10 ng/ml). Moreover, Ntn-1 decreased the increase of hypoxia-induced Bax, cleaved caspase-9, and -3, but blocked the decrease of hypoxia-reduced Bcl-2. Next, in order to examine the Ntn-1-related signaling cascade in the protection of hypoxic injury, we analyzed six Ntn receptors in UCB-MSC. We identified deleted in colorectal cancer (DCC) and integrin (IN) α6β4, except uncoordinated family member (UNC) 5A–C, and neogenin. Among them, IN α6β4 only was detected in lipid raft fractions. In addition, Ntn-1 induced the dissociation of DCC and APPL-1 complex, thereby stimulating the formation of APPL-1 and Akt2 complex. Ntn-1 also reversed the hypoxia-induced decrease of Akt and glycogen synthase kinase 3β (GSK-3β) phosphorylation, which is involved in heat shock factor-1 (HSF-1) expression. Ntn-1-induced phospho-Akt and -GSK-3β were inhibited by DCC function-blocking antibody, IN a6b4 function-blocking antibody, and the Akt inhibitor. Hypoxia and/or Ntn-1 stimulated heat shock protein (HSP)27 expression, which was blocked by HSF-1-specific small interfering RNA (siRNA). Furthermore, HSP27-specific siRNA reversed the Ntn-1-induced increase of phospho-Akt. Additionally, HSP27-specific siRNA attenuated the Ntn-1-reduced loss of mitochondrial membrane injury via the inhibition of cytochrome c (cyt c) release and formation of cyt c and HSP27 complex. Moreover, the inhibition of each signaling protein attenuated Ntn-1-induced blockage of apoptosis. In conclusion, Ntn-1-induced HSP27 protected hypoxic injury-related UCB-MSC apoptosis through DCC- and IN α6β4-dependent Akt, GSK-3β, and HSF-1 signaling pathways.
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Affiliation(s)
- T W Son
- Department of Veterinary Internal Medicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
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30
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Villaflor VM, Salgia R. Targeted agents in non-small cell lung cancer therapy: What is there on the horizon? J Carcinog 2013; 12:7. [PMID: 23599689 PMCID: PMC3622362 DOI: 10.4103/1477-3163.109253] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 01/10/2013] [Indexed: 02/06/2023] Open
Abstract
Lung cancer is a heterogeneous group of diseases. There has been much research in lung cancer over the past decade which has advanced our ability to treat these patients with a more personalized approach. The scope of this paper is to review the literature and give a broad understanding of the current molecular targets for which we currently have therapies as well as other targets for which we may soon have therapies. Additionally, we will cover some of the issues of resistance with these targeted therapies. The molecular targets we intend to discuss are epidermal growth factor receptor (EGFR), Vascular endothelial growth factor (VEGF), anaplastic large-cell lymphoma kinase (ALK), KRAS, C-MET/RON, PIK3CA. ROS-1, RET Fibroblast growth factor receptor (FGFR). Ephrins and their receptors, BRAF, and immunotherapies/vaccines. This manuscript only summarizes the work which has been done to date and in no way is meant to be comprehensive.
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Affiliation(s)
- Victoria M Villaflor
- Department of Medicine, Section of Hematology/Oncology University of Chicago, Chicago, IL, USA
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Li S, Sun Y, Gao D. Role of the nervous system in cancer metastasis. Oncol Lett 2013; 5:1101-1111. [PMID: 23599747 PMCID: PMC3629128 DOI: 10.3892/ol.2013.1168] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 10/17/2012] [Indexed: 12/17/2022] Open
Abstract
The notion that tumors lack innervation was proposed several years ago. However, nerve fibers are irregulatedly found in some tumor tissues. Their terminals interaction with cancer cells are considered to be neuro-neoplastic synapses. Moreover, neural-related factors, which are important players in the development and activity of the nervous system, have been found in cancer cells. Thus, they establish a direct connection between the nervous system and tumor cells. They modulate the process of metastasis, including degradation of base membranes, cancer cell invasion, migration, extravasation and colonization. Peripheral nerve invasion provides another pathway for the spread of cancer cells when blood and lymphatic metastases are absent, which is based on the interactions between the microenvironments of nerve fibers and tumor cells. The nervous system also modulates angiogenesis, the tumor microenvironment, bone marrow, immune functions and inflammatory pathways to influence metastases. Denervation of the tumor has been reported to enhance cancer metastasis. Stress, social isolation and other emotional factors may increase distant metastasis through releasing hormones from the brain, the hypothalamic-pituitary-adrenal axis and autonomic nervous system. Disruption of circadian rhythms will also promote cancer metastasis through direct and indirect actions of the nervous system. Therefore, the nervous system plays an important role in cancer metastasis.
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Affiliation(s)
- Sha Li
- Department of Radiation Oncology, Lanzhou General Hospital of PLA, Lanzhou, Gansu 730050
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32
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Comparative analysis of methods for identifying recurrent copy number alterations in cancer. PLoS One 2012; 7:e52516. [PMID: 23285074 PMCID: PMC3527554 DOI: 10.1371/journal.pone.0052516] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 11/14/2012] [Indexed: 11/19/2022] Open
Abstract
Recurrent copy number alterations (CNAs) play an important role in cancer genesis. While a number of computational methods have been proposed for identifying such CNAs, their relative merits remain largely unknown in practice since very few efforts have been focused on comparative analysis of the methods. To facilitate studies of recurrent CNA identification in cancer genome, it is imperative to conduct a comprehensive comparison of performance and limitations among existing methods. In this paper, six representative methods proposed in the latest six years are compared. These include one-stage and two-stage approaches, working with raw intensity ratio data and discretized data respectively. They are based on various techniques such as kernel regression, correlation matrix diagonal segmentation, semi-parametric permutation and cyclic permutation schemes. We explore multiple criteria including type I error rate, detection power, Receiver Operating Characteristics (ROC) curve and the area under curve (AUC), and computational complexity, to evaluate performance of the methods under multiple simulation scenarios. We also characterize their abilities on applications to two real datasets obtained from cancers with lung adenocarcinoma and glioblastoma. This comparison study reveals general characteristics of the existing methods for identifying recurrent CNAs, and further provides new insights into their strengths and weaknesses. It is believed helpful to accelerate the development of novel and improved methods.
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Abstract
This review is focusing on a critical mediator of embryonic and postnatal development with multiple implications in inflammation, neoplasia, and other pathological situations in brain and peripheral tissues. These morphogenetic guidance and dependence processes are involved in several malignancies targeting the epithelial and immune systems including the progression of human colorectal cancers. We consider the most important findings and their impact on basic, translational, and clinical cancer research. Expected information can bring new cues for innovative, efficient, and safe strategies of personalized medicine based on molecular markers, protagonists, signaling networks, and effectors inherent to the Netrin axis in pathophysiological states.
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Semaphorin-1 and netrin signal in parallel and permissively to position the male ray 1 sensillum in Caenorhabditis elegans. Genetics 2012; 192:959-71. [PMID: 22942127 DOI: 10.1534/genetics.112.144253] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Netrin and semaphorin axon guidance cues have been found to function in the genesis of several mammalian organs; however, little is known about the underlying molecular mechanisms involved. A genetic approach could help to reveal the underpinnings of these mechanisms. The most anterior ray sensillum (ray 1) in the Caenorhabditis elegans male tail is frequently displaced anterior to its normal position in smp-1/semaphorin-1a and plexin-1/plx-1 mutants. Here we report that UNC-6/netrin and its UNC-40/DCC receptor signal in parallel to SMP-1/semaphorin-1a and its PLX-1/plexin-1 receptor to prevent the anterior displacement of ray 1 and that UNC-6 plus SMP-1 signaling can account entirely for this function. We also report that mab-20/semaphorin-2a mutations, which prevent the separation of neighboring rays and cause ray fusions, suppress the anterior displacements of ray 1 caused by deficiencies in SMP-1 and UNC-6 signaling and this is independent of the ray fusion phenotype, whereas overexpression of UNC-40 and PLX-1 cause ray fusions. This suggests that for ray 1 positioning, a balance is struck between a tendency of SMP-1 and UNC-6 signaling to prevent ray 1 from moving away from ray 2 and a tendency of MAB-20/semaphorin-2a signaling to separate all rays from each other. Additional evidence suggests this balance involves the relative adhesion of the ray 1 structural cell to neighboring SET and hyp 7 hypodermal cells. This finding raises the possibility that changes in ray 1 positioning depend on passive movements caused by attachment to the elongating SET cell in opposition to the morphologically more stable hyp 7 cell. Several lines of evidence indicate that SMP-1 and UNC-6 function permissively in the context of ray 1 positioning.
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Wild JRL, Staton CA, Chapple K, Corfe BM. Neuropilins: expression and roles in the epithelium. Int J Exp Pathol 2012; 93:81-103. [PMID: 22414290 DOI: 10.1111/j.1365-2613.2012.00810.x] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Initially found expressed in neuronal and then later in endothelial cells, it is well established that the transmembrane glycoproteins neuropilin-1 (NRP1) and neuropilin-2 (NRP2) play essential roles in axonal growth and guidance and in physiological and pathological angiogenesis. Neuropilin expression and function in epithelial cells has received little attention when compared with neuronal and endothelial cells. Overexpression of NRPs is shown to enhance growth, correlate with invasion and is associated with poor prognosis in various tumour types, especially those of epithelial origin. The contribution of NRP and its ligands to tumour growth and metastasis has spurred a strong interest in NRPs as novel chemotherapy drug targets. Given NRP's role as a multifunctional co-receptor with an ability to bind with disparate ligand families, this has sparked new areas of research implicating NRPs in diverse biological functions. Here, we review the growing body of research demonstrating NRP expression and role in the normal and neoplastic epithelium.
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Affiliation(s)
- Jonathan R L Wild
- Molecular Gastroenterology Research Group, Academic Unit of Surgical Oncology, Department of Oncology, University of Sheffield, The Medical School, Sheffield, UK
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Zhu J, Jiang Z, Gao F, Hu X, Zhou L, Chen J, Luo H, Sun J, Wu S, Han Y, Yin G, Chen M, Han Z, Li X, Huang Y, Zhang W, Zhou F, Chen T, Fa P, Wang Y, Sun L, Leng H, Sun F, Liu Y, Ye M, Yang H, Cai Z, Gui Y, Zhang X. A systematic analysis on DNA methylation and the expression of both mRNA and microRNA in bladder cancer. PLoS One 2011; 6:e28223. [PMID: 22140553 PMCID: PMC3227661 DOI: 10.1371/journal.pone.0028223] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 11/03/2011] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND DNA methylation aberration and microRNA (miRNA) deregulation have been observed in many types of cancers. A systematic study of methylome and transcriptome in bladder urothelial carcinoma has never been reported. METHODOLOGY/PRINCIPAL FINDINGS The DNA methylation was profiled by modified methylation-specific digital karyotyping (MMSDK) and the expression of mRNAs and miRNAs was analyzed by digital gene expression (DGE) sequencing in tumors and matched normal adjacent tissues obtained from 9 bladder urothelial carcinoma patients. We found that a set of significantly enriched pathways disrupted in bladder urothelial carcinoma primarily related to "neurogenesis" and "cell differentiation" by integrated analysis of -omics data. Furthermore, we identified an intriguing collection of cancer-related genes that were deregulated at the levels of DNA methylation and mRNA expression, and we validated several of these genes (HIC1, SLIT2, RASAL1, and KRT17) by Bisulfite Sequencing PCR and Reverse Transcription qPCR in a panel of 33 bladder cancer samples. CONCLUSIONS/SIGNIFICANCE We characterized the profiles between methylome and transcriptome in bladder urothelial carcinoma, identified a set of significantly enriched key pathways, and screened four aberrantly methylated and expressed genes. Conclusively, our findings shed light on a new avenue for basic bladder cancer research.
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Affiliation(s)
- Jialou Zhu
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
- College of Life Science, Wuhan University, Wuhan, China
| | - Zhimao Jiang
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen, China
| | - Fei Gao
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Xueda Hu
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Liang Zhou
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen, China
| | - Jiahao Chen
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Huijuan Luo
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Jihua Sun
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Song Wu
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen, China
| | - Yonghua Han
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen, China
| | | | - Maoshan Chen
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Zujing Han
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Xianxin Li
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen, China
| | - Yi Huang
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen, China
| | - Weixing Zhang
- Department of Urology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Fangjian Zhou
- Department of Urology, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Tong Chen
- Department of Urology, Shenzhen People's Hospital, Shenzhen, China
| | - Pingping Fa
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen, China
| | - Yong Wang
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen, China
| | - Liang Sun
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen, China
| | - Huimin Leng
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen, China
| | - Fenghao Sun
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen, China
- Shantou University Medical College, Shantou, China
| | - Yuchen Liu
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen, China
- Department of Urology, Shenzhen People's Hospital, Shenzhen, China
| | - Mingzhi Ye
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Huanming Yang
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Zhiming Cai
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen, China
- Department of Urology, The Second People's Hospital of Shenzhen, Shenzhen, China
| | - Yaoting Gui
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen, China
- * E-mail: (XZ); (YG)
| | - Xiuqing Zhang
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
- * E-mail: (XZ); (YG)
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