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Ramazi S, Daddzadi M, Sahafnejad Z, Allahverdi A. Epigenetic regulation in lung cancer. MedComm (Beijing) 2023; 4:e401. [PMID: 37901797 PMCID: PMC10600507 DOI: 10.1002/mco2.401] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 09/04/2023] [Accepted: 09/08/2023] [Indexed: 10/31/2023] Open
Abstract
Lung cancer is indeed a major cause of cancer-related deaths worldwide. The development of tumors involves a complex interplay of genetic, epigenetic, and environmental factors. Epigenetic mechanisms, including DNA methylation (DNAm), histone modifications, and microRNA expression, play a crucial role in this process. Changes in DNAm patterns can lead to the silencing of important genes involved in cellular functions, contributing to the development and progression of lung cancer. MicroRNAs and exosomes have also emerged as reliable biomarkers for lung cancer. They can provide valuable information about early diagnosis and treatment assessment. In particular, abnormal hypermethylation of gene promoters and its effects on tumorigenesis, as well as its roles in the Wnt signaling pathway, have been extensively studied. Epigenetic drugs have shown promise in the treatment of lung cancer. These drugs target the aberrant epigenetic modifications that are involved in the development and progression of the disease. Several factors have been identified as drug targets in non-small cell lung cancer. Recently, combination therapy has been discussed as a successful strategy for overcoming drug resistance. Overall, understanding the role of epigenetic mechanisms and their targeting through drugs is an important area of research in lung cancer treatment.
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Affiliation(s)
- Shahin Ramazi
- Department of BiophysicsFaculty of Biological SciencesTarbiat Modares UniversityTehranIran
| | - Meadeh Daddzadi
- Department of BiotechnologyFaculty of Advanced Science and TechnologyTehran Medical SciencesIslamic Azad UniversityTehranIran
| | - Zahra Sahafnejad
- Department of BiophysicsFaculty of Biological SciencesTarbiat Modares UniversityTehranIran
| | - Abdollah Allahverdi
- Department of BiophysicsFaculty of Biological SciencesTarbiat Modares UniversityTehranIran
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Munteanu R, Tomuleasa C, Iuga CA, Gulei D, Ciuleanu TE. Exploring Therapeutic Avenues in Lung Cancer: The Epigenetic Perspective. Cancers (Basel) 2023; 15:5394. [PMID: 38001653 PMCID: PMC10670535 DOI: 10.3390/cancers15225394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/06/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Lung cancer, primarily non-small cell lung carcinoma (NSCLC) and small cell lung carcinoma (SCLC), is distinguished by its high prevalence and marked mortality rates. Traditional therapeutic approaches, encompassing chemotherapy, radiation, and targeted therapies, frequently show limited efficacy due to acquired resistance and notable side effects. The objective of this review is to introduce a fresh perspective on the therapeutic strategies for lung cancer, emphasizing interventions targeting the epigenetic alterations often seen in this malignancy. This review presents the most recent advancements in the field, focusing on both past and current clinical trials related to the modulation of methylation patterns using diverse molecular agents. Furthermore, an in-depth analysis of the challenges and advantages of these methylation-modifying drugs will be provided, assessing their efficacy as individual treatments and their potential for synergy when integrated with prevailing therapeutic regimens.
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Affiliation(s)
- Raluca Munteanu
- Medfuture Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400347 Cluj-Napoca, Romania; (R.M.); (C.T.)
- Academy of Romanian Scientists, Ilfov 3, 050044 Bucharest, Romania
| | - Ciprian Tomuleasa
- Medfuture Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400347 Cluj-Napoca, Romania; (R.M.); (C.T.)
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
- Department of Hematology, Ion Chiricuta Clinical Cancer Center, 400124 Cluj-Napoca, Romania
| | - Cristina-Adela Iuga
- Department of Proteomics and Metabolomics, Research Center for Advanced Medicine–MEDFUTURE, “Iuliu Hatieganu” University of Medicine and Pharmacy Cluj-Napoca, Louis Pasteur Street 6, 400349 Cluj-Napoca, Romania;
- Department of Pharmaceutical Analysis, Faculty of Pharmacy, “Iuliu Hatieganu” University of Medicine and Pharmacy, Louis Pasteur Street 6, 400349 Cluj-Napoca, Romania
| | - Diana Gulei
- Medfuture Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400347 Cluj-Napoca, Romania; (R.M.); (C.T.)
| | - Tudor Eliade Ciuleanu
- Department of Oncology, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
- Department of Oncology, Prof. Dr. Ion Chiricuta Oncology Institute, 400015 Cluj-Napoca, Romania
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Wang H, Zhang W, Ding Z, Ke H, Su D, Wang Q, Xu K. SEMA3G functions as a novel prognostic biomarker associated with Wnt pathway in clear cell renal cell carcinoma. Cell Signal 2023; 111:110868. [PMID: 37633476 DOI: 10.1016/j.cellsig.2023.110868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 08/13/2023] [Accepted: 08/23/2023] [Indexed: 08/28/2023]
Abstract
Renal cell cancer (RCC) is one of the most common cancer, and the incidence of clear cell renal cell cancer rank at the first among multiple subtypes of RCC. Tumor heterogeneity and limited therapies expedite researches and studies on prognostic biomarkers and molecular mechanism. SEMA3G mediates various bimolecular processes but few studies have assessed the influence of SEMA3G on ccRCC. The expression of SEMA3G at mRNA level in ccRCC was analyzed using 4 TCGA datasets. The expression at protein level was verified by immunohistochemistry and western blot. Biological pathway was explored by GSEA and western blot. At both mRNA and protein level, SEMA3G expressed significantly lower in ccRCC tissues compared with normal renal tissues, and the expression was highly associated with clinical stage and pathological grade. Low expression of SEMA3G indicated a poorer overall survival and disease specific survival. Transwell and wound-healing assays showed that overexpressed SEMA3G inhibited the cell motility of renal cancer cells. Upregulated SEMA3G suppressed the invasion and proliferation of both 769-P and 786-O cells. Wnt signaling pathway was tested to work in the interfering of SEMA3G on tumorigenesis and progression of ccRCC. The results provide novel insight into the role of SEMA3G in ccRCC, suggesting the prognostic value and potential suppressor role of SEMA3G.
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Affiliation(s)
- Huanrui Wang
- Department of Urology, Peking University People's Hospital, Beijing 100045, China
| | - Weiyu Zhang
- Department of Urology, Peking University People's Hospital, Beijing 100045, China
| | - Zehua Ding
- Department of Urology, Peking University People's Hospital, Beijing 100045, China
| | - Hanwei Ke
- Department of Urology, Peking University People's Hospital, Beijing 100045, China
| | - Dongyu Su
- Department of Urology, Peking University People's Hospital, Beijing 100045, China
| | - Qi Wang
- Department of Urology, Peking University People's Hospital, Beijing 100045, China
| | - Kexin Xu
- Department of Urology, Peking University People's Hospital, Beijing 100045, China.
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Bica C, Tirpe A, Nutu A, Ciocan C, Chira S, Gurzau ES, Braicu C, Berindan-Neagoe I. Emerging roles and mechanisms of semaphorins activity in cancer. Life Sci 2023; 318:121499. [PMID: 36775114 DOI: 10.1016/j.lfs.2023.121499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/08/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023]
Abstract
Semaphorins are regulatory molecules that are linked to the modulation of several cancer processes, such as angiogenesis, cancer cell invasiveness and metastasis, tumor growth, as well as cancer cell survival. Semaphorin (SEMA) activity depends on the cancer histotypes and their particularities. In broad terms, the effects of SEMAs result from their interaction with specific receptors/co-receptors - Plexins, Neuropilins and Integrins - and the subsequent effects upon the downstream effectors (e.g. PI3K/AKT, MAPK/ERK). The present article serves as an integrative review work, discussing the broad implications of semaphorins in cancer, focusing on cell proliferation/survival, angiogenesis, invasion, metastasis, stemness, and chemo-resistance/response whilst highlighting their heterogeneity as a family. Herein, we emphasized that semaphorins are largely implicated in cancer progression, interacting with the tumor microenvironment components. Whilst some SEMAs (e.g. SEMA3A, SEMA3B) function widely as tumor suppressors, others (e.g. SEMA3C) act as pro-tumor semaphorins. The differences observed in terms of the biological structure of SEMAs and the particularities of each cancer histotypes require that each semaphorin be viewed as a unique entity, and its roles must be researched accordingly. A more in-depth and comprehensive view of the molecular mechanisms that promote and sustain the malignant behavior of cancer cells is of utmost importance.
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Affiliation(s)
- Cecilia Bica
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca 400337, Romania.
| | - Alexandru Tirpe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca 400337, Romania; Faculty of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 8 Victor Babes Street, 400012 Cluj-Napoca, Romania.
| | - Andreea Nutu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca 400337, Romania.
| | - Cristina Ciocan
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca 400337, Romania.
| | - Sergiu Chira
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca 400337, Romania.
| | - Eugen S Gurzau
- Cluj School of Public Health, College of Political, Administrative and Communication Sciences, Babes-Bolyai University, 7 Pandurilor Street, Cluj-Napoca, Romania; Environmental Health Center, 58 Busuiocului Street, 400240 Cluj-Napoca, Romania.
| | - Cornelia Braicu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca 400337, Romania.
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca 400337, Romania.
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Yin Z, Zhao Y, Zhou W, You C, Bai Y, You B, Lu D, Liao S, Zheng L, Sun Y, Wu Y. A 20-Gene Signature Predicting Survival in Patients with Clear Cell Renal Cell Carcinoma Based on Basement Membrane. J Oncol 2023; 2023:1302278. [PMID: 37089260 PMCID: PMC10118896 DOI: 10.1155/2023/1302278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 10/07/2022] [Indexed: 04/25/2023]
Abstract
Objectives The most common subtype of renal cell carcinoma, clear cell renal cell carcinoma (ccRCC), has a high heterogeneity and aggressive nature. The basement membrane (BM) is known to play a vital role in tumor metastasis. BM-related genes remain untested in ccRCC, however, in terms of their prognostic significance. Methods BM-related genes were gleaned from the most recent cutting-edge research. The RNA-seq and clinical data of the ccRCC were obtained from TCGA and GEO databases, respectively. The multigene signature was constructed using the univariate Cox regression and the LASSO regression algorithm. Then, clinical features and prognostic signatures were combined to form a nomogram to predict individual survival probabilities. Using functional enrichment analysis and immune-correlation analysis, we investigated potential enrichment pathways and immunological characteristics associated with BM-related-gene signature. Results In this study, we built a model of 20 BM-related genes and classified them as high-risk or low-risk, with each having its anticipated risk profile. Patients in the high-risk group showed significantly reduced OS compared with patients in the low-risk group in the TCGA cohort, as was confirmed by the testing dataset. Functional analysis showed that the BM-based model was linked to cell-substrate adhesion and tumor-related signaling pathways. Comparative analysis of immune cell infiltration degrees and immune checkpoints reveals a central role for BM-related genes in controlling the interplay between the immune interaction and the tumor microenvironment of ccRCC. Conclusions We combined clinical characteristics known to predict the prognosis of ccRCC patients to create a gene signature associated with BM. Our findings may also be useful for forecasting how well immunotherapies would work against ccRCC. Targeting BM may be a therapeutic alternative for ccRCC, but the underlying mechanism still needs further exploration.
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Affiliation(s)
- Zhenjie Yin
- Department of Urology, Affiliated Sanming First Hospital, Fujian Medical University, Sanming, Fujian 365001, China
| | - Yu Zhao
- Department of Medical and Radiation Oncology, Affiliated Sanming First Hospital, Fujian Medical University, Sanming, Fujian 365001, China
| | - Weiwen Zhou
- Department of Urology, Affiliated Sanming First Hospital, Fujian Medical University, Sanming, Fujian 365001, China
| | - Chengcheng You
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, Hubei 443002, China
| | - Yuanyuan Bai
- Department of Urology, Affiliated Sanming First Hospital, Fujian Medical University, Sanming, Fujian 365001, China
| | - Bingyong You
- Department of Urology, Affiliated Sanming First Hospital, Fujian Medical University, Sanming, Fujian 365001, China
| | - Dongming Lu
- Department of Urology, Affiliated Sanming First Hospital, Fujian Medical University, Sanming, Fujian 365001, China
| | - Shangfan Liao
- Department of Urology, Affiliated Sanming First Hospital, Fujian Medical University, Sanming, Fujian 365001, China
| | - Luoping Zheng
- Department of Urology, Affiliated Sanming First Hospital, Fujian Medical University, Sanming, Fujian 365001, China
| | - Yingming Sun
- Department of Medical and Radiation Oncology, Affiliated Sanming First Hospital, Fujian Medical University, Sanming, Fujian 365001, China
| | - Yongyang Wu
- Department of Urology, Affiliated Sanming First Hospital, Fujian Medical University, Sanming, Fujian 365001, China
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Tao J, Li X, Liang C, Liu Y, Zhou J. Expression of basement membrane genes and their prognostic significance in clear cell renal cell carcinoma patients. Front Oncol 2022; 12:1026331. [DOI: 10.3389/fonc.2022.1026331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/06/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundClear cell renal cell carcinoma (ccRCC) is a malignant tumor with limited treatment options. A recent study confirmed the involvement of basement membrane (BM) genes in the progression of many cancers. Therefore, we studied the role and prognostic significance of BM genes in ccRCC.MethodsCo-expression analysis of ccRCC-related information deposited in The Cancer Genome Atlas database and a BM geneset from a recent study was conducted. The differentially expressed BM genes were validated using quantitative reverse-transcription polymerase chain reaction (qRT-PCR). Least absolute shrinkage and selection operator regression and univariate Cox regression analyses were performed to identify a BM gene signature with prognostic significance for ccRCC. Multivariate Cox regression, time-dependent receiver operating characteristic, Kaplan–Meier, and nomogram analyses were implemented to appraise the prognostic ability of the signature and the findings were further verified using a Gene Expression Omnibus dataset. Additionally, immune cell infiltration and and pathway enrichment analyses were performed using ImmuCellAI and Gene Set Enrichment Analysis (GSEA), respectively. Finally, the DSIGDB dataset was used to screen small-molecule therapeutic drugs that may be useful in treating ccRCC patients.ResultsWe identified 108 BM genes exhibiting different expression levels compared to that in normal kidney tissues, among which 32 genes had prognostic values. The qRT-PCR analyses confirmed that the expression patterns of four of the ten selected genes were the same as the predicted ones. Additionally, we successfully established and validated a ccRCC patient prediction model based on 16 BM genes and observed that the model function is an independent predictor. GSEA revealed that differentially expressed BM genes mainly displayed significant enrichment of tumor and metabolic signaling cascades. The BM gene signature was also associated with immune cell infiltration and checkpoints. Eight small-molecule drugs may have therapeutic effects on ccRCC patients.ConclusionThis study explored the function of BM genes in ccRCC for the first time. Reliable prognostic biomarkers that affect the survival of ccRCC patients were determined, and a BM gene-based prognostic model was established.
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Meng Z, Li FL, Fang C, Yeoman B, Qiu Y, Wang Y, Cai X, Lin KC, Yang D, Luo M, Fu V, Ma X, Diao Y, Giancotti FG, Ren B, Engler AJ, Guan KL. The Hippo pathway mediates Semaphorin signaling. Sci Adv 2022; 8:eabl9806. [PMID: 35613278 PMCID: PMC9132450 DOI: 10.1126/sciadv.abl9806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 04/11/2022] [Indexed: 02/05/2023]
Abstract
Semaphorins were originally identified as axonal guidance molecules, but they also control processes such as vascular development and tumorigenesis. The downstream signaling cascades of Semaphorins in these biological processes remain unclear. Here, we show that the class 3 Semaphorins (SEMA3s) activate the Hippo pathway to attenuate tissue growth, angiogenesis, and tumorigenesis. SEMA3B restoration in lung cancer cells with SEMA3B loss of heterozygosity suppresses cancer cell growth via activating the core Hippo kinases LATS1/2 (large tumor suppressor kinase 1/2). Furthermore, SEMA3 also acts through LATS1/2 to inhibit angiogenesis. We identified p190RhoGAPs as essential partners of the SEMA3A receptor PlexinA in Hippo regulation. Upon SEMA3 treatment, PlexinA interacts with the pseudo-guanosine triphosphatase (GTPase) domain of p190RhoGAP and simultaneously recruits RND GTPases to activate p190RhoGAP, which then stimulates LATS1/2. Disease-associated etiological factors, such as genetic lesions and oscillatory shear, diminish Hippo pathway regulation by SEMA3. Our study thus discovers a critical role of Hippo signaling in mediating SEMA3 physiological function.
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Affiliation(s)
- Zhipeng Meng
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, Miami, FL 33136, USA
| | - Fu-Long Li
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Cao Fang
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Benjamin Yeoman
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yunjiang Qiu
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA 92093, USA
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ying Wang
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, Miami, FL 33136, USA
| | - Xiaomin Cai
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Kimberly C. Lin
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Di Yang
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Min Luo
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Vivian Fu
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Xiaoxiao Ma
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Yarui Diao
- Regeneration Next Initiative, Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Filippo G. Giancotti
- Department of Cancer Biology and David H. Koch Center for Applied Research of GU Cancers, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Herbert Irving Comprehensive Cancer Center and Department of Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10033, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA 92093, USA
| | - Adam J. Engler
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kun-Liang Guan
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
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Hoang PH, Landi MT. DNA Methylation in Lung Cancer: Mechanisms and Associations with Histological Subtypes, Molecular Alterations, and Major Epidemiological Factors. Cancers (Basel) 2022; 14:cancers14040961. [PMID: 35205708 PMCID: PMC8870477 DOI: 10.3390/cancers14040961] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 12/14/2021] [Accepted: 02/11/2022] [Indexed: 01/27/2023] Open
Abstract
Lung cancer is the major leading cause of cancer-related mortality worldwide. Multiple epigenetic factors-in particular, DNA methylation-have been associated with the development of lung cancer. In this review, we summarize the current knowledge on DNA methylation alterations in lung tumorigenesis, as well as their associations with different histological subtypes, common cancer driver gene mutations (e.g., KRAS, EGFR, and TP53), and major epidemiological risk factors (e.g., sex, smoking status, race/ethnicity). Understanding the mechanisms of DNA methylation regulation and their associations with various risk factors can provide further insights into carcinogenesis, and create future avenues for prevention and personalized treatments. In addition, we also highlight outstanding questions regarding DNA methylation in lung cancer to be elucidated in future studies.
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Abstract
Whales are marine creatures known for their enormous size and that live in all the oceans on earth. One of the oldest known organisms is bowhead whales, which can survive up to 200 years, and similarly, other species of whales have shown a remarkable long lifespan. In addition to this, whales are highly resistant to cancer, a disease that is strongly related to aging and the accumulation of damage over time. These two characteristics make whales an interesting model to study and that can provide us with a track both to delay aging and to avoid pathologies associated with it, such as cancer. In the present work, we try to analyze different aspects of whales such as metabolism, hematological and biochemical characteristics, and properties of their genome and transcriptome in order to elucidate possible molecular mechanisms that evolution has provided to these aquatic mammals.
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Affiliation(s)
- Francisco Alejandro Lagunas-Rangel
- Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Mexico City, Mexico; Department of Neuroscience, Functional Pharmacology, Uppsala University, Uppsala, Sweden.
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10
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Tan HW, Xu YM, Qin SH, Chen GF, Lau ATY. Epigenetic regulation of angiogenesis in lung cancer. J Cell Physiol 2021; 236:3194-3206. [PMID: 33078404 DOI: 10.1002/jcp.30104] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 09/08/2020] [Accepted: 09/30/2020] [Indexed: 02/05/2023]
Abstract
Lung cancer is the leading cause of cancer-related deaths worldwide, in which angiogenesis is highly required for lung cancer cell growth and metastasis. Genetic regulation of this multistep process is being studied extensively, however, relatively less is known about the epigenetic regulation of angiogenesis in lung cancer. Several epigenetic alterations contribute to regulating angiogenesis, such as epimodifications of DNA, posttranslational modification of histones, and expression of noncoding RNAs. Here, we review the current knowledge of the epigenetic regulation of angiogenesis and discuss the potential clinical applications of epigenetic-based anticancer therapy in lung cancer. Overall, epigenetic-based therapy will likely emerge as a prominent approach to treat lung cancer in the future.
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Affiliation(s)
- Heng Wee Tan
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong, People's Republic of China
| | - Yan-Ming Xu
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong, People's Republic of China
| | - San-Hai Qin
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong, People's Republic of China
| | - Guo-Feng Chen
- Department of Hepatobiliary Surgery, The Affiliated Huai'an No.1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu, People's Republic of China
| | - Andy T Y Lau
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong, People's Republic of China
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Li GZ, Shen D, Li GH, Wei M, Zheng LJ, Liu ZL, Sun RQ, Zhou SJ, Zhang ZL, Gao YC. Decreased expression of serum semaphorin 3B is associated with poor prognosis of patients with hepatocellular carcinoma. Exp Ther Med 2021; 21:236. [PMID: 33603844 PMCID: PMC7851624 DOI: 10.3892/etm.2021.9667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 12/08/2020] [Indexed: 01/01/2023] Open
Abstract
Semaphorin 3B (SEMA-3B), which belongs to the semaphorin family, has an important role in cell apoptosis and inhibition of angiogenesis. A previous study by our group revealed that SEMA-3B was downregulated in tumor tissues of patients with hepatocellular carcinoma (HCC) and exerts anti-motility and anti-invasion effects on tumor cells. However, the serum levels of SEMA-3B and their clinical significance have remained elusive; therefore, the aim of the present study was to monitor its expression in HCC and investigate its clinical significance. ELISA was used to determine the serum levels of SEMA-3B in 132 patients with HCC and 57 healthy individuals. The association between SEMA-3B and clinicopathological parameters was investigated. Serum SEMA-3B was indicated to be significantly decreased in patients with HCC as compared with that in the controls (P<0.05) and it was negatively associated with tumor size (P=0.039), encapsulation (P=0.002) and TNM stage (P=0.034). The prognosis of patients with low expression of SEMA-3B was poor. In conclusion, the results of the present study revealed that serum SEMA-3B is decreased in HCC and is negatively associated with prognosis; therefore, it may be used as a prognostic marker in HCC.
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Affiliation(s)
- Guang-Zhen Li
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong 250012, P.R. China
| | - Di Shen
- Department of Gynecology and Obstetrics, Shandong Maternity and Child Care Hospital, Jinan, Shandong 250014, P.R. China
| | - Guang-Hong Li
- Department of Endocrinology, The Affiliated Hospital of Taishan Medical College, Tai'an, Shandong 271000, P.R. China
| | - Meng Wei
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong 250012, P.R. China
| | - Li-Jie Zheng
- Department of General Surgery, Qilu Hospital of Shandong University, Qingdao, Shandong 266035, P.R. China
| | - Zeng-Li Liu
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong 250012, P.R. China
| | - Rong-Qi Sun
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong 250012, P.R. China
| | - Shao-Jun Zhou
- Department of General Surgery, Qilu Hospital of Shandong University, Qingdao, Shandong 266035, P.R. China
| | - Zong-Li Zhang
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong 250012, P.R. China
| | - Yan-Chao Gao
- Department of Hepatobiliary Surgery, Liaocheng People's Hospital, Liaocheng, Shandong 252000, P.R. China
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12
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Mastrantonio R, You H, Tamagnone L. Semaphorins as emerging clinical biomarkers and therapeutic targets in cancer. Theranostics 2021; 11:3262-3277. [PMID: 33537086 PMCID: PMC7847692 DOI: 10.7150/thno.54023] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/06/2020] [Indexed: 12/15/2022] Open
Abstract
Semaphorins are a large family of developmental regulatory signals, characterized by aberrant expression in human cancers. These molecules crucially control cell-cell communication, cell migration, invasion and metastasis, tumor angiogenesis, inflammatory and anti-cancer immune responses. Semaphorins comprise secreted and cell surface-exposed molecules and their receptors are mainly found in the Plexin and Neuropilin families, which are further implicated in a signaling network controlling the tumor microenvironment. Accumulating evidence indicates that semaphorins may be considered as novel clinical biomarkers for cancer, especially for the prediction of patient survival and responsiveness to therapy. Moreover, preclinical experimental studies have demonstrated that targeting semaphorin signaling can interfere with tumor growth and/or metastatic dissemination, suggesting their relevance as novel therapeutic targets in cancer; this has also prompted the development of semaphorin-interfering molecules for application in the clinic. Here we will survey, in diverse human cancers, the current knowledge about the relevance of semaphorin family members, and conceptualize potential lines of future research development in this field.
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13
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Abstract
Cell-cell communication is pivotal to guide embryo development, as well as to maintain adult tissues homeostasis and control immune response. Among extracellular factors responsible for this function, are the Semaphorins, a broad family of around 20 different molecular cues conserved in evolution and widely expressed in all tissues. The signaling cascades initiated by semaphorins depend on a family of conserved receptors, called Plexins, and on several additional molecules found in the receptor complexes. Moreover, multiple intracellular pathways have been described to act downstream of semaphorins, highlighting significant diversity in the signaling cascades controlled by this family. Notably, semaphorin expression is altered in many human diseases, such as immunopathologies, neurodegenerative diseases and cancer. This underscores the importance of semaphorins as regulatory factors in the tissue microenvironment and has prompted growing interest for assessing their potential relevance in medicine. This review article surveys the main contexts in which semaphorins have been found to regulate developing and healthy adult tissues, and the signaling cascades implicated in these functions. Vis a vis, we will highlight the main pathological processes in which semaphorins are thought to have a role thereof.
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Affiliation(s)
- Damon Fard
- University of Torino School of Medicine, Torino, Italy
| | - Luca Tamagnone
- Università Cattolica del Sacro Cuore, Rome, Italy; Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Rome, Italy.
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14
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Kushlinskii NE, Utkin DO, Loginov VI, Filippova EA, Burdennyy AM, Kushlinsky DN, Pronina IV, Braga EA. [Clinical significance of methylation of a group of miRNA genes in patients with ovarian cancer.]. Klin Lab Diagn 2020; 65:321-327. [PMID: 32298550 DOI: 10.18821/0869-2084-2020-65-5-321-327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 03/18/2020] [Indexed: 02/05/2023]
Abstract
It was found that the proportion of microRNA genes inactivated by methylation of regulatory CpG islands is several times higher than the genes encoding proteins, which increases their attractiveness as promising markers of cancer. The aim of this work is to evaluate the clinical significance of methylation of 13 tumor-associated microRNA genes (MIR-124a-2, MIR-124a-3, MIR-125-B1, MIR-127, MIR-129-2, MIR-132, MIR-137, MIR-203a, MIR-34b/c, MIR-375, MIR-9-1, MIR-9-3, MIR-339) in 26 patients with ovarian cancer. Methylation level was evaluated by the method of methylation-specific PCR in real time. The data obtained in primary tumors (26), histologically unchanged ovarian tissues (15) and peritoneal metastases (19) were compared using a number of statistical programs. For all 13 genes, an increase in the level of methylation was revealed during the transition from unchanged tissue to primary tumors and further from primary tumors to peritoneal metastases; moreover, in the genes MIR-203a, MIR-375 and MIR-339, the level of methylation in metastases increased most significantly (in 2 and more times). A correlation was observed for the first time, showing a consistency between the increase in methylation level in some miRNA pairs, for example, MIR-129-2/MIR-132 (rs> 0,7; p<0,0001), both in primary tumors and in metastases. An analysis of microRNA gene methylation in clinical samples of ovarian cancer showed a correlation between the observed molecular changes both with the initial stages of tumor formation and with the progression and dissemination of ovarian cancer, with the presence of metastases in a large omentum and with the appearance of ascites. The revealed dependencies deepen the understanding of the mechanism of peritoneal metastasis and can be used to select new diagnostic and prognostic markers of ovarian cancer.
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Affiliation(s)
- N E Kushlinskii
- N.N. Blokhin National Medical Research Center of Oncology, Moscow, 115478, Russian Federation
| | - D O Utkin
- N.N. Blokhin National Medical Research Center of Oncology, Moscow, 115478, Russian Federation
| | - V I Loginov
- The Institute of General Pathology and Pathophysiology of the Ministry of Science and Higher Education of the Russian Federation, Moscow, 125315, Russian Federation
| | - E A Filippova
- The Institute of General Pathology and Pathophysiology of the Ministry of Science and Higher Education of the Russian Federation, Moscow, 125315, Russian Federation
| | - A M Burdennyy
- The Institute of General Pathology and Pathophysiology of the Ministry of Science and Higher Education of the Russian Federation, Moscow, 125315, Russian Federation
| | - D N Kushlinsky
- A.F. Tsyb Medical Radiological Scientific Center - branch of the Federal State Budgetary Institution «National Medical Research Center of Radiology» of the Ministry of Health of the Russian Federation, Obninsk, 249036, Russian Federation
| | - I V Pronina
- The Institute of General Pathology and Pathophysiology of the Ministry of Science and Higher Education of the Russian Federation, Moscow, 125315, Russian Federation
| | - E A Braga
- The Institute of General Pathology and Pathophysiology of the Ministry of Science and Higher Education of the Russian Federation, Moscow, 125315, Russian Federation
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15
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Guo W, Liang X, Liu L, Guo Y, Shen S, Liang J, Dong Z. MiR-6872 host gene SEMA3B and its antisense lncRNA SEMA3B-AS1 function synergistically to suppress gastric cardia adenocarcinoma progression. Gastric Cancer 2019; 22:705-722. [PMID: 30656427 DOI: 10.1007/s10120-019-00924-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 01/03/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Semaphorin 3B (SEMA3B) is frequently inactivated in several carcinomas. However, as the host gene of miR-6872, the roles of SEMA3B, antisense lncRNA SEMA3B-AS1, and miR-6872 in gastric cardia adenocarcinoma (GCA) tumorigenesis have not been clarified. METHODS The expression levels of SEMA3B, SEMA3B-AS1, and miR-6872 were respectively detected by qRT-PCR, western blot, or immunohistochemical staining assays. The methylation status was determined by BGS and BS-MSP methods. In vitro assays were preformed to explore the biological effects of SEMA3B, SEMA3B-AS1, and miR-6872-5p in gastric cancer cells. Chromatin immunoprecipitation assay was used to detect the binding of protein to DNA. The interaction of SEMA3B-AS1 with MLL4 was identified by RNA immunoprecipitation and RNA pull-down assays. RESULTS Frequent downregulation of SEMA3B, SEMA3B-AS1, and miR-6872 was detected in GCA tissues and gastric cancer cells. Aberrant hypermethylation of the promoter region was more tumor specific and was negatively correlated with the expression level of SEMA3B, SEMA3B-AS1, and miR-6872-5p. Transcription factor Sp1 activated SEMA3B or SEMA3B-AS1 transcription and CpG sites hypermethylation within promoter region eliminated Sp1 binding ability. Overexpression of SEMA3B and SEMA3B-AS1 inhibited gastric cancer cell proliferation, migration, and invasion in vitro. SEMA3B-AS1 induced the expression of SEMA3B by interacting with MLL4. ZNF143 might be the target gene of miR-6872-5p and miR-6872-5p functioning synergistically with SEMA3B to suppress cell invasion. Furthermore, SEMA3B, SEMA3B-AS1, and miR-6872-5p expression levels were associated with GCA patients' survival. CONCLUSIONS SEMA3B, SEMA3B-AS1, and miR-6872 may act as tumor suppressors and may serve as potential targets for antitumor therapy.
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Affiliation(s)
- Wei Guo
- Laboratory of Pathology, Hebei Cancer Institute, The Fourth Hospital of Hebei Medical University, Jiankang Road 12, Shijiazhuang, 050011, Hebei, China
| | - Xiaoliang Liang
- Laboratory of Pathology, Hebei Cancer Institute, The Fourth Hospital of Hebei Medical University, Jiankang Road 12, Shijiazhuang, 050011, Hebei, China
| | - Lei Liu
- Department of Thoracic Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Yanli Guo
- Laboratory of Pathology, Hebei Cancer Institute, The Fourth Hospital of Hebei Medical University, Jiankang Road 12, Shijiazhuang, 050011, Hebei, China
| | - Supeng Shen
- Laboratory of Pathology, Hebei Cancer Institute, The Fourth Hospital of Hebei Medical University, Jiankang Road 12, Shijiazhuang, 050011, Hebei, China
| | - Jia Liang
- Laboratory of Pathology, Hebei Cancer Institute, The Fourth Hospital of Hebei Medical University, Jiankang Road 12, Shijiazhuang, 050011, Hebei, China
| | - Zhiming Dong
- Laboratory of Pathology, Hebei Cancer Institute, The Fourth Hospital of Hebei Medical University, Jiankang Road 12, Shijiazhuang, 050011, Hebei, China.
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16
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Dong Z, Liang X, Wu X, Kang X, Guo Y, Shen S, Liang J, Guo W. Promoter hypermethylation-mediated downregulation of tumor suppressor gene SEMA3B and lncRNA SEMA3B-AS1 correlates with progression and prognosis of esophageal squamous cell carcinoma. Clin Exp Metastasis 2019; 36:225-41. [PMID: 30915595 DOI: 10.1007/s10585-019-09964-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 03/22/2019] [Indexed: 02/01/2023]
Abstract
Frequent deletions of tumor-suppressor genes at chromosome 3p21.3 have been detected in esophageal squamous cell carcinoma (ESCC). As a candidate tumor suppressor gene, semaphorin 3B (SEMA3B) is located at 3p21.3 and is frequently inactivated in several tumors. However, the role and inactivation mechanisms of SEMA3B and its antisense long non-coding RNA (lncRNA) SEMA3B-AS1 in the carcinogenesis of ESCC have not been fully elucidated. The present study was conducted to investigate the role, epigenetic inactivation mechanisms, and prognostic value of SEMA3B and SEMA3B-AS1 in ESCC tumorigenesis and prognosis. Frequent downregulation of SEMA3B and SEMA3B-AS1 was detected in esophageal cancer cells and ESCC tissues, and the expression level of SEMA3B and SEMA3B-AS1 in ESCC tissues was correlated with TNM stage and lymph node metastasis. SEMA3B and SEMA3B-AS1 shared the same CpG island in the promoter region and the expression of both genes might be regulated by the promoter methylation status. Furthermore, transcription factor Sp1 activated SEMA3B or SEMA3B-AS1 transcription and the promoter hypermethylation of SEMA3B and SEMA3B-AS1 influenced Sp1 binding ability. Moreover, over-expression of SEMA3B and SEMA3B-AS1 suppressed the viability and invasion of esophageal cancer cells in vitro. SEMA3B-AS1 influenced the protein expression of SEMA3B. SEMA3B or SEMA3B-AS1 expression and promoter methylation status were correlated with ESCC patients' survival. Thus, these findings suggest that SEMA3B and SEMA3B-AS1 may act as tumor suppressors and may serve as potential targets for antitumor therapy.
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Toledano S, Nir-Zvi I, Engelman R, Kessler O, Neufeld G. Class-3 Semaphorins and Their Receptors: Potent Multifunctional Modulators of Tumor Progression. Int J Mol Sci 2019; 20:E556. [PMID: 30696103 DOI: 10.3390/ijms20030556] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/21/2019] [Accepted: 01/22/2019] [Indexed: 12/28/2022] Open
Abstract
Semaphorins are the products of a large gene family containing 28 genes of which 21 are found in vertebrates. Class-3 semaphorins constitute a subfamily of seven vertebrate semaphorins which differ from the other vertebrate semaphorins in that they are the only secreted semaphorins and are distinguished from other semaphorins by the presence of a basic domain at their C termini. Class-3 semaphorins were initially characterized as axon guidance factors, but have subsequently been found to regulate immune responses, angiogenesis, lymphangiogenesis, and a variety of additional physiological and developmental functions. Most class-3 semaphorins transduce their signals by binding to receptors belonging to the neuropilin family which subsequently associate with receptors of the plexin family to form functional class-3 semaphorin receptors. Recent evidence suggests that class-3 semaphorins also fulfill important regulatory roles in multiple forms of cancer. Several class-3 semaphorins function as endogenous inhibitors of tumor angiogenesis. Others were found to inhibit tumor metastasis by inhibition of tumor lymphangiogenesis, by direct effects on the behavior of tumor cells, or by modulation of immune responses. Notably, some semaphorins such as sema3C and sema3E have also been found to potentiate tumor progression using various mechanisms. This review focuses on the roles of the different class-3 semaphorins in tumor progression.
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18
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Iyer AS, Chapoval SP. Neuroimmune Semaphorin 4A in Cancer Angiogenesis and Inflammation: A Promoter or a Suppressor? Int J Mol Sci 2018; 20:ijms20010124. [PMID: 30598022 PMCID: PMC6337608 DOI: 10.3390/ijms20010124] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 12/17/2018] [Accepted: 12/21/2018] [Indexed: 02/06/2023] Open
Abstract
Neuroimmune semaphorin 4A (Sema4A), a member of semaphorin family of transmembrane and secreted proteins, is an important regulator of neuronal and immune functions. In the nervous system, Sema4A primarily regulates the functional activity of neurons serving as an axon guidance molecule. In the immune system, Sema4A regulates immune cell activation and function, instructing a fine tuning of the immune response. Recent studies have shown a dysregulation of Sema4A expression in several types of cancer such as hepatocellular carcinoma, colorectal, and breast cancers. Cancers have been associated with abnormal angiogenesis. The function of Sema4A in angiogenesis and cancer is not defined. Recent studies have demonstrated Sema4A expression and function in endothelial cells. However, the results of these studies are controversial as they report either pro- or anti-angiogenic Sema4A effects depending on the experimental settings. In this mini-review, we discuss these findings as well as our data on Sema4A regulation of inflammation and angiogenesis, which both are important pathologic processes underlining tumorigenesis and tumor metastasis. Understanding the role of Sema4A in those processes may guide the development of improved therapeutic treatments for cancer.
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Affiliation(s)
- Apoorva S Iyer
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Svetlana P Chapoval
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
- Program in Oncology at the Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
- SemaPlex LLC, Ellicott City, MD 21042, USA.
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19
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Loginov VI, Burdennyy AM, Filippova EA, Pronina IV, Kazubskaya TP, Kushlinsky DN, Ermilova VD, Rykov SV, Khodyrev DS, Braga EA. Hypermethylation of miR-107, miR-130b, miR-203a, miR-1258 Genes Associated with Ovarian Cancer Development and Metastasis. Mol Biol 2018. [DOI: 10.1134/s0026893318050102] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Snezhkina AV, Nyushko KM, Zaretsky AR, Shagin DA, Sadritdinova AF, Fedorova MS, Guvatova ZG, Abramov IS, Pudova EA, Alekseev BY, Dmitriev AA, Kudryavtseva AV. Transcription Factor SAP30 Is Involved in the Activation of NETO2 Gene Expression in Clear Cell Renal Cell Carcinoma. Mol Biol 2018. [DOI: 10.1134/s0026893318020152] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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21
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Tang MW, Malvar Fernández B, Newsom SP, van Buul JD, Radstake TRDJ, Baeten DL, Tak PP, Reedquist KA, García S. Class 3 semaphorins modulate the invasive capacity of rheumatoid arthritis fibroblast-like synoviocytes. Rheumatology (Oxford) 2018; 57:909-920. [PMID: 29471421 DOI: 10.1093/rheumatology/kex511] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Indexed: 01/08/2023] Open
Abstract
Objective Class 3 semaphorins regulate diverse cellular processes relevant to the pathology of RA, including immune modulation, angiogenesis, apoptosis and invasive cell migration. Therefore, we analysed the potential role of class 3 semaphorins in the pathology of RA. Methods Protein and mRNA expression in RA synovial tissue, SF and fibroblast-like synoviocytes (FLS) were determined by immunoblotting and quantitative PCR (qPCR). RA FLS migration and invasion were determined using wound closure and transwell invasion assays, respectively. PlexinA1, neuropilin-1 and neuropilin-2 expression was knocked down using small interfering RNA (siRNA). Activation of FLS intracellular signalling pathways was assessed by immunoblotting. Results mRNA expression of semaphorins (Sema)3B, Sema3C, Sema3F and Sema3G was significantly lower in the synovial tissue of early arthritis patients at baseline who developed persistent disease compared with patients with self-limiting disease after 2 years follow-up. Sema3B and Sema3F expression was significantly lower in arthritis patients fulfilling classification criteria for RA compared with those who did not. FLS expression of Sema3A was induced after stimulation with TNF, IL-1β or lipopolysaccharides (LPS), while Sema3B and Sema3F expression was downregulated. Exogenously applied Sema3A induced the migration and invasive capacity of FLS, while stimulation with Sema3B or Sema3F reduced spontaneous FLS migration, and platelet-derived growth factor induced cell invasion, effects associated with differential regulation of MMP expression and mediated by the PlexinA1 and neuropilin-1 and -2 receptors. Conclusion Our data suggest that modulation of class 3 semaphorin signaling could be a novel therapeutic strategy for modulating the invasive behaviour of FLS in RA.
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Affiliation(s)
- Man Wai Tang
- Department of Experimental Immunology and Department of Clinical Immunology and Rheumatology, Amsterdam Rheumatology and Immunology Center, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Beatriz Malvar Fernández
- Department of Experimental Immunology and Department of Clinical Immunology and Rheumatology, Amsterdam Rheumatology and Immunology Center, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Department of Rheumatology and Clinical Immunology and Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Simon P Newsom
- Department of Experimental Immunology and Department of Clinical Immunology and Rheumatology, Amsterdam Rheumatology and Immunology Center, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Jaap D van Buul
- Department of Molecular Cell Biology, Sanquin Research and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Timothy R D J Radstake
- Department of Rheumatology and Clinical Immunology and Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Dominique L Baeten
- Department of Experimental Immunology and Department of Clinical Immunology and Rheumatology, Amsterdam Rheumatology and Immunology Center, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Paul P Tak
- Department of Experimental Immunology and Department of Clinical Immunology and Rheumatology, Amsterdam Rheumatology and Immunology Center, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,GlaxoSmithKline Research and Development, Stevenage, UK.,Department of Medicine, University of Cambridge, Cambridge, UK
| | - Kris A Reedquist
- Department of Experimental Immunology and Department of Clinical Immunology and Rheumatology, Amsterdam Rheumatology and Immunology Center, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Department of Rheumatology and Clinical Immunology and Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Samuel García
- Department of Experimental Immunology and Department of Clinical Immunology and Rheumatology, Amsterdam Rheumatology and Immunology Center, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Department of Rheumatology and Clinical Immunology and Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
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22
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Kudryavtseva AV, Nyushko KM, Zaretsky AR, Shagin DA, Sadritdinova AF, Fedorova MS, Savvateeva MV, Guvatova ZG, Pudova EA, Alekseev BY, Dmitriev AA, Snezhkina AV. Suppression of NR0B2 gene in Clear Cell Renal Cell Carcinoma Is Associated with Hypermethylation of Its Promoter. Mol Biol 2018. [DOI: 10.1134/s0026893318030081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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23
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Marconett CN, Zhou B, Sunohara M, Pouldar TM, Wang H, Liu Y, Rieger ME, Tran E, Flodby P, Siegmund KD, Crandall ED, Laird-Offringa IA, Borok Z. Cross-Species Transcriptome Profiling Identifies New Alveolar Epithelial Type I Cell-Specific Genes. Am J Respir Cell Mol Biol 2017; 56:310-321. [PMID: 27749084 DOI: 10.1165/rcmb.2016-0071oc] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Diseases involving the distal lung alveolar epithelium include chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, and lung adenocarcinoma. Accurate labeling of specific cell types is critical for determining the contribution of each to the pathogenesis of these diseases. The distal lung alveolar epithelium is composed of two cell types, alveolar epithelial type 1 (AT1) and type 2 (AT2) cells. Although cell type-specific markers, most prominently surfactant protein C, have allowed detailed lineage tracing studies of AT2 cell differentiation and the cells' roles in disease, studies of AT1 cells have been hampered by a lack of genes with expression unique to AT1 cells. In this study, we performed genome-wide expression profiling of multiple rat organs together with purified rat AT2, AT1, and in vitro differentiated AT1-like cells, resulting in the identification of 54 candidate AT1 cell markers. Cross-referencing with genes up-regulated in human in vitro differentiated AT1-like cells narrowed the potential list to 18 candidate genes. Testing the top four candidate genes at RNA and protein levels revealed GRAM domain 2 (GRAMD2), a protein of unknown function, as highly specific to AT1 cells. RNA sequencing (RNAseq) confirmed that GRAMD2 is transcriptionally silent in human AT2 cells. Immunofluorescence verified that GRAMD2 expression is restricted to the plasma membrane of AT1 cells and is not expressed in bronchial epithelial cells, whereas reverse transcription-polymerase chain reaction confirmed that it is not expressed in endothelial cells. Using GRAMD2 as a new AT1 cell-specific gene will enhance AT1 cell isolation, the investigation of alveolar epithelial cell differentiation potential, and the contribution of AT1 cells to distal lung diseases.
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Affiliation(s)
- Crystal N Marconett
- Departments of 1 Surgery and.,2 Biochemistry and Molecular Medicine.,3 Norris Comprehensive Cancer Center
| | - Beiyun Zhou
- 3 Norris Comprehensive Cancer Center.,4 Department of Medicine, Will Rogers Institute Pulmonary Research Center, Division of Pulmonary, Critical Care and Sleep Medicine, and
| | - Mitsuhiro Sunohara
- 4 Department of Medicine, Will Rogers Institute Pulmonary Research Center, Division of Pulmonary, Critical Care and Sleep Medicine, and
| | | | - Hongjun Wang
- 4 Department of Medicine, Will Rogers Institute Pulmonary Research Center, Division of Pulmonary, Critical Care and Sleep Medicine, and
| | - Yixin Liu
- 4 Department of Medicine, Will Rogers Institute Pulmonary Research Center, Division of Pulmonary, Critical Care and Sleep Medicine, and
| | - Megan E Rieger
- 4 Department of Medicine, Will Rogers Institute Pulmonary Research Center, Division of Pulmonary, Critical Care and Sleep Medicine, and
| | - Evelyn Tran
- Departments of 1 Surgery and.,2 Biochemistry and Molecular Medicine.,3 Norris Comprehensive Cancer Center
| | - Per Flodby
- 4 Department of Medicine, Will Rogers Institute Pulmonary Research Center, Division of Pulmonary, Critical Care and Sleep Medicine, and
| | - Kimberly D Siegmund
- 5 Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Edward D Crandall
- 4 Department of Medicine, Will Rogers Institute Pulmonary Research Center, Division of Pulmonary, Critical Care and Sleep Medicine, and
| | - Ite A Laird-Offringa
- Departments of 1 Surgery and.,2 Biochemistry and Molecular Medicine.,3 Norris Comprehensive Cancer Center
| | - Zea Borok
- 2 Biochemistry and Molecular Medicine.,3 Norris Comprehensive Cancer Center.,4 Department of Medicine, Will Rogers Institute Pulmonary Research Center, Division of Pulmonary, Critical Care and Sleep Medicine, and
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24
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Loginov VI, Pronina IV, Burdennyi AM, Pereyaslova EA, Braga EA, Kazubskaya TP, Kushlinskii NE. Role of Methylation in the Regulation of Apoptosis Genes APAF1, DAPK1, and BCL2 in Breast Cancer. Bull Exp Biol Med 2017; 162:797-800. [PMID: 28429233 DOI: 10.1007/s10517-017-3716-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Indexed: 12/11/2022]
Abstract
Changes in the levels of expression of proapoptotic genes APAF1 and DAPK1 and antiapoptotic gene BCL2 were studied by real time PCR in specimens of tumors and histologically intact tissue from 28 patients with breast cancer. The expression of APAF1 and DAPK1 was below the normal in the majority of tumor samples (p<0.05), while the level of BCL2 mRNA more often surpassed the normal (p<0.1). Study of the same sample of specimens by methylspecific PCR showed predominance of APAF1 and DAPK1 hypermethylation (p<0.05 and p<0.1, respectively) and more frequent hypomethylation of BCL2. A significant correlation between changes in the levels of expression and methylation (r=0.40-0.49; p<0.05) was detected for all three genes (APAF1, DAPK1, and BCL2). The results suggest that methylation play an important role in the regulation of these apoptosis system genes in breast cancer.
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Pronina IV, Klimov EA, Burdennyy AM, Beresneva EV, Fridman MV, Ermilova VD, Kazubskaya TP, Karpukhin AV, Braga EA, Loginov VI. Methylation of the genes for the microRNAs miR-129-2 and miR-9-1, changes in their expression, and activation of their potential target genes in clear cell renal cell carcinoma. Mol Biol 2017. [DOI: 10.1134/s0026893316060169] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Neufeld G, Mumblat Y, Smolkin T, Toledano S, Nir-Zvi I, Ziv K, Kessler O. The role of the semaphorins in cancer. Cell Adh Migr 2016; 10:652-674. [PMID: 27533782 PMCID: PMC5160032 DOI: 10.1080/19336918.2016.1197478] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 05/19/2016] [Accepted: 05/30/2016] [Indexed: 12/16/2022] Open
Abstract
The semaphorins were initially characterized as axon guidance factors, but have subsequently been implicated also in the regulation of immune responses, angiogenesis, organ formation, and a variety of additional physiological and developmental functions. The semaphorin family contains more then 20 genes divided into 7 subfamilies, all of which contain the signature sema domain. The semaphorins transduce signals by binding to receptors belonging to the neuropilin or plexin families. Additional receptors which form complexes with these primary semaphorin receptors are also frequently involved in semaphorin signaling. Recent evidence suggests that semaphorins also fulfill important roles in the etiology of multiple forms of cancer. Some semaphorins have been found to function as bona-fide tumor suppressors and to inhibit tumor progression by various mechanisms while other semaphorins function as inducers and promoters of tumor progression.
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Affiliation(s)
- Gera Neufeld
- Cancer Research and Vascular Biology Center, The Bruce Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel
| | - Yelena Mumblat
- Cancer Research and Vascular Biology Center, The Bruce Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel
| | - Tatyana Smolkin
- Cancer Research and Vascular Biology Center, The Bruce Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel
| | - Shira Toledano
- Cancer Research and Vascular Biology Center, The Bruce Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel
| | - Inbal Nir-Zvi
- Cancer Research and Vascular Biology Center, The Bruce Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel
| | - Keren Ziv
- Cancer Research and Vascular Biology Center, The Bruce Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel
| | - Ofra Kessler
- Cancer Research and Vascular Biology Center, The Bruce Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel
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Neufeld G, Mumblat Y, Smolkin T, Toledano S, Nir-Zvi I, Ziv K, Kessler O. The semaphorins and their receptors as modulators of tumor progression. Drug Resist Updat 2016; 29:1-12. [DOI: 10.1016/j.drup.2016.08.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Revised: 07/31/2016] [Accepted: 08/23/2016] [Indexed: 12/16/2022]
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Loginov VI, Burdennyy AM, Pronina IV, Khokonova VV, Kurevljov SV, Kazubskaya TP, Kushlinskii NE, Braga EA. Novel miRNA genes hypermethylated in breast cancer. Mol Biol 2016. [DOI: 10.1134/s0026893316050101] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Wu ST, Ku WC, Huang CJ, Wang YC, Lin CM, Chen SK. Cellular effects induced by 17-β-estradiol to reduce the survival of renal cell carcinoma cells. J Biomed Sci 2016; 23:67. [PMID: 27680214 PMCID: PMC5041337 DOI: 10.1186/s12929-016-0282-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 08/23/2016] [Indexed: 12/21/2022] Open
Abstract
Background Renal cell carcinoma (RCC) is an adult malignancy with 2:1 men-to-women ratio, which implies the possible role of sex hormones in RCC carcinogenesis. One of the predominant sex hormones in women before menopause, 17-β-estradiol (or E2), may regulate RCC growth by cellular mechanisms that are still not fully understood. Methods The expression levels of E2 receptors (ER1 and ER2) were determined in different RCC cell lines. The DNA damage response induced by E2 was determined by a DNA double-strand break marker γH2AX. To study the possible effect of E2 on oxidative stress response, RCC cells were stained with 2,7-dichlorofluorescein diacetate and analyzed by flow cytometry. Upregulation of nuclear factor (erythroid-derived 2)-like 2 (Nrf2) ser40 phosphorylation in response to oxidative stress was detected by immunoblotting. Finally, annexin V/propidium iodide (PI) double staining assay was used to determine E2-induced cellular apoptosis. Results Variable expression of ER1 and ER2 were found in the RCC cell lines studied (786-O, A498, and ACHN), in which ACHN and A498 showed highest and lowest ER expression, respectively. In A498 cells, E2 induced DNA double-strand breaks with positive staining of γH2AX. On the other hand, the level of reactive oxidative species were elevated in ACHN cells after E2 treatment. The E2-induced oxidative stress also induced the Ser40 phosphorylation and nuclear translocation of Nrf2. Finally, we also demonstrated that E2 induced apoptosis as revealed by annexin V/PI double staining. Conclusions In this study, we demonstrated the cellular effects of E2 on DNA repair, ROS production as well as Nrf2 activation, and apoptosis in RCC cell lines. Together these cellular alterations may contribute to the reduced viability of RCC cells following E2 treatment.
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Affiliation(s)
- Sheng-Tang Wu
- Division of Urology, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Wei-Chi Ku
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei, Taiwan
| | - Chi-Jung Huang
- Department of Biochemistry, National Defense Medical Center, Taipei, Taiwan.,Department of Medical Research, Cathay General Hospital, Taipei, Taiwan
| | - Yen-Chieh Wang
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei, Taiwan.,Department of Surgery, Sijhih Cathay General Hospital, No. 2, Ln. 59, Jiancheng Rd., Sijhih Dist., New Taipei, 22174, Taiwan
| | - Chih-Ming Lin
- Department of Surgery, Cathay General Hospital, Taipei, Taiwan
| | - Shao-Kuan Chen
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei, Taiwan. .,Department of Surgery, Sijhih Cathay General Hospital, No. 2, Ln. 59, Jiancheng Rd., Sijhih Dist., New Taipei, 22174, Taiwan.
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López-Úbeda R, Muñoz M, Vieira L, Hunter RHF, Coy P, Canovas S. The oviductal transcriptome is influenced by a local ovarian effect in the sow. J Ovarian Res 2016; 9:44. [PMID: 27448656 PMCID: PMC4957888 DOI: 10.1186/s13048-016-0252-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 07/03/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Oviducts participate in fertilization and early embryo development, and they are influenced by systemic and local circulation. Local functional interplay between ovary, oviduct and uterus is important, as deduced from the previously observed differences in hormone concentrations, presence of sperm, or patterns of motility in the oviduct after unilateral ovariectomy (UO). However, the consequences of unilateral ovariectomy on the oviductal transcriptome remain unexplored. In this study, we have investigated the consequences of UO in a higher animal model as the pig. METHODS The influence of UO was analyzed on the number of ovulations on the contra ovary, which was increased, and on the ipsilateral oviductal transcriptome. Microarray analysis was performed and the results were validated by PCR. Differentially expressed genes (DEGs) with a fold change ≥ 2 and a false discovery rate of 10 % were analyzed by Ingenuity Pathway Analysis (IPA) to identify the main biofunctions affected by UO. RESULTS Data revealed two principal effects in the ipsilateral oviduct after UO: i) down-regulation of genes involved in the survival of sperm in the oviduct and early embryonic development, and ii) up-regulation of genes involved in others functions as protection against external agents and tumors. CONCLUSIONS Results showed that unilateral ovariectomy results in an increased number of ovulation points on the contra ovary and changes in the transcriptome of the ipsilateral oviduct with consequences on key biological process that could affect fertility output.
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Affiliation(s)
- Rebeca López-Úbeda
- Department of Physiology, Veterinary Faculty, University of Murcia, Campus de Espinardo, 30100, Murcia, Spain.,International Excellence Campus for Higher Education and Research (Campus Mare Nostrum), Murcia, Spain
| | - Marta Muñoz
- Centro de Biotecnología Animal - SERIDA, Deva, Gijón, Asturias, Spain
| | - Luis Vieira
- Department of Physiology, Veterinary Faculty, University of Murcia, Campus de Espinardo, 30100, Murcia, Spain.,International Excellence Campus for Higher Education and Research (Campus Mare Nostrum), Murcia, Spain
| | | | - Pilar Coy
- Department of Physiology, Veterinary Faculty, University of Murcia, Campus de Espinardo, 30100, Murcia, Spain. .,International Excellence Campus for Higher Education and Research (Campus Mare Nostrum), Murcia, Spain. .,IMIB-Arrixaca (Institute for Biomedical Research of Murcia), Murcia, Spain.
| | - Sebastian Canovas
- Department of Physiology, Veterinary Faculty, University of Murcia, Campus de Espinardo, 30100, Murcia, Spain. .,International Excellence Campus for Higher Education and Research (Campus Mare Nostrum), Murcia, Spain. .,IMIB-Arrixaca (Institute for Biomedical Research of Murcia), Murcia, Spain.
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Tang H, Wu Y, Liu M, Qin Y, Wang H, Wang L, Li S, Zhu H, He Z, Luo J, Wang H, Wang Q, Luo S. SEMA3B improves the survival of patients with esophageal squamous cell carcinoma by upregulating p53 and p21. Oncol Rep 2016; 36:900-8. [PMID: 27349960 DOI: 10.3892/or.2016.4901] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 02/18/2016] [Indexed: 12/16/2022] Open
Abstract
As one of the most common malignancies, esophageal squamous cell carcinoma (ESCC) is ranked as the sixth leading cause of cancer-related death worldwide. In our previous study, by employing cDNA microarray analysis, semaphorin 3B (SEMA3B) was found to be significantly downregulated in ESCC. In the present study, SEMA3B downregulation at the mRNA level was found in 34 of 60 primary ESCCs (56.7%) and in 6 of 9 ESCC cell lines (66.7%) by transcription-polymerase chain reaction (RT-PCR). Moreover, immunohistochemical (IHC) staining of SEMA3B in a tissue microarray further indicated that downregulated expression of SEMA3B protein was found in 125 of 222 (56.3%) ESCC cases and downregulation of SEMA3B protein was significantly correlated with lymph node metastasis (P=0.000), advanced clinicopathological stage (P=0.001) and poor disease-specific survival (P=0.017) of ESCC patients. In addition, functional studies demonstrated that the SEMA3B gene could suppress the tumorigenic ability of ESCC cells and cell motility. Furthermore, it was found that by upregulating p53 and p21 expression and inhibiting Akt (Ser473) phosphorylation, SEMA3B could induce cell cycle arrest at G1/S phase. Taken together, our results suggest that SEMA3B may be an important tumor-suppressor gene in the malignant progression of ESCC, as well as a valuable prognostic marker for ESCC patients.
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Affiliation(s)
- Hong Tang
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan 450008, P.R. China
| | - Yufeng Wu
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan 450008, P.R. China
| | - Ming Liu
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong, SAR, L10-56, P.R. China
| | - Yanru Qin
- Department of Clinical Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Haiying Wang
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan 450008, P.R. China
| | - Lili Wang
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan 450008, P.R. China
| | - Shaomei Li
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan 450008, P.R. China
| | - Hui Zhu
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan 450008, P.R. China
| | - Zheng He
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan 450008, P.R. China
| | - Junpeng Luo
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan 450008, P.R. China
| | - Hongyan Wang
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan 450008, P.R. China
| | - Qiming Wang
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan 450008, P.R. China
| | - Suxia Luo
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan 450008, P.R. China
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Krasnov GS, Dmitriev AA, Melnikova NV, Zaretsky AR, Nasedkina TV, Zasedatelev AS, Senchenko VN, Kudryavtseva AV. CrossHub: a tool for multi-way analysis of The Cancer Genome Atlas (TCGA) in the context of gene expression regulation mechanisms. Nucleic Acids Res 2016; 44:e62. [PMID: 26773058 PMCID: PMC4838350 DOI: 10.1093/nar/gkv1478] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 12/05/2015] [Indexed: 02/07/2023] Open
Abstract
The contribution of different mechanisms to the regulation of gene expression varies for different tissues and tumors. Complementation of predicted mRNA–miRNA and gene–transcription factor (TF) relationships with the results of expression correlation analyses derived for specific tumor types outlines the interactions with functional impact in the current biomaterial. We developed CrossHub software, which enables two-way identification of most possible TF–gene interactions: on the basis of ENCODE ChIP-Seq binding evidence or Jaspar prediction and co-expression according to the data of The Cancer Genome Atlas (TCGA) project, the largest cancer omics resource. Similarly, CrossHub identifies mRNA–miRNA pairs with predicted or validated binding sites (TargetScan, mirSVR, PicTar, DIANA microT, miRTarBase) and strong negative expression correlations. We observed partial consistency between ChIP-Seq or miRNA target predictions and gene–TF/miRNA co-expression, demonstrating a link between these indicators. Additionally, CrossHub expression-methylation correlation analysis can be used to identify hypermethylated CpG sites or regions with the greatest potential impact on gene expression. Thus, CrossHub is capable of outlining molecular portraits of a specific gene and determining the three most common sources of expression regulation: promoter/enhancer methylation, miRNA interference and TF-mediated activation or repression. CrossHub generates formatted Excel workbooks with the detailed results. CrossHub is freely available at https://sourceforge.net/projects/crosshub/.
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Affiliation(s)
- George S Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia N.N. Blokhin Russian Cancer Research Center, Moscow 115478, Russia Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Moscow 119121, Russia
| | - Alexey A Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Nataliya V Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Andrew R Zaretsky
- M.M. Shemyakin-Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Tatiana V Nasedkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia N.N. Blokhin Russian Cancer Research Center, Moscow 115478, Russia
| | - Alexander S Zasedatelev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia N.N. Blokhin Russian Cancer Research Center, Moscow 115478, Russia
| | - Vera N Senchenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Anna V Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia N.N. Blokhin Russian Cancer Research Center, Moscow 115478, Russia
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Pronina IV, Loginov VI, Burdennyy AM, Fridman MV, Kazubskaya TP, Dmitriev AA, Braga EA. Expression and DNA methylation alterations of seven cancer-associated 3p genes and their predicted regulator miRNAs (miR-129-2, miR-9-1) in breast and ovarian cancers. Gene 2016; 576:483-91. [PMID: 26519551 DOI: 10.1016/j.gene.2015.10.059] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 10/14/2015] [Accepted: 10/25/2015] [Indexed: 01/05/2023]
Abstract
The methylation of promoter CpG islands and interactions between microRNAs (miRNAs) and messenger RNAs (mRNAs) of target genes are considered two crucial epigenetic mechanisms for inducing gene and pathway deregulation in tumors. Here, the expression levels of seven cancer-associated 3p genes (RASSF1(isoform A), RARB(isoform 2), SEMA3B, RHOA, GPX1, NKIRAS1, and CHL1) and their predicted regulator miRNAs (miR-129-2, miR-9-1) were analyzed in breast (BC, 40 samples) and ovarian (OC, 14 samples) cancers using RT-PCR and qPCR. We first revealed a negative correlation between the level of the miR-129-2 precursor and RASSF1(A) and GPX1 mRNA levels in BC (Spearman's correlation coefficient (rs) was − 0.26 in both cases). Similar results were observed for the miR-129-2 precursor and the RASSF1(A), GPX1, RARB(2), and CHL1 genes in OC (rs was in the range − 0.48 to − 0.54). Using methylation-specific PCR, a significant correlation was shown between promoter hypermethylation and the down-regulation of the RASSF1(A), GPX1, RARB(2), SEMA3B, MIR-129-2, and MIR-9-1 genes in BC (rs = 0.41 to 0.75) and of the RASSF1(A) gene in OC (rs = 0.67). We first demonstrated a high hypermethylation frequency of MIR-129-2 and SEMA3B (up to 45 to 48%) in both BC (69 samples) and OC (41 samples). Moreover, we observed a positive correlation between the hypermethylation of MIR-129-2 and the up-regulation of the RASSF1(A) and GPX1 genes in BC (rs = 0.38 and 0.42, respectively). QPCR analysis of the expression of RASSF1(A) and mature miR-129-2 in additional BC sample set (24 samples) revealed a negative correlation between them (rs = − 0.41) that strengthened the results obtained during the analysis of miR-129-2 precursor level. In summary, the obtained data indicate the involvement of methylation in the down-regulation of the studied coding and miRNA genes and suggest the involvement of miR-129-2 in the deregulation of RASSF1(A) via a direct interaction or/and mediators in common pathways (according to KEGG, Gene Ontology (FDR < 0.01), and GeneCards data) in the examined gynecological tumors.
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