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Liu Y. CWGCNA: an R package to perform causal inference from the WGCNA framework. NAR Genom Bioinform 2024; 6:lqae042. [PMID: 38666214 PMCID: PMC11044439 DOI: 10.1093/nargab/lqae042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 03/17/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
WGCNA (weighted gene co-expression network analysis) is a very useful tool for identifying co-expressed gene modules and detecting their correlations to phenotypic traits. Here, we explored more possibilities about it and developed the R package CWGCNA (causal WGCNA), which works from the traditional WGCNA pipeline but mines more information. It couples a mediation model with WGCNA, so the causal relationships among WGCNA modules, module features, and phenotypes can be found, demonstrating whether the module change causes the phenotype change or vice versa. After that, when annotating the module gene set functions, it uses a novel network-based method, considering the modules' topological structures and capturing their influence on the gene set functions. In addition to conducting these biological explorations, CWGCNA also contains a machine learning section to perform clustering and classification on multi-omics data, given the increasing popularity of this data type. Some basic functions, such as differential feature identification, are also available in our package. Its effectiveness is proved by the performance on three single or multi-omics datasets, showing better performance than existing methods. CWGCNA is available at: https://github.com/yuabrahamliu/CWGCNA.
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Affiliation(s)
- Yu Liu
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
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Yuan M, Yao L, Chen P, Wang Z, Liu P, Xiong Z, Hu X, Li L, Jiang Y. Human umbilical cord mesenchymal stem cells inhibit liver fibrosis via the microRNA-148a-5p/SLIT3 axis. Int Immunopharmacol 2023; 125:111134. [PMID: 37918086 DOI: 10.1016/j.intimp.2023.111134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/08/2023] [Accepted: 10/23/2023] [Indexed: 11/04/2023]
Abstract
BACKGROUND Human umbilical cord-derived mesenchymal stem cells (hUC-MSCs) have garnered considerable attention as prospective modalities of treatment for liver fibrosis (LF). The inhibition of hepatic stellate cell (HSC) activation underlies the anti-fibrotic effects of hUC-MSCs. However, the precise mechanism by which hUC-MSCs impede HSC activation remains unclarified. We aimed to elucidate the intrinsic mechanisms underlying the therapeutic effects of hUC-MSCs in LF patients. METHODS Mice with liver cirrhosis induced by carbon tetrachloride (CCl4) were used as experimental models and administered hUC-MSCs via tail-vein injection. The alterations in inflammation and fibrosis were evaluated through histopathological examinations. RNA sequencing (RNA-seq) and bioinformatics analysis were then conducted to investigate the therapeutic mechanism of hUC-MSCs. Finally, an in-vitro experiment involving the co-cultivation of hUC-MSCs or hUC-MSC-derived exosomes (MSC-Exos) with LX2 cells was performed to validate the potential mechanism underlying the hepatoprotective effects of hUC-MSCs in LF patients. RESULTS hUC-MSC therapy significantly improved liver function and alleviated LF in CCl4-induced mice. High-throughput RNA-Seq analysis identified 1142 differentially expressed genes that were potentially involved in mediating the therapeutic effects of hUC-MSCs. These genes play an important role in regulating the extracellular matrix. miRNA expression data (GSE151098) indicated that the miR-148a-5p level was downregulated in LF samples, but restored following hUC-MSC treatment. miR-148a-5p was delivered to LX2 cells by hUC-MSCs via the exosome pathway, and the upregulated expression of miR-148a-5p significantly suppressed the expression of the activated phenotype of LX2 cells. SLIT3 was identified within the pool of potential target genes regulated by miR-148a-5p. Furthermore, hUC-MSC administration upregulated the expression of miR-148a-5p, which played a crucial role in suppressing the expression of SLIT3, thereby palliating fibrosis. CONCLUSIONS hUC-MSCs inhibit the activation of HSCs through the miR-148a-5p/SLIT3 pathway and are thus capable of alleviating LF.
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Affiliation(s)
- Mengqin Yuan
- Department of Infectious Diseases, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Lichao Yao
- Department of Infectious Diseases, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Ping Chen
- Department of Infectious Diseases, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Zheng Wang
- Department of Infectious Diseases, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Pingji Liu
- Department of Infectious Diseases, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Zhiyu Xiong
- Department of Infectious Diseases, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Xue Hu
- Department of Infectious Diseases, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Lanjuan Li
- Department of Infectious Diseases, Renmin Hospital of Wuhan University, Wuhan 430060, China; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310053, China.
| | - Yingan Jiang
- Department of Infectious Diseases, Renmin Hospital of Wuhan University, Wuhan 430060, China.
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Tawk B, Rein K, Schwager C, Knoll M, Wirkner U, Hörner-Rieber J, Liermann J, Kurth I, Balermpas P, Rödel C, Linge A, Löck S, Lohaus F, Tinhofer I, Krause M, Stuschke M, Grosu AL, Zips D, Combs SE, Belka C, Stenzinger A, Herold-Mende C, Baumann M, Schirmacher P, Debus J, Abdollahi A. DNA-Methylome-Based Tumor Hypoxia Classifier Identifies HPV-Negative Head and Neck Cancer Patients at Risk for Locoregional Recurrence after Primary Radiochemotherapy. Clin Cancer Res 2023; 29:3051-3064. [PMID: 37058257 PMCID: PMC10425733 DOI: 10.1158/1078-0432.ccr-22-3790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/16/2023] [Accepted: 04/11/2023] [Indexed: 04/15/2023]
Abstract
PURPOSE Tumor hypoxia is a paradigmatic negative prognosticator of treatment resistance in head and neck squamous cell carcinoma (HNSCC). The lack of robust and reliable hypoxia classifiers limits the adaptation of stratified therapies. We hypothesized that the tumor DNA methylation landscape might indicate epigenetic reprogramming induced by chronic intratumoral hypoxia. EXPERIMENTAL DESIGN A DNA-methylome-based tumor hypoxia classifier (Hypoxia-M) was trained in the TCGA (The Cancer Genome Atlas)-HNSCC cohort based on matched assignments using gene expression-based signatures of hypoxia (Hypoxia-GES). Hypoxia-M was validated in a multicenter DKTK-ROG trial consisting of human papillomavirus (HPV)-negative patients with HNSCC treated with primary radiochemotherapy (RCHT). RESULTS Although hypoxia-GES failed to stratify patients in the DKTK-ROG, Hypoxia-M was independently prognostic for local recurrence (HR, 4.3; P = 0.001) and overall survival (HR, 2.34; P = 0.03) but not distant metastasis after RCHT in both cohorts. Hypoxia-M status was inversely associated with CD8 T-cell infiltration in both cohorts. Hypoxia-M was further prognostic in the TCGA-PanCancer cohort (HR, 1.83; P = 0.04), underscoring the breadth of this classifier for predicting tumor hypoxia status. CONCLUSIONS Our findings highlight an unexplored avenue for DNA methylation-based classifiers as biomarkers of tumoral hypoxia for identifying high-risk features in patients with HNSCC tumors. See related commentary by Heft Neal and Brenner, p. 2954.
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Affiliation(s)
- Bouchra Tawk
- German Cancer Research Center (DKFZ), Heidelberg, Germany and German Cancer Consortium (DKTK), Core Center Heidelberg, Germany
- Clinical Cooperation Unit Translational Radiation Oncology, National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Molecular and Translational Radiation Oncology, Department of Radiation Oncology, Heidelberg Faculty of Medicine (MFHD) and Heidelberg University Hospital (UKHD), Heidelberg Ion-Beam Therapy Center (HIT), Heidelberg, Germany
- Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Oncology (NCRO), Heidelberg University and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Katrin Rein
- German Cancer Research Center (DKFZ), Heidelberg, Germany and German Cancer Consortium (DKTK), Core Center Heidelberg, Germany
- Clinical Cooperation Unit Translational Radiation Oncology, National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Molecular and Translational Radiation Oncology, Department of Radiation Oncology, Heidelberg Faculty of Medicine (MFHD) and Heidelberg University Hospital (UKHD), Heidelberg Ion-Beam Therapy Center (HIT), Heidelberg, Germany
- Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Oncology (NCRO), Heidelberg University and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christian Schwager
- German Cancer Research Center (DKFZ), Heidelberg, Germany and German Cancer Consortium (DKTK), Core Center Heidelberg, Germany
- Clinical Cooperation Unit Translational Radiation Oncology, National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Molecular and Translational Radiation Oncology, Department of Radiation Oncology, Heidelberg Faculty of Medicine (MFHD) and Heidelberg University Hospital (UKHD), Heidelberg Ion-Beam Therapy Center (HIT), Heidelberg, Germany
- Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Oncology (NCRO), Heidelberg University and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Maximilian Knoll
- German Cancer Research Center (DKFZ), Heidelberg, Germany and German Cancer Consortium (DKTK), Core Center Heidelberg, Germany
- Clinical Cooperation Unit Translational Radiation Oncology, National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Molecular and Translational Radiation Oncology, Department of Radiation Oncology, Heidelberg Faculty of Medicine (MFHD) and Heidelberg University Hospital (UKHD), Heidelberg Ion-Beam Therapy Center (HIT), Heidelberg, Germany
- Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Oncology (NCRO), Heidelberg University and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ute Wirkner
- German Cancer Research Center (DKFZ), Heidelberg, Germany and German Cancer Consortium (DKTK), Core Center Heidelberg, Germany
- Clinical Cooperation Unit Translational Radiation Oncology, National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Molecular and Translational Radiation Oncology, Department of Radiation Oncology, Heidelberg Faculty of Medicine (MFHD) and Heidelberg University Hospital (UKHD), Heidelberg Ion-Beam Therapy Center (HIT), Heidelberg, Germany
- Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Oncology (NCRO), Heidelberg University and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Juliane Hörner-Rieber
- German Cancer Research Center (DKFZ), Heidelberg, Germany and German Cancer Consortium (DKTK), Core Center Heidelberg, Germany
- Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Oncology (NCRO), Heidelberg University and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jakob Liermann
- German Cancer Research Center (DKFZ), Heidelberg, Germany and German Cancer Consortium (DKTK), Core Center Heidelberg, Germany
- Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Oncology (NCRO), Heidelberg University and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ina Kurth
- German Cancer Research Center (DKFZ), Heidelberg, Germany and German Cancer Consortium (DKTK), Core Center Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Dresden, Germany
- OncoRay – National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden - Rossendorf, Dresden, Germany
| | - Panagiotis Balermpas
- German Cancer Research Center (DKFZ), Heidelberg, Germany and German Cancer Consortium (DKTK), partner site, Frankfurt, Germany
- Department of Radiation Oncology, University Hospital Zurich, Zurich, Switzerland
| | - Claus Rödel
- German Cancer Research Center (DKFZ), Heidelberg, Germany and German Cancer Consortium (DKTK), partner site, Frankfurt, Germany
- Department of Radiotherapy and Oncology, Goethe-University Frankfurt, Frankfurt, Germany
| | - Annett Linge
- German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Dresden, Germany
- OncoRay – National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden - Rossendorf, Dresden, Germany
- Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Helmholtz Association and Helmholtz-Zentrum Dresden – Rossendorf (HZDR), Dresden, Germany
| | - Steffen Löck
- German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Dresden, Germany
- OncoRay – National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden - Rossendorf, Dresden, Germany
- Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Fabian Lohaus
- German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Dresden, Germany
- OncoRay – National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden - Rossendorf, Dresden, Germany
- Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Helmholtz Association and Helmholtz-Zentrum Dresden – Rossendorf (HZDR), Dresden, Germany
| | - Ingeborg Tinhofer
- German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Berlin, Germany
- Department of Radiooncology and Radiotherapy, Charité University Hospital, Berlin, Germany
| | - Mechtild Krause
- German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Dresden, Germany
- OncoRay – National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden - Rossendorf, Dresden, Germany
- Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Helmholtz Association and Helmholtz-Zentrum Dresden – Rossendorf (HZDR), Dresden, Germany
| | - Martin Stuschke
- German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Essen, Germany
- Department of Radiotherapy, Medical Faculty, University of Duisburg-Essen, Essen, Germany
| | - Anca Ligia Grosu
- German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Freiburg, Germany
- Department of Radiation Oncology, University of Freiburg, Freiburg, Germany
| | - Daniel Zips
- German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Berlin, Germany
- Department of Radiooncology and Radiotherapy, Charité University Hospital, Berlin, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany, German Cancer Consortium (DKTK), partner site Tuebingen, Germany
- Department of Radiation Oncology, Faculty of Medicine and University Hospital Tübingen, Eberhard Karls Universität Tübingen, Germany
| | - Stephanie E. Combs
- German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Munich, Germany
- Department of Radiation Oncology, Technische Universität München, Munich, Germany
| | - Claus Belka
- German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Munich, Germany
- Department of Radiation Oncology, University Hospital Ludwig-Maximilians-University of Munich, Munich, Germany
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Albrecht Stenzinger
- German Cancer Research Center (DKFZ), Heidelberg, Germany and German Cancer Consortium (DKTK), Core Center Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Christel Herold-Mende
- Division of Experimental Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Michael Baumann
- German Cancer Research Center (DKFZ), Heidelberg, Germany and German Cancer Consortium (DKTK), Core Center Heidelberg, Germany
- Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Oncology (NCRO), Heidelberg University and German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Dresden, Germany
- OncoRay – National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden - Rossendorf, Dresden, Germany
- Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Peter Schirmacher
- German Cancer Research Center (DKFZ), Heidelberg, Germany and German Cancer Consortium (DKTK), Core Center Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Jürgen Debus
- German Cancer Research Center (DKFZ), Heidelberg, Germany and German Cancer Consortium (DKTK), Core Center Heidelberg, Germany
- Clinical Cooperation Unit Translational Radiation Oncology, National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Molecular and Translational Radiation Oncology, Department of Radiation Oncology, Heidelberg Faculty of Medicine (MFHD) and Heidelberg University Hospital (UKHD), Heidelberg Ion-Beam Therapy Center (HIT), Heidelberg, Germany
- Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Oncology (NCRO), Heidelberg University and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Amir Abdollahi
- German Cancer Research Center (DKFZ), Heidelberg, Germany and German Cancer Consortium (DKTK), Core Center Heidelberg, Germany
- Clinical Cooperation Unit Translational Radiation Oncology, National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Molecular and Translational Radiation Oncology, Department of Radiation Oncology, Heidelberg Faculty of Medicine (MFHD) and Heidelberg University Hospital (UKHD), Heidelberg Ion-Beam Therapy Center (HIT), Heidelberg, Germany
- Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Oncology (NCRO), Heidelberg University and German Cancer Research Center (DKFZ), Heidelberg, Germany
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Feng L, Shu HP, Sun LL, Tu YC, Liao QQ, Yao LJ. Role of the SLIT-ROBO signaling pathway in renal pathophysiology and various renal diseases. Front Physiol 2023; 14:1226341. [PMID: 37497439 PMCID: PMC10366692 DOI: 10.3389/fphys.2023.1226341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 06/30/2023] [Indexed: 07/28/2023] Open
Abstract
SLIT ligand and its receptor ROBO were initially recognized for their role in axon guidance in central nervous system development. In recent years, as research has advanced, the role of the SLIT-ROBO signaling pathway has gradually expanded from axonal repulsion to cell migration, tumor development, angiogenesis, and bone metabolism. As a secreted protein, SLIT regulates various pathophysiological processes in the kidney, such as proinflammatory responses and fibrosis progression. Many studies have shown that SLIT-ROBO is extensively involved in various aspects of kidney development and maintenance of structure and function. The SLIT-ROBO signaling pathway also plays an important role in different types of kidney disease. This article reviews the advances in the study of the SLIT-ROBO pathway in various renal pathophysiological and kidney disorders and proposes new directions for further research in this field.
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Li L, Yang W, Jia D, Zheng S, Gao Y, Wang G. Establishment of a N1-methyladenosine-related risk signature for breast carcinoma by bioinformatics analysis and experimental validation. Breast Cancer 2023:10.1007/s12282-023-01458-1. [PMID: 37178414 DOI: 10.1007/s12282-023-01458-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 04/09/2023] [Indexed: 05/15/2023]
Abstract
OBJECTIVES Breast carcinoma (BRCA) has resulted in a huge health burden globally. N1-methyladenosine (m1A) RNA methylation has been proven to play key roles in tumorigenesis. Nevertheless, the function of m1A RNA methylation-related genes in BRCA is indistinct. METHODS The RNA sequencing (RNA-seq), copy-number variation (CNV), single-nucleotide variant (SNV), and clinical data of BRCA were acquired via The Cancer Genome Atlas (TCGA) database. In addition, the GSE20685 dataset, the external validation set, was acquired from the Gene Expression Omnibus (GEO) database. 10 m1A RNA methylation regulators were obtained from the previous literature, and further analyzed through differential expression analysis by rank-sum test, mutation by SNV data, and mutual correlation by Pearson Correlation Analysis. Furthermore, the differentially expressed m1A-related genes were selected through overlapping m1A-related module genes obtained by weighted gene co-expression network analysis (WGCNA), differentially expressed genes (DEGs) in BRCA and DEGs between high- and low- m1A score subgroups. The m1A-related model genes in the risk signature were derived by univariate Cox and least absolute shrinkage and selection operator (LASSO) regression analyses. In addition, a nomogram was built through univariate and multivariate Cox analyses. After that, the immune infiltration between the high- and low-risk groups was investigated through ESTIMATE and CIBERSORT. Finally, the expression trends of model genes in clinical BRCA samples were further confirmed by quantitative real-time PCR (RT‒qPCR). RESULTS Eighty-five differentially expressed m1A-related genes were obtained. Among them, six genes were selected as prognostic biomarkers to build the risk model. The validation results of the risk model showed that its prediction was reliable. In addition, Cox independent prognosis analysis revealed that age, risk score, and stage were independent prognostic factors for BRCA. Moreover, 13 types of immune cells were different between the high- and low-risk groups and the immune checkpoint molecules TIGIT, IDO1, LAG3, ICOS, PDCD1LG2, PDCD1, CD27, and CD274 were significantly different between the two risk groups. Ultimately, RT-qPCR results confirmed that the model genes MEOX1, COL17A1, FREM1, TNN, and SLIT3 were significantly up-regulated in BRCA tissues versus normal tissues. CONCLUSIONS An m1A RNA methylation regulator-related prognostic model was constructed, and a nomogram based on the prognostic model was constructed to provide a theoretical reference for individual counseling and clinical preventive intervention in BRCA.
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Affiliation(s)
- Leilei Li
- Department of Pathology, Kunming Medical University, Kunming, Yunnan, 650500, People's Republic of China
| | - Wenhui Yang
- Department of Digestive Oncology, Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030032, People's Republic of China
| | - Daqi Jia
- Department of Pathology, Kunming Medical University, Kunming, Yunnan, 650500, People's Republic of China
| | - Shiqi Zheng
- Department of Pathology, Kunming Medical University, Kunming, Yunnan, 650500, People's Republic of China
| | - Yuzhe Gao
- Department of Breast Surgery, Guizhou Provincial People's Hospital, Guiyang, Guizhou, 550002, People's Republic of China.
| | - Guanghui Wang
- Department of Breast Surgery, Guizhou Provincial People's Hospital, Guiyang, Guizhou, 550002, People's Republic of China.
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Cui Y, Wang X, Zhang L, Liu W, Ning J, Gu R, Cui Y, Cai L, Xing Y. A novel epithelial-mesenchymal transition (EMT)-related gene signature of predictive value for the survival outcomes in lung adenocarcinoma. Front Oncol 2022; 12:974614. [PMID: 36185284 PMCID: PMC9521574 DOI: 10.3389/fonc.2022.974614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/30/2022] [Indexed: 11/24/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is a remarkably heterogeneous and aggressive disease with dismal prognosis of patients. The identification of promising prognostic biomarkers might enable effective diagnosis and treatment of LUAD. Aberrant activation of epithelial-mesenchymal transition (EMT) is required for LUAD initiation, progression and metastasis. With the purpose of identifying a robust EMT-related gene signature (E-signature) to monitor the survival outcomes of LUAD patients. In The Cancer Genome Atlas (TCGA) database, least absolute shrinkage and selection operator (LASSO) analysis and cox regression analysis were conducted to acquire prognostic and EMT-related genes. A 4 EMT-related and prognostic gene signature, comprising dickkopf-like protein 1 (DKK1), lysyl oxidase-like 2 (LOXL2), matrix Gla protein (MGP) and slit guidance ligand 3 (SLIT3), was identified. By the usage of datum derived from TCGA database and Western blotting analysis, compared with adjacent tissue samples, DKK1 and LOXL2 protein expression in LUAD tissue samples were significantly higher, whereas the trend of MGP and SLIT3 expression were opposite. Concurrent with upregulation of epithelial markers and downregulation of mesenchymal markers, knockdown of DKK1 and LOXL2 impeded the migration and invasion of LUAD cells. Simultaneously, MGP and SLIT3 silencing promoted metastasis and induce EMT of LUAD cells. In the TCGA-LUAD set, receiver operating characteristic (ROC) analysis indicated that our risk model based on the identified E-signature was superior to those reported in literatures. Additionally, the E-signature carried robust prognostic significance. The validity of prediction in the E-signature was validated by the three independent datasets obtained from Gene Expression Omnibus (GEO) database. The probabilistic nomogram including the E-signature, pathological T stage and N stage was constructed and the nomogram demonstrated satisfactory discrimination and calibration. In LUAD patients, the E-signature risk score was associated with T stage, N stage, M stage and TNM stage. GSEA (gene set enrichment analysis) analysis indicated that the E-signature might be linked to the pathways including GLYCOLYSIS, MYC TARGETS, DNA REPAIR and so on. In conclusion, our study explored an innovative EMT based prognostic signature that might serve as a potential target for personalized and precision medicine.
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Affiliation(s)
- Yimeng Cui
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Xin Wang
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Lei Zhang
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Wei Liu
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jinfeng Ning
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Ruixue Gu
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yaowen Cui
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Li Cai
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
- *Correspondence: Ying Xing, ; Li Cai,
| | - Ying Xing
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
- *Correspondence: Ying Xing, ; Li Cai,
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Trefzer TB, Schneider MA, Jechow K, Chua RL, Muley T, Winter H, Kriegsmann M, Meister M, Eils R, Conrad C. Intratumoral Heterogeneity and Immune Modulation in Lung Adenocarcinoma in Female Smokers and Never Smokers. Cancer Res 2022; 82:3116-3129. [PMID: 35819252 PMCID: PMC9437562 DOI: 10.1158/0008-5472.can-21-3836] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 04/13/2022] [Accepted: 07/08/2022] [Indexed: 01/07/2023]
Abstract
SIGNIFICANCE Single-cell analysis of healthy lung tissue and lung cancer reveals distinct tumor cell populations, including cells with differential immune modulating capacity between smokers and never smokers, which could guide future therapeutic strategies.
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Affiliation(s)
- Timo B. Trefzer
- Charité - Universitätsmedizin Berlin and Berlin Institute of Health, Digital Health Center, Berlin, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marc A. Schneider
- Translational Research Unit, Thoraxklinik, Heidelberg University Hospital, Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Katharina Jechow
- Charité - Universitätsmedizin Berlin and Berlin Institute of Health, Digital Health Center, Berlin, Germany
| | - Robert Lorenz Chua
- Charité - Universitätsmedizin Berlin and Berlin Institute of Health, Digital Health Center, Berlin, Germany
| | - Thomas Muley
- Translational Research Unit, Thoraxklinik, Heidelberg University Hospital, Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Hauke Winter
- Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany.,Department of Surgery, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
| | - Mark Kriegsmann
- Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany.,Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Michael Meister
- Translational Research Unit, Thoraxklinik, Heidelberg University Hospital, Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Roland Eils
- Charité - Universitätsmedizin Berlin and Berlin Institute of Health, Digital Health Center, Berlin, Germany.,Health Data Science Unit, Heidelberg University Hospital and BioQuant, Heidelberg, Germany
| | - Christian Conrad
- Charité - Universitätsmedizin Berlin and Berlin Institute of Health, Digital Health Center, Berlin, Germany.,Corresponding Author: Christian Conrad, Charité - Universitätsmedizin Berlin and Berlin Institute of Health, Digital Health Center, Kapelle-Ufer 2, Berlin 10117, Germany. Phone: 4930-4505-43097; E-mail:
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8
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Aberrant Methylation of SLIT2 Gene in Plasma Cell-Free DNA of Non-Small Cell Lung Cancer Patients. Cancers (Basel) 2022; 14:cancers14020296. [PMID: 35053460 PMCID: PMC8773699 DOI: 10.3390/cancers14020296] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/02/2022] [Accepted: 01/04/2022] [Indexed: 12/04/2022] Open
Abstract
Simple Summary Despite significant advances in the detection, prevention, and treatment of lung cancer, the prognosis of the patients is still very poor due in part to micrometastasis of cancer cells to surrounding tissues at the time of diagnosis. Therefore, identifying biomarkers for early detection of lung cancer is very important for prolonging the lifespan of patients with lung cancer. The methylation statuses of SLIT1, SLIT2, SLIT3 genes were analyzed in bronchial washing, bronchial biopsy, sputum, tumor and matched normal tissues, or plasma samples obtained from a total of 208 non-small cell lung cancer (NSCLC) patients and 121 cancer-free patients to understand the feasibility of the genes as biomarkers for early detection and survival prediction of NSCLC. The present study suggests that aberrant methylation of SLIT2 in plasma cell-free DNA might be a potential biomarker for the early detection and prognosis prediction of NSCLC patient. Abstract This study aimed to understand aberrant methylation of SLITs genes as a biomarker for the early detection and prognosis prediction of non-small cell lung cancer (NSCLC). Methylation levels of SLITs were determined using the Infinium HumanMethylation450 BeadChip or pyrosequencing. Five CpGs at the CpG island of SLIT1, SLIT2 or SLIT3 genes were significantly (Bonferroni corrected p < 0.05) hypermethylated in tumor tissues obtained from 42 NSCLC patients than in matched normal tissues. Methylation levels of these CpGs did not differ significantly between bronchial washings obtained from 76 NSCLC patients and 60 cancer-free patients. However, methylation levels of SLIT2 gene were significantly higher in plasma cell-free DNA of 72 NSCLC patients than in that of 61 cancer-free patients (p = 0.001, Wilcoxon rank sum test). Prediction of NSCLC using SLIT2 methylation was achieved with a sensitivity of 73.7% and a specificity of 61.9% in a plasma test dataset (N = 40). A Cox proportional hazards model showed that SLIT2 hypermethylation in plasma cell-free DNA was significantly associated with poor recurrence-free survival (hazards ratio = 2.19, 95% confidence interval = 1.21–4.36, p = 0.01). The present study suggests that aberrant methylation of SLIT2 in plasma cell-free DNA is a valuable biomarker for the early detection of NSCLC and prediction of recurrence-free survival. However, further research is needed with larger sample size to confirm results.
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9
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Ozhan A, Tombaz M, Konu O. Discovery of Cancer-Specific and Independent Prognostic Gene Subsets of the Slit-Robo Family Using TCGA-PANCAN Datasets. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:782-795. [PMID: 34757814 DOI: 10.1089/omi.2021.0097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The Slit-Robo family of axon guidance molecules works in concert, playing important roles in organ development and cancer. Expressions of individual Slit-Robo genes have been used in calculating univariable hazard ratios (HRuni) for predicting cancer prognosis in the literature. However, Slit-Robo members do not act independently; hence, hazard ratios from multivariable Cox regression (HRmulti) on the whole gene set can further lead to identification of cancer-specific, novel, and independent prognostic gene pairs or modules. Herein, we obtained mRNA expressions of the Slit-Robo family consisting of four Robos (ROBO1/2/3/4) and three Slits (SLIT1/2/3), along with four types of survival outcome across cancers found in the Cancer Genome Atlas (TCGA). We used cluster heat maps to visualize closely associated pairs/modules of prognostic genes across 33 different cancers. We found a smaller number of significant genes in HRmulti than in HRuni, suggesting that the former analysis was less redundant. High ROBO4 expression emerged as relatively protective within the family, in both types of HR analyses. Multivariable Cox regression, on the other hand, revealed significantly more HR signatures containing Slit-Robo pairs acting in opposing directions than those containing Slit-Slit or Robo-Robo pairs for disease-specific survival. Furthermore, we discovered, through the online app SmulTCan's lasso regression, Slit-Robo gene subsets that significantly differentiated between high- versus low-risk prognosis patient groups, particularly for renal cancers and low-grade glioma. The statistical pipeline reported herein can help test independent and significant pairs/modules within a codependent gene family for cancer prognostication, and thus should also prove useful in personalized/precision medicine research.
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Affiliation(s)
- Ayse Ozhan
- UNAM-National Nanotechnology Research Center, Institute of Material Science and Nanotechnology, Bilkent University, Ankara, Turkey
| | - Melike Tombaz
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara, Turkey
| | - Ozlen Konu
- UNAM-National Nanotechnology Research Center, Institute of Material Science and Nanotechnology, Bilkent University, Ankara, Turkey.,Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara, Turkey.,Interdisciplinary Graduate Program in Neuroscience, Aysel Sabuncu Brain Research Center, Bilkent University, Ankara, Turkey
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10
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Protein Ligands in the Secretome of CD36 + Fibroblasts Induce Growth Suppression in a Subset of Breast Cancer Cell Lines. Cancers (Basel) 2021; 13:cancers13184521. [PMID: 34572749 PMCID: PMC8469330 DOI: 10.3390/cancers13184521] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/03/2021] [Accepted: 09/05/2021] [Indexed: 01/07/2023] Open
Abstract
Simple Summary Human breast cancers are not fully autonomous. They are dependent on nutrients and growth-promoting signals provided by stromal cells. In order to instruct the surrounding cells to provide essential growth factors, cancer cells co-opt normal signaling molecules and mechanisms. To inhibit or potentially reverse tumor growth, our goal is to emulate this signaling and reprogram the microenvironment. For example, in a healthy mammary gland, fibroblasts (FBs) overexpress CD36; and the downregulation of CD36 is one of the hallmarks of cancer-associated FBs. Therefore, in this project, we hypothesized that signaling from CD36+ FBs could cause growth suppression in a subset of breast cancer cell lines. We then designed a series of experiments to validate this growth suppression and identified responsible secreted factors by the CD36+ FBs. These experiments suggested that three protein ligands are primarily responsible for growth suppression in a subset of breast cancer cell lines. Abstract Reprogramming the tumor stroma is an emerging approach to circumventing the challenges of conventional cancer therapies. This strategy, however, is hampered by the lack of a specific molecular target. We previously reported that stromal fibroblasts (FBs) with high expression of CD36 could be utilized for this purpose. These studies are now expanded to identify the secreted factors responsible for tumor suppression. Methodologies included 3D colonies, fluorescent microscopy coupled with quantitative techniques, proteomics profiling, and bioinformatics analysis. The results indicated that the conditioned medium (CM) of the CD36+ FBs caused growth suppression via apoptosis in the triple-negative cell lines of MDA-MB-231, BT549, and Hs578T, but not in the ERBB2+ SKBR3. Following the proteomics and bioinformatic analysis of the CM of CD36+ versus CD36− FBs, we determined KLF10 as one of the transcription factors responsible for growth suppression. We also identified FBLN1, SLIT3, and PENK as active ligands, where their minimum effective concentrations were determined. Finally, in MDA-MB-231, we showed that a mixture of FBLN1, SLIT3, and PENK could induce an amount of growth suppression similar to the CM of CD36+ FBs. In conclusion, our findings suggest that these ligands, secreted by CD36+ FBs, can be targeted for breast cancer treatment.
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11
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Marulanda K, Brokaw D, Gambarian M, Pareta R, McQuilling JP, Opara EC, McLean SE. Controlled Delivery of Slit3 Proteins from Alginate Microbeads Inhibits In Vitro Angiogenesis. J Surg Res 2021; 264:90-98. [PMID: 33794389 DOI: 10.1016/j.jss.2021.01.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 12/15/2020] [Accepted: 01/25/2021] [Indexed: 11/19/2022]
Abstract
BACKGROUND The Slit-Robo pathway is a key regulator of angiogenesis and cellular function in experimental models. Slit3 proteins exhibit both proangiogenic and antiangiogenic properties, but the exact mechanism remains unclear. It is theorized that Slit3 may be a potential treatment for vascular diseases and cancer. METHODS Slit3 labeled with I-125 was encapsulated in microbeads composed of low-viscosity alginate of high-glucuronic acid content, first coated with poly-L-ornithine for various durations and finally with low-viscosity high mannuronic acid. Gamma counter was used to measure microbead encapsulation efficiency and Slit3 release. Markers of angiogenesis were assessed with Boyden chamber, scratch wound, and Matrigel tube formation assays using human umbilical vein and mouse endothelial cells. RESULTS On incubation of Slit3-loaded microbeads, there was an initial burst phase release of Slit3 for the first 24 h followed by sustained release for 6 to 12 d. Microbead composition determined encapsulation efficiency and rate of release; Slit3 encapsulation was most efficient in microbeads with lower low-viscosity alginate of high-glucuronic acid content concentrations (1.5%) and no poly-L-ornithine coating. Compared with controls (media alone), Slit3 microbeads significantly inhibited in vitro cellular migration, endothelial cell migration for wound closure at 24 and 48 h and endothelial tube formation (P < 0.001, respectively). CONCLUSIONS Slit3 can be effectively encapsulated and delivered via a controlled release pattern using alginate microbeads. Microbead encapsulation reduces in vitro endothelial tube formation and inhibits cellular migration to impair angiogenesis. Thus, Slit3 microparticles may be explored as a therapeutic option to mitigate tumor proliferation.
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Affiliation(s)
- Kathleen Marulanda
- Department of Surgery, University of North Carolina, Chapel Hill, North Carolina
| | - Dylan Brokaw
- Department of Surgery, University of North Carolina, Chapel Hill, North Carolina
| | - Maria Gambarian
- Department of Surgery, University of North Carolina, Chapel Hill, North Carolina
| | - Rajesh Pareta
- Wake Forest Institute for Regenerative Medicine, Wake Forest University School of Medicine, Winston Salem, North Carolina
| | - John P McQuilling
- Wake Forest Institute for Regenerative Medicine, Wake Forest University School of Medicine, Winston Salem, North Carolina
| | - Emmanuel C Opara
- Wake Forest Institute for Regenerative Medicine, Wake Forest University School of Medicine, Winston Salem, North Carolina
| | - Sean E McLean
- Department of Surgery, University of North Carolina, Chapel Hill, North Carolina.
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12
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Identification of Key circRNAs in Non-Small Cell Lung Cancer. Am J Med Sci 2021; 361:98-105. [DOI: 10.1016/j.amjms.2020.08.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 05/31/2020] [Accepted: 08/07/2020] [Indexed: 12/14/2022]
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13
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Jones TK, Christie JD. Discovery through Diversity: Insights into the Genetics of Lung Function in Latino Youth. Am J Respir Crit Care Med 2020; 202:913-914. [PMID: 32692576 PMCID: PMC7528776 DOI: 10.1164/rccm.202006-2404ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Tiffanie K Jones
- Division of Pulmonary, Allergy, and Critical Care Medicine and Center for Translational Lung Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Jason D Christie
- Division of Pulmonary, Allergy, and Critical Care Medicine and Center for Translational Lung Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
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14
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Lee EY, Mak ACY, Hu D, Sajuthi S, White MJ, Keys KL, Eckalbar W, Bonser L, Huntsman S, Urbanek C, Eng C, Jain D, Abecasis G, Kang HM, Germer S, Zody MC, Nickerson DA, Erle D, Ziv E, Rodriguez-Santana J, Seibold MA, Burchard EG. Whole-Genome Sequencing Identifies Novel Functional Loci Associated with Lung Function in Puerto Rican Youth. Am J Respir Crit Care Med 2020; 202:962-972. [PMID: 32459537 PMCID: PMC7528787 DOI: 10.1164/rccm.202002-0351oc] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/27/2020] [Indexed: 12/22/2022] Open
Abstract
Rationale: Puerto Ricans have the highest childhood asthma prevalence in the United States (23.6%); however, the etiology is uncertain.Objectives: In this study, we sought to uncover the genetic architecture of lung function in Puerto Rican youth with and without asthma who were recruited from the island (n = 836).Methods: We used admixture-mapping and whole-genome sequencing data to discover genomic regions associated with lung function. Functional roles of the prioritized candidate SNPs were examined with chromatin immunoprecipitation sequencing, RNA sequencing, and expression quantitative trait loci data.Measurements and Main Results: We discovered a genomic region at 1q32 that was significantly associated with a 0.12-L decrease in the lung volume of exhaled air (95% confidence interval, -0.17 to -0.07; P = 6.62 × 10-8) with each allele of African ancestry. Within this region, two SNPs were expression quantitative trait loci of TMEM9 in nasal airway epithelial cells and MROH3P in esophagus mucosa. The minor alleles of these SNPs were associated with significantly decreased lung function and decreased TMEM9 gene expression. Another admixture-mapping peak was observed on chromosome 5q35.1, indicating that each Native American ancestry allele was associated with a 0.15-L increase in lung function (95% confidence interval, 0.08-0.21; P = 5.03 × 10-6). The region-based association tests identified four suggestive windows that harbored candidate rare variants associated with lung function.Conclusions: We identified common and rare genetic variants that may play a critical role in lung function among Puerto Rican youth. We independently validated an inflammatory pathway that could potentially be used to develop more targeted treatments and interventions for patients with asthma.
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Affiliation(s)
- Eunice Y. Lee
- Department of Bioengineering and Therapeutic Sciences and
- Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Angel C. Y. Mak
- Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Donglei Hu
- Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Satria Sajuthi
- Department of Pediatrics, Center for Genes, Environment, and Health, and
| | - Marquitta J. White
- Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Kevin L. Keys
- Department of Medicine, University of California, San Francisco, San Francisco, California
| | | | - Luke Bonser
- Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Scott Huntsman
- Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Cydney Urbanek
- Department of Pediatrics, Center for Genes, Environment, and Health, and
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, San Francisco, California
| | | | - Gonçalo Abecasis
- Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan
- Regeneron Pharmaceuticals, Tarrytown, New York
| | - Hyun M. Kang
- Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan
| | | | | | - Deborah A. Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington
- Northwest Genomics Center, Seattle, Washington
- Brotman Baty Institute, Seattle, Washington
| | - David Erle
- Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Elad Ziv
- Department of Medicine, University of California, San Francisco, San Francisco, California
| | | | - Max A. Seibold
- Department of Pediatrics, Center for Genes, Environment, and Health, and
- Department of Pediatrics, National Jewish Health, Denver, Colorado
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado–Anschutz Medical Campus, Aurora, Colorado
| | - Esteban G. Burchard
- Department of Bioengineering and Therapeutic Sciences and
- Department of Medicine, University of California, San Francisco, San Francisco, California
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15
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Wang S, Huang S, Johnson S, Rosin V, Lee J, Colomb E, Witt R, Jaworski A, Weiss SJ, Si M. Tissue-specific angiogenic and invasive properties of human neonatal thymus and bone MSCs: Role of SLIT3-ROBO1. Stem Cells Transl Med 2020; 9:1102-1113. [PMID: 32470195 PMCID: PMC7445019 DOI: 10.1002/sctm.19-0448] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 04/05/2020] [Accepted: 05/03/2020] [Indexed: 12/13/2022] Open
Abstract
Although mesenchymal stem/stromal cells (MSCs) are being explored in numerous clinical trials as proangiogenic and proregenerative agents, the influence of tissue origin on the therapeutic qualities of these cells is poorly understood. Complicating the functional comparison of different types of MSCs are the confounding effects of donor age, genetic background, and health status of the donor. Leveraging a clinical setting where MSCs can be simultaneously isolated from discarded but healthy bone and thymus tissues from the same neonatal patients, thereby controlling for these confounding factors, we performed an in vitro and in vivo paired comparison of these cells. We found that both neonatal thymus (nt)MSCs and neonatal bone (nb)MSCs expressed different pericytic surface marker profiles. Further, ntMSCs were more potent in promoting angiogenesis in vitro and in vivo and they were also more motile and efficient at invading ECM in vitro. These functional differences were in part mediated by an increased ntMSC expression of SLIT3, a factor known to activate endothelial cells. Further, we discovered that SLIT3 stimulated MSC motility and fibrin gel invasion via ROBO1 in an autocrine fashion. Consistent with our findings in human MSCs, we found that SLIT3 and ROBO1 were expressed in the perivascular cells of the neonatal murine thymus gland and that global SLIT3 or ROBO1 deficiency resulted in decreased neonatal murine thymus gland vascular density. In conclusion, ntMSCs possess increased proangiogenic and invasive behaviors, which are in part mediated by the paracrine and autocrine effects of SLIT3.
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Affiliation(s)
- Shuyun Wang
- Department of Cardiac Surgery, Section of Pediatric Cardiovascular SurgeryUniversity of MichiganAnn ArborMichiganUSA
| | - Shan Huang
- Department of Cardiac Surgery, Section of Pediatric Cardiovascular SurgeryUniversity of MichiganAnn ArborMichiganUSA
| | - Sean Johnson
- Department of Cardiac Surgery, Section of Pediatric Cardiovascular SurgeryUniversity of MichiganAnn ArborMichiganUSA
| | - Vadim Rosin
- Department of Cardiac Surgery, Section of Pediatric Cardiovascular SurgeryUniversity of MichiganAnn ArborMichiganUSA
| | - Jeffrey Lee
- Department of Cardiac Surgery, Section of Pediatric Cardiovascular SurgeryUniversity of MichiganAnn ArborMichiganUSA
| | - Eric Colomb
- Department of Cardiac Surgery, Section of Pediatric Cardiovascular SurgeryUniversity of MichiganAnn ArborMichiganUSA
| | - Russell Witt
- Department of General SurgeryBrigham and Women's HospitalMassachusettsUSA
| | | | - Stephen J. Weiss
- Department of Internal MedicineUniversity of MichiganAnn ArborMichiganUSA
| | - Ming‐Sing Si
- Department of Cardiac Surgery, Section of Pediatric Cardiovascular SurgeryUniversity of MichiganAnn ArborMichiganUSA
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16
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Gerashchenko TS, Zolotaryova SY, Kiselev AM, Tashireva LA, Novikov NM, Krakhmal NV, Cherdyntseva NV, Zavyalova MV, Perelmuter VM, Denisov EV. The Activity of KIF14, Mieap, and EZR in a New Type of the Invasive Component, Torpedo-Like Structures, Predetermines the Metastatic Potential of Breast Cancer. Cancers (Basel) 2020; 12:E1909. [PMID: 32679794 PMCID: PMC7409151 DOI: 10.3390/cancers12071909] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/29/2020] [Accepted: 07/13/2020] [Indexed: 12/29/2022] Open
Abstract
Intratumor morphological heterogeneity reflects patterns of invasive growth and is an indicator of the metastatic potential of breast cancer. In this study, we used this heterogeneity to identify molecules associated with breast cancer invasion and metastasis. The gene expression microarray data were used to identify genes differentially expressed between solid, trabecular, and other morphological arrangements of tumor cells. Immunohistochemistry was applied to evaluate the association of the selected proteins with metastasis. RNA-sequencing was performed to analyze the molecular makeup of metastatic tumor cells. High frequency of metastases and decreased metastasis-free survival were detected in patients either with positive expression of KIF14 or Mieap or negative expression of EZR at the tips of the torpedo-like structures in breast cancers. KIF14- and Mieap-positive and EZR-negative cells were mainly detected in the torpedo-like structures of the same breast tumors; however, their transcriptomic features differed. KIF14-positive cells showed a significant upregulation of genes involved in ether lipid metabolism. Mieap-positive cells were enriched in genes involved in mitophagy. EZR-negative cells displayed upregulated genes associated with phagocytosis and the chemokine-mediated signaling pathway. In conclusion, the positive expression of KIF14 and Mieap and negative expression of EZR at the tips of the torpedo-like structures are associated with breast cancer metastasis.
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Affiliation(s)
- Tatiana S. Gerashchenko
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 634009 Tomsk, Russia; (T.S.G.); (S.Y.Z.); (A.M.K.); (N.M.N.)
| | - Sofia Y. Zolotaryova
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 634009 Tomsk, Russia; (T.S.G.); (S.Y.Z.); (A.M.K.); (N.M.N.)
| | - Artem M. Kiselev
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 634009 Tomsk, Russia; (T.S.G.); (S.Y.Z.); (A.M.K.); (N.M.N.)
- Institute of Cytology, Russian Academy of Sciences, 194064 Saint Petersburg, Russia
| | - Liubov A. Tashireva
- Department of General and Molecular Pathology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 634009 Tomsk, Russia; (L.A.T.); (M.V.Z.); (V.M.P.)
| | - Nikita M. Novikov
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 634009 Tomsk, Russia; (T.S.G.); (S.Y.Z.); (A.M.K.); (N.M.N.)
| | - Nadezhda V. Krakhmal
- Department of Pathological Anatomy, Siberian State Medical University, 634050 Tomsk, Russia;
| | - Nadezhda V. Cherdyntseva
- Laboratory of Molecular Oncology and Immunology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 634009 Tomsk, Russia;
| | - Marina V. Zavyalova
- Department of General and Molecular Pathology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 634009 Tomsk, Russia; (L.A.T.); (M.V.Z.); (V.M.P.)
- Department of Pathological Anatomy, Siberian State Medical University, 634050 Tomsk, Russia;
| | - Vladimir M. Perelmuter
- Department of General and Molecular Pathology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 634009 Tomsk, Russia; (L.A.T.); (M.V.Z.); (V.M.P.)
| | - Evgeny V. Denisov
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 634009 Tomsk, Russia; (T.S.G.); (S.Y.Z.); (A.M.K.); (N.M.N.)
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17
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Yuan M, Xie F, Xia X, Zhong K, Lian L, Zhang S, Yuan L, Ye J. UNC5C‑knockdown enhances the growth and metastasis of breast cancer cells by potentiating the integrin α6/β4 signaling pathway. Int J Oncol 2020; 56:139-150. [PMID: 31789389 PMCID: PMC6910211 DOI: 10.3892/ijo.2019.4931] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Accepted: 11/13/2019] [Indexed: 02/06/2023] Open
Abstract
Unc‑5 Netrin Receptor C (UNC5C) is a netrin‑1 dependence receptor that mediates the induction of apoptosis in the absence of netrin‑1. The present study found that UNC5C is heterogeneously expressed in breast cancer cell lines. By knocking down UNC5C in SK‑BR‑3 and ZR‑75‑30 cells and overexpressing UNC5c in MDA‑MB‑231 cells, it was demonstrated that UNC5C exerts an inhibitory effect on the growth and metastasis of breast cancer cells. The mechanism involved a UNC5C‑knockdown‑induced enhancement of matrix metalloproteinase (MMP)3, MMP7, MMP9 and MMP10 expression via activation of the PI3K/AKT, ERK and p38 MAPK signaling pathways. Notably, UNC5C directly interacted with integrin α6, which is involved in the growth and metastasis of breast cancer cells. Additionally, UNC5C‑knockdown enhanced the phosphorylation of FAK and SRC, which are key kinases in the netrin‑1/Unc5C and netrin‑1/integrin α6/β4 signaling pathways. This suggests that netrin‑1 functions as an integrator for both the netrin‑1/Unc5C and netrin‑1/integrin α6/β4 signaling pathways. UNC5C‑knockdown potentiated netrin‑1/integrin α6/β4 signaling. Given that UNC5C‑knockdown inhibited integrin‑liked protein kinase phosphorylation at Thr‑173, at least in SK‑BR‑3 cells, this may be an inhibitory phosphorylation site rather than activating phosphorylation site for relaying integrin signaling.
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Affiliation(s)
- Mingjing Yuan
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102
| | - Fuan Xie
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102
- Organ Transplantation Institute, School of Medicine, Xiamen University, Xiamen, Fujian 361102
| | - Xianyuan Xia
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102
| | - Kai Zhong
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102
| | - Lanlan Lian
- Department of Laboratory Medicine, Xiang'an Hospital of Xiamen University, Xiamen University, Xiamen, Fujian 361102
| | - Shihui Zhang
- School of Life Science, Central South University, Changsha, Hunan 410083, P.R. China
| | - Li Yuan
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102
| | - Jun Ye
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102
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Kuligina ES, Sokolenko AP, Bizin IV, Romanko AA, Zagorodnev KA, Anisimova MO, Krylova DD, Anisimova EI, Mantseva MA, Varma AK, Hasan SK, Ni VI, Koloskov AV, Suspitsin EN, Venina AR, Aleksakhina SN, Sokolova TN, Milanović AM, Schürmann P, Prokofyeva DS, Bermisheva MA, Khusnutdinova EK, Bogdanova N, Dörk T, Imyanitov EN. Exome sequencing study of Russian breast cancer patients suggests a predisposing role for USP39. Breast Cancer Res Treat 2019; 179:731-742. [DOI: 10.1007/s10549-019-05492-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 11/07/2019] [Indexed: 12/11/2022]
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19
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Zhong W, Peng Y, Yue E, Huang B, Zhang W, Zhao Z, Jiang J, Wang Q, Zhao H. Gingival crevicular fluid levels of SLIT3 are increased in periodontal disease. Oral Dis 2019; 26:182-192. [PMID: 31696592 DOI: 10.1111/odi.13227] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 10/25/2019] [Accepted: 10/30/2019] [Indexed: 12/01/2022]
Abstract
This study aims to investigate the levels of SLIT3 in gingival crevicular fluid (GCF) of healthy and periodontal disease subjects, and their correlations to periodontal disease. A total of 45 periodontal patients and 45 periodontally healthy volunteers were enrolled. The clinical parameters, radiographic bone loss and the levels of SLIT3, receptor activator of NF-κB ligand (RANKL) and osteoprotegerin (OPG) in GCF were measured. The prevalences of Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia in subgingival plaque were also analyzed. The expression of SLIT3 and RANKL was detected in the periodontium of experimental periodontitis in rats and lipopolysaccharide (LPS)-induced mouse macrophage. The total amounts and concentrations of SLIT3 and RANKL were significantly higher in periodontitis than those in healthy, while the level of OPG was significantly lower (p < .05). Significant positive correlations were observed between the level of GCF SLIT3 and clinical attachment level and radiographic bone loss (p < .05). There existed a significant positive correlation between SLIT3 and RANKL (p < .05). Increased expression of SLIT3 and RANKL was observed in the periodontium of periodontal rats. SLIT3 expression was induced by LPS stimulation in macrophages. These results suggest that SLIT3 may act as a diagnostic indicator of periodontal disease and should be further investigated.
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Affiliation(s)
- Wei Zhong
- Department of Stomatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Youmei Peng
- Henan Key Laboratory for Pharmacology of Liver Diseases, Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Erli Yue
- Department of Stomatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Bin Huang
- Department of Stomatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wei Zhang
- Department of Stomatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhe Zhao
- Department of Stomatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jinhua Jiang
- Henan Key Laboratory for Pharmacology of Liver Diseases, Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Qingduan Wang
- Henan Key Laboratory for Pharmacology of Liver Diseases, Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Hongyu Zhao
- Department of Stomatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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20
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Jiang Z, Liang G, Xiao Y, Qin T, Chen X, Wu E, Ma Q, Wang Z. Targeting the SLIT/ROBO pathway in tumor progression: molecular mechanisms and therapeutic perspectives. Ther Adv Med Oncol 2019; 11:1758835919855238. [PMID: 31217826 PMCID: PMC6557020 DOI: 10.1177/1758835919855238] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 05/07/2019] [Indexed: 01/14/2023] Open
Abstract
The SLITs (SLIT1, SLIT2, and SLIT3) are a family of secreted proteins that mediate positional interactions between cells and their environment during development by signaling through ROBO receptors (ROBO1, ROBO2, ROBO3, and ROBO4). The SLIT/ROBO signaling pathway has been shown to participate in axonal repulsion, axon guidance, and neuronal migration in the nervous system and the formation of the vascular system. However, the role of the SLIT/ROBO pathway has not been thoroughly clarified in tumor development. The SLIT/ROBO pathway can produce both beneficial and detrimental effects in the growth of malignant cells. It has been confirmed that SLIT/ROBO play contradictory roles in tumorigenesis. Here, we discuss the tumor promotion and tumor suppression roles of the SLIT/ROBO pathway in tumor growth, angiogenesis, migration, and the tumor microenvironment. Understanding these roles will help us develop more effective cancer therapies.
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Affiliation(s)
- Zhengdong Jiang
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Gang Liang
- Department of Hepatobiliary Surgery, No. 215 Hospital of Shaanxi Nuclear Industry, Xianyang, Shaanxi, China
| | - Ying Xiao
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Tao Qin
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xin Chen
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Erxi Wu
- Department of Neurosurgery, Neuroscience Institute, Baylor Scott and White Health, Temple, TX, USA
| | - Qingyong Ma
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Zheng Wang
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
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21
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Wang J, Yu XF, OUYang N, Luo QL, Zhao SY, Guan XF, Chen T, Li JX. Multi-platform analysis of methylation-regulated genes in human lung adenocarcinoma. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2019; 82:37-45. [PMID: 30626254 DOI: 10.1080/15287394.2018.1551645] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Lung adenocarcinoma (LUAD) is the most frequent pathological type of lung cancer that has a poor prognosis and high mortality rate. DNA methylation plays a critical role in various biological processes during development, while dysregulation results in pathological consequences. Thus, this study aimed to identify DNA methylation-regulated genes involved in LUAD occurrence. Initially, 300 downregulated and 168 upregulated mRNA expression levels were identified in two databases: Gene Expression Omnibus (GEO) and The Cancer Genome Atlas. In addition, GEO was utilized to detect 243 DNA hyper-methylated sites. Based on our observations, it was possible to correlate downregulation of mRNA expression and DNA hyper-methylation of six genes (ABCA3, COX7A1, HOXA5, SLIT3, SOX17, and SPARCL1). Functional analysis of the six genes indicated that these genes are predominantly enriched in cancer-related pathways and may promote carcinogenesis by regulating epithelialmesenchymal transition processes. In conclusion, our study identified a panel of DNA methylation-regulated genes involved in LUAD and may serve as potential epigenetic markers for this type of carcinoma.
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Affiliation(s)
- Jin Wang
- a Department of Toxicology, School of Public Health , Medical College of Soochow University , Suzhou , Jiangsu , China
- b Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases , Suzhou , Jiangsu , China
| | - Xiao-Fan Yu
- a Department of Toxicology, School of Public Health , Medical College of Soochow University , Suzhou , Jiangsu , China
- b Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases , Suzhou , Jiangsu , China
| | - Nan OUYang
- a Department of Toxicology, School of Public Health , Medical College of Soochow University , Suzhou , Jiangsu , China
| | - Qiu-Lin Luo
- a Department of Toxicology, School of Public Health , Medical College of Soochow University , Suzhou , Jiangsu , China
| | - Shi-Yu Zhao
- a Department of Toxicology, School of Public Health , Medical College of Soochow University , Suzhou , Jiangsu , China
| | - Xi-Fei Guan
- a Department of Toxicology, School of Public Health , Medical College of Soochow University , Suzhou , Jiangsu , China
| | - Tao Chen
- a Department of Toxicology, School of Public Health , Medical College of Soochow University , Suzhou , Jiangsu , China
- b Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases , Suzhou , Jiangsu , China
| | - Jian-Xiang Li
- a Department of Toxicology, School of Public Health , Medical College of Soochow University , Suzhou , Jiangsu , China
- b Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases , Suzhou , Jiangsu , China
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22
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Lee HY, Chen YJ, Li CC, Li WM, Hsu YL, Yeh HC, Ke HL, Huang CN, Li CF, Wu WJ, Kuo PL. Deduction of Novel Genes Potentially Involved in Upper Tract Urothelial Carcinoma Using Next-Generation Sequencing and Bioinformatics Approaches. Int J Med Sci 2019; 16:93-105. [PMID: 30662333 PMCID: PMC6332486 DOI: 10.7150/ijms.29560] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 10/31/2018] [Indexed: 12/13/2022] Open
Abstract
Upper tract urothelial carcinoma (UTUC) is a relatively uncommon cancer worldwide, however it accounts for approximately 30% of urothelial cancer in the Taiwanese population. The aim of the current study is to identify differential molecular signatures and novel miRNA regulations in UTUC, using next-generation sequencing and bioinformatics approaches. Two pairs of UTUC tumor and non-tumor tissues were collected during surgical resection, and RNAs extracted for deep sequencing. There were 317 differentially expressed genes identified in UTUC tissues, and the systematic bioinformatics analyses indicated dysregulated genes were enriched in biological processes related to aberration in cell cycle and matrisome-related genes. Additionally, 15 candidate genes with potential miRNA-mRNA interactions were identified. Using the clinical outcome prediction database, low expression of SLIT3 was found to be a prognostic predictor of poor survival in urothelial cancer, and a novel miRNA, miR-34a-5p, was a potential regulator of SLIT3, which may infer the potential role of miR-34a-5p-SLIT3 regulation in the altered tumor microenvironment in UTUC. Our findings suggested novel miRNA target with SLIT3 regulation exerts potential prognostic value in UTUC, and future investigation is necessary to explore the role of SLIT3 in the tumor development and progression of UTUC.
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Affiliation(s)
- Hsiang-Ying Lee
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Urology, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung, Taiwan.,Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Yi-Jen Chen
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Physical Medicine and Rehabilitation, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Ching-Chia Li
- Department of Urology, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung, Taiwan.,Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wei-Ming Li
- Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Urology, Ministry of Health and Welfare Pingtung Hospital, Pingtung, Taiwan
| | - Ya-Ling Hsu
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Hsin-Chih Yeh
- Department of Urology, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung, Taiwan.,Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Hung-Lung Ke
- Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chun-Nung Huang
- Department of Urology, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung, Taiwan.,Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chien-Feng Li
- Department of Pathology, Chi Mei Medical Center, Tainan, Taiwan
| | - Wen-Jeng Wu
- Department of Urology, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung, Taiwan.,Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Po-Lin Kuo
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung 807, Taiwan.,Institute of Medical Science and Technology, National Sun Yat-Sen University, Kaohsiung, Taiwan
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23
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Tanaka H, Kuwano Y, Nishikawa T, Rokutan K, Nishida K. ZNF350 promoter methylation accelerates colon cancer cell migration. Oncotarget 2018; 9:36750-36769. [PMID: 30613364 PMCID: PMC6298409 DOI: 10.18632/oncotarget.26353] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 10/24/2018] [Indexed: 12/21/2022] Open
Abstract
Diversification of transcriptomic and epigenomic states may occur during the expansion of colorectal cancers. Certain cancer cells lose their epithelial characters and gain mesenchymal properties, known as epithelial-mesenchymal transition (EMT), and they aggressively migrate into the non-tumorigenic extracellular matrix. In this study, we isolated a subpopulation with accelerated baseline motility (MG cells) and an immotile one (non-MG cells) from a colon cancer cell line (HCT116). Gene expression signatures of the MG cells indicated that this subpopulation was likely an EMT hybrid. The MG cells substantially lost their migratory properties after treatment with a methyltransferase inhibitor, 5-azacytidine, suggesting a role of DNA methylation in this process. Global transcriptome assays of both types of cells with or without 5-azacytidine treatment identified 640 genes, whose expression might be methylation-dependently down-regulated in the MG cells. Global methylation analysis revealed that 35 out of the 640 genes were hyper-methylated in the MG cells. Among them, we focused on the anti-oncogene ZNF350, which encodes a zinc-finger and BRCA1-interacting protein. Notably, ZNF350 knockdown accelerated migration of the non-MG cells, while overexpression of ZNF350 in the MG cells significantly impaired their migration. Finally, pyrosequence analysis together with dual luciferase assays of serially truncated fragments of the ZNF350 promoter (-268 to +49 bp) indicated that three hyper-methylated sites were possibly responsible for the basal promoter activity of ZNF350. Taken together, our results suggest that hyper-methylation of the ZNF350 proximal promoter may be one of the crucial determinants for acquiring increased migratory capabilities in colon cancer cells.
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Affiliation(s)
- Hiroki Tanaka
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Yuki Kuwano
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Tatsuya Nishikawa
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Kazuhito Rokutan
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Kensei Nishida
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
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24
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Sun X, Tian Y, Zheng Q, Zheng R, Lin A, Chen T, Zhu Y, Lai M. A novel discriminating colorectal cancer model for differentiating normal and tumor tissues. Epigenomics 2018; 10:1463-1475. [DOI: 10.2217/epi-2018-0063] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- Xiaohui Sun
- Department of Epidemiology & Biostatistics, School of Public Health, Zhejiang University, Hangzhou 310058, Zhejiang, PR China
| | - Yiping Tian
- Key Laboratory of Disease Proteomics of Zhejiang Province & Department of Pathology, School of Medicine, Zhejiang University, Hangzhou 310058, PR China
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou 310022, PR China
| | - Qianqian Zheng
- Department of Epidemiology & Biostatistics, School of Public Health, Zhejiang University, Hangzhou 310058, Zhejiang, PR China
| | - Ruizhi Zheng
- Department of Epidemiology & Biostatistics, School of Public Health, Zhejiang University, Hangzhou 310058, Zhejiang, PR China
| | - Aifen Lin
- Human Tissue Bank/Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, 317000, PR China
| | - Tianhui Chen
- Group of Molecular Epidemiology & Cancer Precision Prevention, Zhejiang Academy of Medical Sciences, Hangzhou, PR China
| | - Yimin Zhu
- Department of Epidemiology & Biostatistics, School of Public Health, Zhejiang University, Hangzhou 310058, Zhejiang, PR China
| | - Maode Lai
- Key Laboratory of Disease Proteomics of Zhejiang Province & Department of Pathology, School of Medicine, Zhejiang University, Hangzhou 310058, PR China
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25
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Ng L, Chow AKM, Man JHW, Yau TCC, Wan TMH, Iyer DN, Kwan VHT, Poon RTP, Pang RWC, Law WL. Suppression of Slit3 induces tumor proliferation and chemoresistance in hepatocellular carcinoma through activation of GSK3β/β-catenin pathway. BMC Cancer 2018; 18:621. [PMID: 29859044 PMCID: PMC5984734 DOI: 10.1186/s12885-018-4326-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 04/03/2018] [Indexed: 01/05/2023] Open
Abstract
Background It is essential to understand the mechanisms responsible for hepatocellular carcinoma (HCC) progression and chemoresistance in order to identify prognostic biomarkers as well as potential therapeutic avenues. Recent findings have shown that SLIT3 appears to function as a novel tumor suppressor gene in various types of cancers, yet its clinical correlation and role in HCC has not been understood clearly. Methods We determined the transcript levels of Slit3 in tumor and adjacent normal tissues within two cohorts (N = 40 and 25) of HCC patients, and correlated the gene expression with the clinicopathological data. Subsequently, the functional effects and underlying molecular mechanisms of Slit3 overexpression and/or repression were studied using cell-line and mouse models. Results Our results demonstrated a repression in Slit3 expression in nearly 50% of the HCC patients, while the overall expression of Slit3 inversely correlated with the size of the tumor in both cohorts of patients. Stable down-regulation of Slit3 in HCC cell-lines induced cell proliferation in vitro and tumor growth in vivo, while stable Slit3 overexpression repressed these effects. Molecular investigations showed that the stable Slit3 repression-induced cell proliferation was associated with a higher expression of β-catenin and a repressed GSK3β activity. Moreover, Slit3-repression induced chemoresistance to sorafenib, oxaliplatin and 5-FU through impairment of β-catenin degradation and induction of cyclin D3 and survivin levels. The effects induced by stable Slit3-repression were diminished by transient repression of β-catenin by siRNA approach. Conclusion This study suggests that Slit3 acts as a tumor suppressor in HCC by repressing the tumor growth and thus tumor progression. Low Slit3 level indicates a poor response of HCC cells to chemotherapy. Restoration or overexpression of Slit3 is a potential therapeutic approach to repress the tumor growth and enhance the efficacy of chemotherapeutic agents. Electronic supplementary material The online version of this article (10.1186/s12885-018-4326-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lui Ng
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Ariel K M Chow
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Johnny H W Man
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Thomas C C Yau
- Centre for Cancer Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Timothy M H Wan
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Deepak N Iyer
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Virginia H T Kwan
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Ronnie T P Poon
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong.,Centre for Cancer Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Roberta W C Pang
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong. .,Centre for Cancer Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong.
| | - Wai-Lun Law
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
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26
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Luo Y, Xuan Z, Zhu X, Zhan P, Wang Z. Long non-coding RNAs RP5-821D11.7, APCDD1L-AS1 and RP11-277P12.9 were associated with the prognosis of lung squamous cell carcinoma. Mol Med Rep 2018; 17:7238-7248. [PMID: 29568882 PMCID: PMC5928681 DOI: 10.3892/mmr.2018.8770] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 02/20/2018] [Indexed: 12/14/2022] Open
Abstract
Lung squamous cell carcinoma (LUSC), a type of non-small cell lung carcinoma, has a poor therapeutic response, high relapse rate and poor prognosis. The present study was designed to reveal the key long non-coding RNAs (lncRNAs) associated with the prognosis of LUSC. The lncRNA expression profiles of LUSC and adjacent samples were downloaded from The Cancer Genome Atlas database. Based on the edgeR and DEseq packages, the differentially expressed lncRNAs (DELs) between LUSC and adjacent samples were obtained and the intersecting DELs were regarded as significant DELs. Subsequently, a prognostic risk model was established using Cox regression analysis and its classification effect was detected by survival analysis. Using survival analysis, the effect of the prognostic risk model was assessed in the validation set and other types of cancer. Finally, the co-expression genes of key lncRNAs were screened using the Multi-Experiment Matrix tool and the STRING database, and their functions were predicted via enrichment analysis using the Database for Annotation, Visualization and Integrated Discovery tool. A total of 2,041 significant DELs between LUSC and adjacent samples were screened. The prognostic risk model consisting of RP5-821D11.7, APCDD1L-AS1 and RP11-277P12.9 was established, which had a good classification effect. Cox multivariate regression analysis demonstrated that risk score may serve as an independent prognostic factor. Furthermore, certain co-expression genes of RP5-821D11.7 (including proliferating cell nuclear antigen), APCDD1L-AS1 (including semaphorin 5A, semaphorin 6D, ADAMTS like 1, ADAM metallopeptidase with thrombospondin type 1 motif 6, slit guidance ligand 3, and tenascin C) and RP11-277P12.9 (including Wnt family member 2B) were identified. Additionally, ‘positive regulation of cell migration’ and ‘proteinaceous extracellular matrix’ were enriched. In conclusion, the expression levels of the lncRNAs RP5-821D11.7, APCDD1L-AS1 and RP11-277P12.9 may affect the prognosis of LUSC.
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Affiliation(s)
- Yanzhuo Luo
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250021, P.R. China
| | - Zhaobo Xuan
- Department of Neurosurgery, The First Hospital Affiliated to Jiamusi University, Jiamusi, Heilongjiang 154002, P.R. China
| | - Xiaofeng Zhu
- Department of Thoracic Surgery, The First Hospital Affiliated to Jiamusi University, Jiamusi, Heilongjiang 154002, P.R. China
| | - Peng Zhan
- Department of Thoracic Surgery, The First Hospital Affiliated to Jiamusi University, Jiamusi, Heilongjiang 154002, P.R. China
| | - Zhou Wang
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250021, P.R. China
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27
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SUV39H2 promotes colorectal cancer proliferation and metastasis via tri-methylation of the SLIT1 promoter. Cancer Lett 2018; 422:56-69. [PMID: 29458143 DOI: 10.1016/j.canlet.2018.02.023] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 01/30/2018] [Accepted: 02/12/2018] [Indexed: 01/01/2023]
Abstract
Suppressor of variegation 3-9 homolog 2 (SUV39H2) is a member of the SUV39H subfamily of lysine methyltransferases. Its role in colorectal cancer (CRC) proliferation and metastasis has remained unexplored. Here, we determined that SUV39H2 was upregulated in CRC tissues compared with that in adjacent non-neoplastic tissues. Further statistical analysis revealed that high SUV39H2 expression was strongly associated with distant metastasis (P = 0.016) and TNM stage (P = 0.038) and predicted a shorter overall survival (OS; P = 0.018) and progression-free survival (PFS; P = 0.018) time for CRC patients. Both in vitro and in vivo assays demonstrated that ectopically expressed SUV39H2 enhanced CRC proliferation and metastasis, while SUV39H2 knockdown inhibited CRC proliferation and metastasis. A molecular screen of SUV39H2 targets found that SUV39H2 negatively regulated the expression of SLIT guidance ligand 1 (SLIT1). Moreover, rescue assays suggested that SLIT1 could antagonize the function of SUV39H2 in CRC. Mechanistic studies indicated that SUV39H2 can directly bind to the SLIT1 promoter, suppressing SLIT1 transcription by catalyzing histone H3 lysine 9 (H3K9) tri-methylation. In summary, we propose that SUV39H2 can predict CRC patient prognosis and stimulate CRC malignant phenotypes via SLIT1 promoter tri-methylation.
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Yuan M, Guo H, Li J, Sui C, Qin Y, Wang J, Khan YH, Ye L, Xie F, Wang H, Yuan L, Ye J. Slit2 and Robo1 induce opposing effects on metastasis of hepatocellular carcinoma Sk-hep-1 cells. Int J Oncol 2016; 49:305-15. [PMID: 27176045 DOI: 10.3892/ijo.2016.3506] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 03/28/2016] [Indexed: 11/05/2022] Open
Abstract
The neural guidance molecular, Slit2, and its cognate receptor, Robo1, play critical roles in the development of the nervous system, nevertheless, their functions are not limited to this system. Numerous studies have shown decreased Slit2 expression in a wide variety of cancers, highlighting its potential as a tumor suppressor. However, the Slit2/Robo1 signaling axis was reported to induce either suppressive or stimulatory effects on tumor growth and metastasis, depending on cellular context. There is a paucity of information on the effects of the Slit2/Robo1 signaling axis on the growth and metastasis of human hepatocellular carcinoma (HCC). Large-scale data mining of the Oncomine database has revealed heterogeneous expression of Slit2 in HCC. We screened the Sk-hep-1, a cell line showing a relatively high level of Slit2, and low level of Robo1 expression. After Slit2 knockdown and Robo1 overexpression in these cells, we found Slit2 and Robo1 exerted opposing effects on tumor growth and metastasis both in in vitro and in vivo models. Slit2 knockdown and Robo1 overexpression in Sk-hep-1 cells promoted tumor growth and metastasis, suggesting a negative and positive role for Slit2 and Robo1, respectively, in tumor progression. Robo1 overexpression upregulated matrix metalloproteinase (MMP)2, -9 and membrane-type1 MMP (MT1-MMP) expression, stimulated MMP2, but not MMP9 activation, and downregulated expression of TIMP1 and 2. The PI3K/Akt signaling pathway is of importance in regulating MMP2 expression in Sk-hep-1 cells, since Robo1 overexpression stimulated phosphorylation of Akt while the PI3K inhibitor LY294002, significantly inhibited the upregulation of MMP2 and also the enhanced cell invasion induced by Robo1 overexpression. We postulate that Robo1 promotes tumor invasion partly by the upregulation of MMP2 after activation of PI3K/Akt signaling pathway. Notably, Slit2 knockdown caused the upregulation of Robo1 expression both at the mRNA and protein levels. Thus, the stimulatory effects of Slit2 knockdown on tumor progression can be ascribed, at least in part, to the upregulation of Robo1 and its positive role in tumor progression.
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Affiliation(s)
- Mingjing Yuan
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, P.R. China
| | - Hui Guo
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, P.R. China
| | - Jing Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, P.R. China
| | - Chengzhi Sui
- The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, P.R. China
| | - Ying Qin
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, P.R. China
| | - Jingjing Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, P.R. China
| | - Yasir Hayat Khan
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, P.R. China
| | - Liying Ye
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, P.R. China
| | - Fuan Xie
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, P.R. China
| | - Heng Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, P.R. China
| | - Li Yuan
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, P.R. China
| | - Jun Ye
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, P.R. China
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Transcriptional profiling revealed the anti-proliferative effect of MFN2 deficiency and identified risk factors in lung adenocarcinoma. Tumour Biol 2016; 37:8643-55. [DOI: 10.1007/s13277-015-4702-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 12/20/2015] [Indexed: 01/11/2023] Open
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He F, Zuo L. Redox Roles of Reactive Oxygen Species in Cardiovascular Diseases. Int J Mol Sci 2015; 16:27770-80. [PMID: 26610475 PMCID: PMC4661917 DOI: 10.3390/ijms161126059] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/06/2015] [Accepted: 11/11/2015] [Indexed: 02/07/2023] Open
Abstract
Cardiovascular disease (CVD), a major cause of mortality in the world, has been extensively studied over the past decade. However, the exact mechanism underlying its pathogenesis has not been fully elucidated. Reactive oxygen species (ROS) play a pivotal role in the progression of CVD. Particularly, ROS are commonly engaged in developing typical characteristics of atherosclerosis, one of the dominant CVDs. This review will discuss the involvement of ROS in atherosclerosis, specifically their effect on inflammation, disturbed blood flow and arterial wall remodeling. Pharmacological interventions target ROS in order to alleviate oxidative stress and CVD symptoms, yet results are varied due to the paradoxical role of ROS in CVD. Lack of effectiveness in clinical trials suggests that understanding the exact role of ROS in the pathophysiology of CVD and developing novel treatments, such as antioxidant gene therapy and nanotechnology-related antioxidant delivery, could provide a therapeutic advance in treating CVDs. While genetic therapies focusing on specific antioxidant expression seem promising in CVD treatments, multiple technological challenges exist precluding its immediate clinical applications.
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Affiliation(s)
- Feng He
- Department of Kinesiology, California State University-Chico, Chico, CA 95929, USA.
| | - Li Zuo
- Molecular Physiology and Rehabilitation Research Lab, Radiologic Sciences and Respiratory Therapy Division, School of Health and Rehabilitation Sciences, the Ohio State University College of Medicine, Columbus, OH 43210, USA.
- Interdisciplinary Biophysics Graduate Program, the Ohio State University, Columbus, OH 43210, USA.
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Yang M, Liu R, Li X, Liao J, Pu Y, Pan E, Wang Y, Yin L. Epigenetic Repression of miR-218 Promotes Esophageal Carcinogenesis by Targeting ROBO1. Int J Mol Sci 2015; 16:27781-95. [PMID: 26610476 PMCID: PMC4661920 DOI: 10.3390/ijms161126062] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/11/2015] [Accepted: 11/12/2015] [Indexed: 12/17/2022] Open
Abstract
miR-218, consisting of miR-218-1 at 4p15.31 and miR-218-2 at 5q35.1, was significantly decreased in esophageal squamous cell carcinoma (ESCC) in our previous study. The aim of this study was to determine whether aberrant methylation is associated with miR-218 repression. Bisulfite sequencing analysis (BSP), methylation specific PCR (MSP), and 5-aza-2'-deoxycytidine treatment assay were applied to determine the methyaltion status of miR-218 in cells and clinical samples. In vitro assays were performed to explore the role of miR-218. Results showed that miR-218-1 was significantly CpG hypermethylated in tumor tissues (81%, 34/42) compared with paired non-tumor tissues (33%, 14/42) (p < 0.05). However, no statistical difference was found in miR-218-2. Accordingly, expression of miR-218 was negatively correlated with miR-218-1 methylation status (p < 0.05). After demethylation treatment by 5-aza-2'-deoxycytidine, there was a 2.53- and 2.40-fold increase of miR-218 expression in EC109 and EC9706, respectively. miR-218 suppressed cell proliferation and arrested cells at G1 phase by targeting 3' untranslated region (3'UTR) of roundabout guidance receptor 1 (ROBO1). A negative correlation was found between miR-218 and ROBO1 mRNA expression in clinical samples. In conclusion, our results support that aberrant CpG hypermethylation at least partly accounts for miR-218 silencing in ESCC, which impairs its tumor-suppressive function.
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Affiliation(s)
- Miao Yang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China.
| | - Ran Liu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China.
| | - Xiajun Li
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China.
| | - Juan Liao
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China.
| | - Yuepu Pu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China.
| | - Enchun Pan
- Huaian Center for Disease Control and Prevention, Huaian 223001, China.
| | - Yi Wang
- Huaian Center for Disease Control and Prevention, Huaian 223001, China.
| | - Lihong Yin
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China.
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