1
|
Xu G, Zhao Y, Bai Y, Lin Y. Study of hub nodes of transcription factor-target gene regulatory network and immune mechanism for type 2 diabetes based on chip analysis of GEO database. Front Mol Biosci 2024; 11:1410004. [PMID: 38855325 PMCID: PMC11157018 DOI: 10.3389/fmolb.2024.1410004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 05/08/2024] [Indexed: 06/11/2024] Open
Abstract
Identification of novel therapeutic targets for type 2 diabetes is a key area of contemporary research. In this study, we screened differentially expressed genes in type 2 diabetes through the GEO database and sought to identify the key virulence factors for type 2 diabetes through a transcription factor regulatory network. Our findings may help identify new therapeutic targets for type 2 diabetes. Data pertaining to the humoral (whole blood) gene expression profile of diabetic patients were obtained from the NCBI's GEO Datasets database and gene sets with differential expression were identified. Subsequently, the TRED transcriptional regulatory element database was integrated to build a gene regulatory network for type 2 diabetes. Functional analysis (GO-Analysis) and Pathway-analysis of differentially expressed genes were performed using the DAVID database and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Finally, gene-disease correlation analysis was performed using the DAVID online annotation tool. A total of 236 pathogenic genes, four transcription factors related to the pathogenic genes, and 261 corresponding target genes were identified. A transcription factor-target gene regulatory network for type 2 diabetes was constructed. Most of the key factors of the transcription factor-target gene regulatory network for type 2 diabetes were found closely related to the immune metabolic system and the functions of cell proliferation and transformation.
Collapse
Affiliation(s)
- Guangyu Xu
- College of Pharmacy, Beihua University, Jilin, China
| | - Yuehan Zhao
- College of Pharmacy, Beihua University, Jilin, China
| | - Yu Bai
- College of Pharmacy, Jilin Medical University, Jilin, China
| | - Yan Lin
- School of Basic Medical Sciences, Beihua University, Jilin, China
| |
Collapse
|
2
|
Colucci M, Zumerle S, Bressan S, Gianfanti F, Troiani M, Valdata A, D'Ambrosio M, Pasquini E, Varesi A, Cogo F, Mosole S, Dongilli C, Desbats MA, Contu L, Revankdar A, Chen J, Kalathur M, Perciato ML, Basilotta R, Endre L, Schauer S, Othman A, Guccini I, Saponaro M, Maraccani L, Bancaro N, Lai P, Liu L, Pernigoni N, Mele F, Merler S, Trotman LC, Guarda G, Calì B, Montopoli M, Alimonti A. Retinoic acid receptor activation reprograms senescence response and enhances anti-tumor activity of natural killer cells. Cancer Cell 2024; 42:646-661.e9. [PMID: 38428412 PMCID: PMC11003464 DOI: 10.1016/j.ccell.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 12/19/2023] [Accepted: 02/07/2024] [Indexed: 03/03/2024]
Abstract
Cellular senescence can exert dual effects in tumors, either suppressing or promoting tumor progression. The senescence-associated secretory phenotype (SASP), released by senescent cells, plays a crucial role in this dichotomy. Consequently, the clinical challenge lies in developing therapies that safely enhance senescence in cancer, favoring tumor-suppressive SASP factors over tumor-promoting ones. Here, we identify the retinoic-acid-receptor (RAR) agonist adapalene as an effective pro-senescence compound in prostate cancer (PCa). Reactivation of RARs triggers a robust senescence response and a tumor-suppressive SASP. In preclinical mouse models of PCa, the combination of adapalene and docetaxel promotes a tumor-suppressive SASP that enhances natural killer (NK) cell-mediated tumor clearance more effectively than either agent alone. This approach increases the efficacy of the allogenic infusion of human NK cells in mice injected with human PCa cells, suggesting an alternative therapeutic strategy to stimulate the anti-tumor immune response in "immunologically cold" tumors.
Collapse
Affiliation(s)
- Manuel Colucci
- Institute of Oncology Research (IOR), CH6500 Bellinzona, Switzerland; Università della Svizzera Italiana, CH6900 Lugano, Switzerland; Faculty of Biology and Medicine, University of Lausanne UNIL, CH1011 Lausanne, Switzerland
| | - Sara Zumerle
- Veneto Institute of Molecular Medicine (VIMM) & Department of Medicine, University of Padova, Padova, Italy
| | - Silvia Bressan
- Institute of Oncology Research (IOR), CH6500 Bellinzona, Switzerland; Università della Svizzera Italiana, CH6900 Lugano, Switzerland; Veneto Institute of Molecular Medicine (VIMM) & Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Federico Gianfanti
- Institute of Oncology Research (IOR), CH6500 Bellinzona, Switzerland; Università della Svizzera Italiana, CH6900 Lugano, Switzerland; Veneto Institute of Molecular Medicine (VIMM) & Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Martina Troiani
- Institute of Oncology Research (IOR), CH6500 Bellinzona, Switzerland; Università della Svizzera Italiana, CH6900 Lugano, Switzerland; Bioinformatics Core Unit, Swiss Institute of Bioinformatics, TI, Bellinzona, Switzerland
| | - Aurora Valdata
- Institute of Oncology Research (IOR), CH6500 Bellinzona, Switzerland; Department of Health Sciences and Technology (D-HEST) ETH Zurich, Zurich, CH, Switzerland
| | - Mariantonietta D'Ambrosio
- Institute of Oncology Research (IOR), CH6500 Bellinzona, Switzerland; MRC London Institute of Medical Sciences (LMS), London, UK
| | - Emiliano Pasquini
- Institute of Oncology Research (IOR), CH6500 Bellinzona, Switzerland; Università della Svizzera Italiana, CH6900 Lugano, Switzerland
| | - Angelica Varesi
- Institute of Oncology Research (IOR), CH6500 Bellinzona, Switzerland; Università della Svizzera Italiana, CH6900 Lugano, Switzerland
| | - Francesca Cogo
- Institute of Oncology Research (IOR), CH6500 Bellinzona, Switzerland; Università della Svizzera Italiana, CH6900 Lugano, Switzerland
| | - Simone Mosole
- Institute of Oncology Research (IOR), CH6500 Bellinzona, Switzerland; Università della Svizzera Italiana, CH6900 Lugano, Switzerland
| | - Cristina Dongilli
- Institute of Oncology Research (IOR), CH6500 Bellinzona, Switzerland; Università della Svizzera Italiana, CH6900 Lugano, Switzerland
| | - Maria Andrea Desbats
- Veneto Institute of Molecular Medicine (VIMM) & Department of Medicine, University of Padova, Padova, Italy
| | - Liliana Contu
- Veneto Institute of Molecular Medicine (VIMM) & Department of Medicine, University of Padova, Padova, Italy
| | - Ajinkya Revankdar
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Jingjing Chen
- Department of Cell Biology, Harvard Medical School, Boston, MA 02215, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Madhuri Kalathur
- Children's GMP, LLC, St. Jude Children's Research Hospital, 262 Danny Thomas Place Mail Stop 920 Memphis, TN 38105, USA
| | - Maria Luna Perciato
- School of Clinical Dentistry, University of Sheffield, Sheffield S10 2TA, UK
| | - Rossella Basilotta
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98166 viale Ferdinando D'Alcontres, Italy
| | - Laczko Endre
- Functional Genomics Center Zurich, ETHZ and University of Zurich, Zurich, CH, Switzerland
| | - Stefan Schauer
- Functional Genomics Center Zurich, ETHZ and University of Zurich, Zurich, CH, Switzerland
| | - Alaa Othman
- Functional Genomics Center Zurich, ETHZ and University of Zurich, Zurich, CH, Switzerland
| | - Ilaria Guccini
- Department of Health Sciences and Technology (D-HEST) ETH Zurich, Zurich, CH, Switzerland
| | - Miriam Saponaro
- Veneto Institute of Molecular Medicine (VIMM) & Department of Medicine, University of Padova, Padova, Italy
| | - Luisa Maraccani
- Institute of Oncology Research (IOR), CH6500 Bellinzona, Switzerland; Veneto Institute of Molecular Medicine (VIMM) & Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Nicolò Bancaro
- Institute of Oncology Research (IOR), CH6500 Bellinzona, Switzerland; Università della Svizzera Italiana, CH6900 Lugano, Switzerland
| | - Ping Lai
- Institute of Oncology Research (IOR), CH6500 Bellinzona, Switzerland; Università della Svizzera Italiana, CH6900 Lugano, Switzerland
| | - Lei Liu
- Institute of Oncology Research (IOR), CH6500 Bellinzona, Switzerland; Università della Svizzera Italiana, CH6900 Lugano, Switzerland
| | - Nicolò Pernigoni
- Institute of Oncology Research (IOR), CH6500 Bellinzona, Switzerland; Università della Svizzera Italiana, CH6900 Lugano, Switzerland
| | - Federico Mele
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Sara Merler
- Section of Innovation Biomedicine - Oncology Area, Department of Engineering for Innovation Medicine, University of Verona and Verona University and Hospital Trust, Verona, Italy
| | - Lloyd C Trotman
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Greta Guarda
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Bianca Calì
- Institute of Oncology Research (IOR), CH6500 Bellinzona, Switzerland; Università della Svizzera Italiana, CH6900 Lugano, Switzerland
| | - Monica Montopoli
- Veneto Institute of Molecular Medicine (VIMM) & Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Andrea Alimonti
- Institute of Oncology Research (IOR), CH6500 Bellinzona, Switzerland; Università della Svizzera Italiana, CH6900 Lugano, Switzerland; Veneto Institute of Molecular Medicine (VIMM) & Department of Medicine, University of Padova, Padova, Italy; Department of Health Sciences and Technology (D-HEST) ETH Zurich, Zurich, CH, Switzerland; Oncology Institute of Southern Switzerland, Ente Ospedaliero Cantonale, Bellinzona, Switzerland.
| |
Collapse
|
3
|
Xu G, Yang Y, Lin Y, Bai Y. GEO dataset mining analysis reveals novel Staphylococcus aureus virulence gene regulatory networks and diagnostic targets in mice. Front Mol Biosci 2024; 11:1381334. [PMID: 38606287 PMCID: PMC11007229 DOI: 10.3389/fmolb.2024.1381334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 03/18/2024] [Indexed: 04/13/2024] Open
Abstract
Staphylococcus (S.) aureus infection is a serious, worldwide health concern, particularly in many communities and hospitals. Understanding the S. aureus pathogenetic regulatory network will provide significant insights into diagnostic target screening to improve clinical treatment of diseases caused by S. aureus. We screened differentially expressed genes between normal mice and S. aureus-infected mice. We used the Gene Expression Omnibus (GEO) DataSets database for functional analysis (GO-analysis) and the DAVID and KEGG databases for signaling pathway analyses. We next integrated the gene and pathway analyses with Transcriptional Regulatory Element Database (TRED) to build an antimicrobial resistance gene regulatory network of S. aureus. We performed association analysis of network genes and diseases using DAVID online annotation tools. We identified a total of 437 virulence genes and 15 transcription factors (TFs), as well as 444 corresponding target genes, in the S. aureus TF regulatory network. We screened seven key network nodes (Met, Mmp13, Il12b, Il4, Tnf, Ptgs2, and Ctsl), four key transcription factors (Jun, C3, Spil, and Il6) and an important signaling pathway (TNF). We hypothesized that the cytokine activity and growth factor activity of S. aureus are combinatorically cross-regulated by Met, Mmp13, Il12b, Il4, Tnf, Ptgs2, and Ctsl genes, the TFs Jun, C3, Spi1, and Il6, as well as the immune response, cellular response to lipopolysaccharide, and inflammatory response. Our study provides information and reference values for the molecular understanding of the S. aureus pathogenetic gene regulatory network.
Collapse
Affiliation(s)
- Guangyu Xu
- College of Pharmacy, Beihua University, Jilin, China
| | - Yue Yang
- College of Pharmacy, Beihua University, Jilin, China
| | - Yan Lin
- School of Basic Medical Sciences, Beihua University, Jilin, China
| | - Yu Bai
- College of Pharmacy, Jilin Medical University, Jilin, China
| |
Collapse
|
4
|
Xie L, Wu S, Guo X. An important resource and analytic platform for human and mouse cardiovascular-related cis-regulatory elements. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 34:102033. [PMID: 37808923 PMCID: PMC10556829 DOI: 10.1016/j.omtn.2023.102033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Affiliation(s)
- Longxiang Xie
- Institute of Biomedical Informatics, Bioinformatics Center, Henan Provincial Engineering Center for Tumor Molecular Medicine, Academy for Advanced Interdisciplinary Studies, School of Basic Medical Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Shengnan Wu
- Institute of Biomedical Informatics, Bioinformatics Center, Henan Provincial Engineering Center for Tumor Molecular Medicine, Academy for Advanced Interdisciplinary Studies, School of Basic Medical Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Xiangqian Guo
- Institute of Biomedical Informatics, Bioinformatics Center, Henan Provincial Engineering Center for Tumor Molecular Medicine, Academy for Advanced Interdisciplinary Studies, School of Basic Medical Sciences, Henan University, Kaifeng, Henan 475004, China
| |
Collapse
|
5
|
Chen Q, Hu C, Lu W, Hang T, Shao Y, Chen C, Wang Y, Li N, Jin L, Wu W, Wang H, Zeng X, Xie W. Characteristics of alveolar macrophages in bronchioalveolar lavage fluids from active tuberculosis patients identified by single-cell RNA sequencing. J Biomed Res 2022; 36:167-180. [PMID: 35635159 PMCID: PMC9179115 DOI: 10.7555/jbr.36.20220007] [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] [Indexed: 12/04/2022] Open
Abstract
Tuberculosis (TB), is an infectious disease caused by Mycobacterium tuberculosis (M. tuberculosis), and presents with high morbidity and mortality. Alveolar macrophages play an important role in TB pathogenesis although there is heterogeneity and functional plasticity. This study aimed to show the characteristics of alveolar macrophages from bronchioalveolar lavage fluid (BALF) in active TB patients. Single-cell RNA sequencing (scRNA-seq) was performed on BALF cells from three patients with active TB and additional scRNA-seq data from three healthy adults were established as controls. Transcriptional profiles were analyzed and compared by differential geneexpression and functional enrichment analysis. We applied pseudo-temporal trajectory analysis to investigate correlations and heterogeneity within alveolar macrophage subclusters. Alveolar macrophages from active TB patients at the single-cell resolution are described. We found that TB patients have higher cellular percentages in five macrophage subclusters. Alveolar macrophage subclusters with increased percentages were involved in inflammatory signaling pathways as well as the basic macrophage functions. The TB-increased alveolar macrophage subclusters might be derived from M1-like polarization state, before switching to an M2-like polarization state with the development ofM. tuberculosis infection. Cell-cell communications of alveolar macrophages also increased and enhanced in active TB patients. Overall, our study demonstrated the characteristics of alveolar macrophages from BALF in active TB patients by using scRNA-seq.
Collapse
Affiliation(s)
- Qianqian Chen
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Chunmei Hu
- Department of Tuberculosis, the Second Hospital of Nanjing, Nanjing, Jiangsu 210029, China
| | - Wei Lu
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, Jiangsu 210029, China
| | - Tianxing Hang
- Department of Tuberculosis, the Second Hospital of Nanjing, Nanjing, Jiangsu 210029, China
| | - Yan Shao
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, Jiangsu 210029, China
| | - Cheng Chen
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, Jiangsu 210029, China
| | - Yanli Wang
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Nan Li
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Linling Jin
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Wei Wu
- Department of Bioinformatics, Nanjing Medical University, Nanjing, Jiangsu 210029, China
- School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210029, China
| | - Hong Wang
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
- Weiping Xie, Xiaoning Zeng, and Hong Wang. Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu 210029, China. Tel/Fax: +86-25-68306030/+86-25-68306030. E-mails:
,
, and
| | - Xiaoning Zeng
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
- Weiping Xie, Xiaoning Zeng, and Hong Wang. Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu 210029, China. Tel/Fax: +86-25-68306030/+86-25-68306030. E-mails:
,
, and
| | - Weiping Xie
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
- Weiping Xie, Xiaoning Zeng, and Hong Wang. Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu 210029, China. Tel/Fax: +86-25-68306030/+86-25-68306030. E-mails:
,
, and
| |
Collapse
|
6
|
iDEP Web Application for RNA-Seq Data Analysis. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2284:417-443. [PMID: 33835455 DOI: 10.1007/978-1-0716-1307-8_22] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
RNA sequencing (RNA-seq) has become a routine method for transcriptomic profiling. We developed a user-friendly web app called iDEP (integrated differential expression and pathway analysis) to help biologists interpret read counts or other types of expression matrices derived from read mapping. With iDEP, users can easily conduct exploratory data analysis, identify differentially expressed genes, and perform pathway analysis. Due to its intuitive user interface and massive annotation database, iDEP is being widely adopted for interactive analysis of RNA-seq data. Using a public dataset on the effect of heat shock on mouse with and without functional Hsf1, we demonstrate how users can prepare data files and conduct in-depth analysis. We also discuss the importance of critical interpretion of results (avoid p-hacking and rationalizing) and validation of significant pathways by using different methods and independent annotation databases.
Collapse
|
7
|
Katayama S, Shiraishi K, Gorai N, Andou M. A CRISPR/Cas9-based method for targeted DNA methylation enables cancer initiation in B lymphocytes. ADVANCED GENETICS (HOBOKEN, N.J.) 2021; 2:e10040. [PMID: 36618443 PMCID: PMC9744502 DOI: 10.1002/ggn2.10040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 02/01/2021] [Accepted: 02/09/2021] [Indexed: 01/11/2023]
Abstract
Targeted DNA methylation is important for understanding transcriptional modulation and epigenetic diseases. Although CRISPR-Cas9 has potential for this purpose, it has not yet been successfully used to efficiently introduce DNA methylation and induce epigenetic diseases. We herein developed a new system that enables the replacement of an unmethylated promoter with a methylated promoter through microhomology-mediated end joining-based knock-in. We successfully introduced an approximately 100% DNA methylation ratio at the cancer-associated gene SP3 in HEK293 cells. Moreover, engineered SP3 promoter hypermethylation led to transcriptional suppression in human B lymphocytes and induced B-cell lymphoma. Our system provides a promising framework for targeted DNA methylation and cancer initiation through epimutations.
Collapse
Affiliation(s)
| | | | - Naoki Gorai
- IMRA Japan Co., Ltd.SapporoJapan,AISIN AW Co., Ltd.AnjouJapan
| | | |
Collapse
|
8
|
Su W, Liu ML, Yang YH, Wang JS, Li SH, Lv H, Dao FY, Yang H, Lin H. PPD: A Manually Curated Database for Experimentally Verified Prokaryotic Promoters. J Mol Biol 2021; 433:166860. [PMID: 33539888 DOI: 10.1016/j.jmb.2021.166860] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/13/2020] [Accepted: 01/27/2021] [Indexed: 12/16/2022]
Abstract
As a key region, promoter plays a key role in transcription regulation. A eukaryotic promoter database called EPD has been constructed to store eukaryotic POL II promoters. Although there are some promoter databases for specific prokaryotic species or specific promoter type, such as RegulonDB for Escherichia coli K-12, DBTBS for Bacillus subtilis and Pro54DB for sigma 54 promoter, because of the diversity of prokaryotes and the development of sequencing technology, huge amounts of prokaryotic promoters are scattered in numerous published articles, which is inconvenient for researchers to explore the process of gene regulation in prokaryotes. In this study, we constructed a Prokaryotic Promoter Database (PPD), which records the experimentally validated promoters in prokaryotes, from published articles. Up to now, PPD has stored 129,148 promoters across 63 prokaryotic species manually extracted from published papers. We provided a friendly interface for users to browse, search, blast, visualize, submit and download data. The PPD will provide relatively comprehensive resources of prokaryotic promoter for the study of prokaryotic gene transcription. The PPD is freely available and easy accessed at http://lin-group.cn/database/ppd/.
Collapse
Affiliation(s)
- Wei Su
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Meng-Lu Liu
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Yu-He Yang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Jia-Shu Wang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Shi-Hao Li
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hao Lv
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Fu-Ying Dao
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hui Yang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hao Lin
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
| |
Collapse
|
9
|
Ataei A, Poorebrahim M, Rajabpour A, Rizvanov A, Shahriar Arab S. Topological Analysis of Regulatory Networks Reveals Functionally Key Genes and miRNAs Involved in the Differentiation of Mesenchymal Stem Cells. IRANIAN JOURNAL OF BIOTECHNOLOGY 2021; 19:e2565. [PMID: 34179189 PMCID: PMC8217530 DOI: 10.30498/ijb.2021.2565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Background The details of molecular mechanisms underlying the differentiation of Mesenchymal Stem Cells (MSCs) into specific lineages are not well understood. Objectives We aimed to construct the interactome network and topology analysis of bone marrow mesenchymal stem cell of CAGE data. Applying the enrichment results, we wanted to introduce the common genes and hub-microRNA and hub-genes of these giant network. Materials and Methods In this study, we constructed gene regulatory networks for each non-mesenchymal cell lineage according to their gene expression profiles obtained from FANTOM5 database. The putative interactions of TF-gene and protein-protein were determined using TRED, STRING, HPRD and GeneMANIA servers. In parallel, a regulatory network including corresponding miRNAs and total differentially expressed genes (DEGs) was constructed for each cell lineage. Results The results indicated that analysis of networks' topology can significantly distinguish the hub regulatory genes and miRNAs involved in the differentiation of MSCs. The functional annotation of identified hub genes and miRNAs revealed that several signal transduction pathways i.e. AKT, WNT and TGFβ and cell proliferation related pathways play a pivotal role in the regulation of MSCs differentiation. We also classified cell lineages into two groups based on their predicted miRNA profiles. Conclusions In conclusion, we found a number of hub genes and miRNAs which seem to have key regulatory functions during differentiation of MSCs. Our results also introduce a number of new regulatory genes and miRNAs which can be considered as the new candidates for genetic manipulation of MSCs in vitro.
Collapse
Affiliation(s)
- Atousa Ataei
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia.,Equal contribution
| | - Mansour Poorebrahim
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, University of Medical Sciences, Tehran, Iran.,Equal contribution
| | - Azam Rajabpour
- Cellular and Molecular Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Albert Rizvanov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Seyed Shahriar Arab
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| |
Collapse
|
10
|
Kim C, Beilina A, Smith N, Li Y, Kim M, Kumaran R, Kaganovich A, Mamais A, Adame A, Iba M, Kwon S, Lee WJ, Shin SJ, Rissman RA, You S, Lee SJ, Singleton AB, Cookson MR, Masliah E. LRRK2 mediates microglial neurotoxicity via NFATc2 in rodent models of synucleinopathies. Sci Transl Med 2020; 12:eaay0399. [PMID: 33055242 PMCID: PMC8100991 DOI: 10.1126/scitranslmed.aay0399] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 09/04/2019] [Accepted: 03/31/2020] [Indexed: 12/15/2022]
Abstract
Synucleinopathies are neurodegenerative disorders characterized by abnormal α-synuclein deposition that include Parkinson's disease, dementia with Lewy bodies, and multiple system atrophy. The pathology of these conditions also includes neuronal loss and neuroinflammation. Neuron-released α-synuclein has been shown to induce neurotoxic, proinflammatory microglial responses through Toll-like receptor 2, but the molecular mechanisms involved are poorly understood. Here, we show that leucine-rich repeat kinase 2 (LRRK2) plays a critical role in the activation of microglia by extracellular α-synuclein. Exposure to α-synuclein was found to enhance LRRK2 phosphorylation and activity in mouse primary microglia. Furthermore, genetic and pharmacological inhibition of LRRK2 markedly diminished α-synuclein-mediated microglial neurotoxicity via lowering of tumor necrosis factor-α and interleukin-6 expression in mouse cultures. We determined that LRRK2 promoted a neuroinflammatory cascade by selectively phosphorylating and inducing nuclear translocation of the immune transcription factor nuclear factor of activated T cells, cytoplasmic 2 (NFATc2). NFATc2 activation was seen in patients with synucleinopathies and in a mouse model of synucleinopathy, where administration of an LRRK2 pharmacological inhibitor restored motor behavioral deficits. Our results suggest that modulation of LRRK2 and its downstream signaling mediator NFATc2 might be therapeutic targets for treating synucleinopathies.
Collapse
Affiliation(s)
- Changyoun Kim
- Molecular Neuropathology Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Alexandria Beilina
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nathan Smith
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, NE 68588, USA
| | - Yan Li
- Protein/Peptide Sequencing Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Minhyung Kim
- Departments of Surgery and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Ravindran Kumaran
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alice Kaganovich
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adamantios Mamais
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anthony Adame
- Department of Neurosciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Michiyo Iba
- Molecular Neuropathology Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Somin Kwon
- Molecular Neuropathology Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Won-Jae Lee
- Department of Biomedical Sciences, Neuroscience Research Institute, and Department of Medicine, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Soo-Jean Shin
- Department of Biomedical Sciences, Neuroscience Research Institute, and Department of Medicine, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Robert A Rissman
- Department of Neurosciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sungyong You
- Departments of Surgery and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Seung-Jae Lee
- Department of Biomedical Sciences, Neuroscience Research Institute, and Department of Medicine, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Andrew B Singleton
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark R Cookson
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eliezer Masliah
- Molecular Neuropathology Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA.
| |
Collapse
|
11
|
Ma J, Xia LL, Yao XQ, Zheng SM, Li S, Xu LS, Sha WH, Li ZS. BARX2 expression is downregulated by CpG island hypermethylation and is associated with suppressed cell proliferation and invasion of gastric cancer cells. Oncol Rep 2020; 43:1805-1818. [PMID: 32236603 PMCID: PMC7160541 DOI: 10.3892/or.2020.7558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 02/21/2020] [Indexed: 12/18/2022] Open
Abstract
BarH-like homeobox 2 (BARX2), a homeobox gene, is associated with several types of cancers. The present study aimed to determine whether DNA methylation downregulates BARX2 expression and whether BARX2 is associated with suppression of gastric carcinogenesis. BARX2 protein expression in normal and cancerous gastric tissues and various gastric cancer (GC) cell lines was detected using immunohistochemical and western blot assays. BARX2 mRNA levels were detected using both reverse transcription-polymerase chain reaction (RT-PCR) and quantitative PCR (qPCR). Promoter hypermethylation in GC cells was detected using methylation-specific PCR or bisulfite DNA sequencing PCR. Effects of BARX2 expression on GC cell proliferation, clonal formation, and migration were evaluated after lentivirus-BARX2 transfection. The effect of stable BARX2 transfection on tumor formation was assessed in a nude xenograft mouse model. BARX2 was strongly expressed in the normal gastric mucosa, but weakly or not expressed in GC tissues and most GC cell lines. BARX2 expression was negatively correlated with DNMT (a marker for DNA methylation) expression in the gastric tissues. The BARX2 promoter fragment was hypermethylated in the GC cell lines. Overexpression of BARX2 significantly inhibited GC cell proliferation, clonal formation, and migration. Stable BARX2 transfection inhibited tumor formation in xenograft mice, which was correlated with decreased expression of E-cadherin, proliferation markers, and matrix metalloproteinases. In conclusion, BARX2 expression is aberrantly reduced in GC, which is associated with increased DNA methylation of its promoter. BARX2 inhibits GC cell proliferation, migration, and tumor formation, suggesting that BARX2 acts as a tumor suppressor in gastric carcinogenesis.
Collapse
Affiliation(s)
- Juan Ma
- Department of Gastroenterology and Hepatology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, and Guangdong Provincial Geriatrics Institute, Guangzhou, Guangdong 510080, P.R. China
| | - Ling-Ling Xia
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong 518000, P.R. China
| | - Xue-Qing Yao
- Department of General Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, P.R. China
| | - Shi-Min Zheng
- Department of Gastroenterology and Hepatology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, and Guangdong Provincial Geriatrics Institute, Guangzhou, Guangdong 510080, P.R. China
| | - Shi Li
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong 518000, P.R. China
| | - Li-Shu Xu
- Department of Gastroenterology and Hepatology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, and Guangdong Provincial Geriatrics Institute, Guangzhou, Guangdong 510080, P.R. China
| | - Wei-Hong Sha
- Department of Gastroenterology and Hepatology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, and Guangdong Provincial Geriatrics Institute, Guangzhou, Guangdong 510080, P.R. China
| | - Ze-Song Li
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong 518000, P.R. China
| |
Collapse
|
12
|
Study on the Antibreast Cancer Mechanism and Bioactive Components of Si-Wu-Tang by Cell Type-Specific Molecular Network. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2020; 2020:2345970. [PMID: 32256636 PMCID: PMC7091537 DOI: 10.1155/2020/2345970] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 02/13/2020] [Indexed: 01/14/2023]
Abstract
Si-Wu-Tang (SWT), a traditional Chinese herbal formula, has shown an effect on antibreast cancer. However, the mechanisms and bioactive components of SWT are still unclear. Fortunately, cell type-specific molecular network has provided an effective method. This study integrated the data of formula components, all types of biomolecules in the human body, and nonexpressed protein in breast cancer cells and constructed the breast cancer cell network and the biological network that SWT acted on the breast cancer-related targets by Entity Grammar System (EGS). Biological network showed 59 bioactive components acting on 15 breast cancer-related targets. The antibreast cancer mechanisms were summarized by enrichment analysis: regulation of cell death, response to hormone stimulation, response to organic substance, regulation of phosphorylation of amino acids, regulation of cell proliferation, regulation of signal transmission, and affection of gland development. In addition, we discovered that verbascoside played the role of antibreast cancer by inhibiting cell proliferation, but there was not a report on this effect. The results of CCK8 and western blot were consistent with the antibreast cancer effect of verbascoside based on biological network. Biological network modeling by EGS and network analysis provide an effective way for uncovering the mechanism and identifying the bioactive components of SWT.
Collapse
|
13
|
Jex AR, Svärd S, Hagen KD, Starcevich H, Emery-Corbin SJ, Balan B, Nosala C, Dawson SC. Recent advances in functional research in Giardia intestinalis. ADVANCES IN PARASITOLOGY 2020; 107:97-137. [PMID: 32122532 PMCID: PMC7878119 DOI: 10.1016/bs.apar.2019.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This review considers current advances in tools to investigate the functional biology of Giardia, it's coding and non-coding genes, features and cellular and molecular biology. We consider major gaps in current knowledge of the parasite and discuss the present state-of-the-art in its in vivo and in vitro cultivation. Advances in in silico tools, including for the modelling non-coding RNAs and genomic elements, as well as detailed exploration of coding genes through inferred homology to model organisms, have provided significant, primary level insight. Improved methods to model the three-dimensional structure of proteins offer new insights into their function, and binding interactions with ligands, other proteins or precursor drugs, and offer substantial opportunities to prioritise proteins for further study and experimentation. These approaches can be supplemented by the growing and highly accessible arsenal of systems-based methods now being applied to Giardia, led by genomic, transcriptomic and proteomic methods, but rapidly incorporating advanced tools for detection of real-time transcription, evaluation of chromatin states and direct measurement of macromolecular complexes. Methods to directly interrogate and perturb gene function have made major leaps in recent years, with CRISPr-interference now available. These approaches, coupled with protein over-expression, fluorescent labelling and in vitro and in vivo imaging, are set to revolutionize the field and herald an exciting time during which the field may finally realise Giardia's long proposed potential as a model parasite and eukaryote.
Collapse
Affiliation(s)
- Aaron R Jex
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC, Australia; Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia.
| | - Staffan Svärd
- Centre for Biomedicine, Uppsala University, Uppsala, Sweden
| | - Kari D Hagen
- College of Biological Sciences, University of California-Davis, Davis, CA, United States
| | - Hannah Starcevich
- College of Biological Sciences, University of California-Davis, Davis, CA, United States
| | - Samantha J Emery-Corbin
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC, Australia
| | - Balu Balan
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC, Australia
| | - Chris Nosala
- College of Biological Sciences, University of California-Davis, Davis, CA, United States
| | - Scott C Dawson
- College of Biological Sciences, University of California-Davis, Davis, CA, United States
| |
Collapse
|
14
|
Hörhold F, Eisel D, Oswald M, Kolte A, Röll D, Osen W, Eichmüller SB, König R. Reprogramming of macrophages employing gene regulatory and metabolic network models. PLoS Comput Biol 2020; 16:e1007657. [PMID: 32097424 PMCID: PMC7059956 DOI: 10.1371/journal.pcbi.1007657] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 03/06/2020] [Accepted: 01/14/2020] [Indexed: 12/20/2022] Open
Abstract
Upon exposure to different stimuli, resting macrophages undergo classical or alternative polarization into distinct phenotypes that can cause fatal dysfunction in a large range of diseases, such as systemic infection leading to sepsis or the generation of an immunosuppressive tumor microenvironment. Investigating gene regulatory and metabolic networks, we observed two metabolic switches during polarization. Most prominently, anaerobic glycolysis was utilized by M1-polarized macrophages, while the biosynthesis of inosine monophosphate was upregulated in M2-polarized macrophages. Moreover, we observed a switch in the urea cycle. Gene regulatory network models revealed E2F1, MYC, PPARγ and STAT6 to be the major players in the distinct signatures of these polarization events. Employing functional assays targeting these regulators, we observed the repolarization of M2-like cells into M1-like cells, as evidenced by their specific gene expression signatures and cytokine secretion profiles. The predicted regulators are essential to maintaining the M2-like phenotype and function and thus represent potential targets for the therapeutic reprogramming of immunosuppressive M2-like macrophages.
Collapse
Affiliation(s)
- Franziska Hörhold
- Center for Sepsis Control and Care, University Hospital, Jena, Germany
| | - David Eisel
- Research Group GMP & T Cell Therapy, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Biopharmaceutical New Technologies (BioNTech) Corporation, Mainz, Germany
| | - Marcus Oswald
- Center for Sepsis Control and Care, University Hospital, Jena, Germany
| | - Amol Kolte
- Center for Sepsis Control and Care, University Hospital, Jena, Germany
| | - Daniela Röll
- Center for Sepsis Control and Care, University Hospital, Jena, Germany
| | - Wolfram Osen
- Research Group GMP & T Cell Therapy, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan B. Eichmüller
- Research Group GMP & T Cell Therapy, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rainer König
- Center for Sepsis Control and Care, University Hospital, Jena, Germany
| |
Collapse
|
15
|
Liu ZG, Li Y, Jiao JH, Long H, Xin ZY, Yang XY. MicroRNA regulatory pattern in spinal cord ischemia-reperfusion injury. Neural Regen Res 2020; 15:2123-2130. [PMID: 32394971 PMCID: PMC7716024 DOI: 10.4103/1673-5374.280323] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
After spinal cord injury, dysregulated miRNAs appear and can participate in inflammatory responses, as well as the inhibition of apoptosis and axon regeneration through multiple pathways. However, the functions of miRNAs in spinal cord ischemia-reperfusion injury progression remain unclear. miRCURY LNATM Arrays were used to analyze miRNA expression profiles of rats after 90 minutes of ischemia followed by reperfusion for 24 and 48 hours. Furthermore, subsequent construction of aberrantly expressed miRNA regulatory patterns involved cell survival, proliferation, and apoptosis. Remarkably, the mitogen-activated protein kinase (MAPK) signaling pathway was the most significantly enriched pathway among 24- and 48-hour groups. Bioinformatics analysis and quantitative reverse transcription polymerase chain reaction confirmed the persistent overexpression of miR-22-3p in both groups. These results suggest that the aberrant miRNA regulatory network is possibly regulated MAPK signaling and continuously affects the physiological and biochemical status of cells, thus participating in the regulation of spinal cord ischemia-reperfusion injury. As such, miR-22-3p may play sustained regulatory roles in spinal cord ischemia-reperfusion injury. All experimental procedures were approved by the Animal Ethics Committee of Jilin University, China [approval No. 2020 (Research) 01].
Collapse
Affiliation(s)
- Zhi-Gang Liu
- Department of Orthopedics, The Second Hospital of Jilin University, Changchun, Jilin Province, China
| | - Yin Li
- School of Public Health, Jilin University, Changchun, Jilin Province, China
| | - Jian-Hang Jiao
- Department of Orthopedics, The Second Hospital of Jilin University, Changchun, Jilin Province, China
| | - Hao Long
- Pain Clinic, The Sixth Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Zhuo-Yuan Xin
- The Key Laboratory of Zoonosis Search, Chinese Ministry of Education, College of Basic Medicine, Jilin University, Changchun, Jilin Province, China
| | - Xiao-Yu Yang
- Department of Orthopedics, The Second Hospital of Jilin University, Changchun, Jilin Province, China
| |
Collapse
|
16
|
Poos AM, Kordaß T, Kolte A, Ast V, Oswald M, Rippe K, König R. Modelling TERT regulation across 19 different cancer types based on the MIPRIP 2.0 gene regulatory network approach. BMC Bioinformatics 2019; 20:737. [PMID: 31888467 PMCID: PMC6937852 DOI: 10.1186/s12859-019-3323-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 12/16/2019] [Indexed: 01/15/2023] Open
Abstract
Background Reactivation of the telomerase reverse transcriptase gene TERT is a central feature for unlimited proliferation of the majority of cancers. However, the underlying regulatory processes are only partly understood. Results We assembled regulator binding information from serveral sources to construct a generic human and mouse gene regulatory network. Advancing our “Mixed Integer linear Programming based Regulatory Interaction Predictor” (MIPRIP) approach, we identified the most common and cancer-type specific regulators of TERT across 19 different human cancers. The results were validated by using the well-known TERT regulation by the ETS1 transcription factor in a subset of melanomas with mutations in the TERT promoter. Our improved MIPRIP2 R-package and the associated generic regulatory networks are freely available at https://github.com/KoenigLabNM/MIPRIP. Conclusion MIPRIP 2.0 identified common as well as tumor type specific regulators of TERT. The software can be easily applied to transcriptome datasets to predict gene regulation for any gene and disease/condition under investigation.
Collapse
Affiliation(s)
- Alexandra M Poos
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany.,Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Theresa Kordaß
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.,Research Group GMP & T Cell Therapy, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Amol Kolte
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Volker Ast
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Marcus Oswald
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany
| | - Rainer König
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany.
| |
Collapse
|
17
|
Chen X, Gu J, Wang X, Jung JG, Wang TL, Hilakivi-Clarke L, Clarke R, Xuan J. CRNET: an efficient sampling approach to infer functional regulatory networks by integrating large-scale ChIP-seq and time-course RNA-seq data. Bioinformatics 2019; 34:1733-1740. [PMID: 29280996 DOI: 10.1093/bioinformatics/btx827] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 12/20/2017] [Indexed: 12/28/2022] Open
Abstract
Motivation NGS techniques have been widely applied in genetic and epigenetic studies. Multiple ChIP-seq and RNA-seq profiles can now be jointly used to infer functional regulatory networks (FRNs). However, existing methods suffer from either oversimplified assumption on transcription factor (TF) regulation or slow convergence of sampling for FRN inference from large-scale ChIP-seq and time-course RNA-seq data. Results We developed an efficient Bayesian integration method (CRNET) for FRN inference using a two-stage Gibbs sampler to estimate iteratively hidden TF activities and the posterior probabilities of binding events. A novel statistic measure that jointly considers regulation strength and regression error enables the sampling process of CRNET to converge quickly, thus making CRNET very efficient for large-scale FRN inference. Experiments on synthetic and benchmark data showed a significantly improved performance of CRNET when compared with existing methods. CRNET was applied to breast cancer data to identify FRNs functional at promoter or enhancer regions in breast cancer MCF-7 cells. Transcription factor MYC is predicted as a key functional factor in both promoter and enhancer FRNs. We experimentally validated the regulation effects of MYC on CRNET-predicted target genes using appropriate RNAi approaches in MCF-7 cells. Availability and implementation R scripts of CRNET are available at http://www.cbil.ece.vt.edu/software.htm. Contact xuan@vt.edu. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Xi Chen
- Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
| | - Jinghua Gu
- Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
| | - Xiao Wang
- Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
| | - Jin-Gyoung Jung
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD 21231, USA
| | - Tian-Li Wang
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD 21231, USA
| | - Leena Hilakivi-Clarke
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Robert Clarke
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Jianhua Xuan
- Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
| |
Collapse
|
18
|
Koh HWL, Fermin D, Vogel C, Choi KP, Ewing RM, Choi H. iOmicsPASS: network-based integration of multiomics data for predictive subnetwork discovery. NPJ Syst Biol Appl 2019; 5:22. [PMID: 31312515 PMCID: PMC6616462 DOI: 10.1038/s41540-019-0099-y] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 06/14/2019] [Indexed: 12/15/2022] Open
Abstract
Computational tools for multiomics data integration have usually been designed for unsupervised detection of multiomics features explaining large phenotypic variations. To achieve this, some approaches extract latent signals in heterogeneous data sets from a joint statistical error model, while others use biological networks to propagate differential expression signals and find consensus signatures. However, few approaches directly consider molecular interaction as a data feature, the essential linker between different omics data sets. The increasing availability of genome-scale interactome data connecting different molecular levels motivates a new class of methods to extract interactive signals from multiomics data. Here we developed iOmicsPASS, a tool to search for predictive subnetworks consisting of molecular interactions within and between related omics data types in a supervised analysis setting. Based on user-provided network data and relevant omics data sets, iOmicsPASS computes a score for each molecular interaction, and applies a modified nearest shrunken centroid algorithm to the scores to select densely connected subnetworks that can accurately predict each phenotypic group. iOmicsPASS detects a sparse set of predictive molecular interactions without loss of prediction accuracy compared to alternative methods, and the selected network signature immediately provides mechanistic interpretation of the multiomics profile representing each sample group. Extensive simulation studies demonstrate clear benefit of interaction-level modeling. iOmicsPASS analysis of TCGA/CPTAC breast cancer data also highlights new transcriptional regulatory network underlying the basal-like subtype as positive protein markers, a result not seen through analysis of individual omics data.
Collapse
Affiliation(s)
- Hiromi W. L. Koh
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Damian Fermin
- University of Michigan Medical School, Ann Arbor, MI USA
| | - Christine Vogel
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003 USA
| | - Kwok Pui Choi
- Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
| | - Rob M. Ewing
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Hyungwon Choi
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
| |
Collapse
|
19
|
Ahn H, Jo K, Jeong D, Pak M, Hur J, Jung W, Kim S. PropaNet: Time-Varying Condition-Specific Transcriptional Network Construction by Network Propagation. FRONTIERS IN PLANT SCIENCE 2019; 10:698. [PMID: 31258543 PMCID: PMC6587906 DOI: 10.3389/fpls.2019.00698] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 05/09/2019] [Indexed: 06/09/2023]
Abstract
Transcription factor (TF) has a significant influence on the state of a cell by regulating multiple down-stream genes. Thus, experimental and computational biologists have made great efforts to construct TF gene networks for regulatory interactions between TFs and their target genes. Now, an important research question is how to utilize TF networks to investigate the response of a plant to stress at the transcription control level using time-series transcriptome data. In this article, we present a new computational network, PropaNet, to investigate dynamics of TF networks from time-series transcriptome data using two state-of-the-art network analysis techniques, influence maximization and network propagation. PropaNet uses the influence maximization technique to produce a ranked list of TFs, in the order of TF that explains differentially expressed genes (DEGs) better at each time point. Then, a network propagation technique is used to select a group of TFs that explains DEGs best as a whole. For the analysis of Arabidopsis time series datasets from AtGenExpress, we used PlantRegMap as a template TF network and performed PropaNet analysis to investigate transcriptional dynamics of Arabidopsis under cold and heat stress. The time varying TF networks showed that Arabidopsis responded to cold and heat stress quite differently. For cold stress, bHLH and bZIP type TFs were the first responding TFs and the cold signal influenced histone variants, various genes involved in cell architecture, osmosis and restructuring of cells. However, the consequences of plants under heat stress were up-regulation of genes related to accelerating differentiation and starting re-differentiation. In terms of energy metabolism, plants under heat stress show elevated metabolic process and resulting in an exhausted status. We believe that PropaNet will be useful for the construction of condition-specific time-varying TF network for time-series data analysis in response to stress. PropaNet is available at http://biohealth.snu.ac.kr/software/PropaNet.
Collapse
Affiliation(s)
- Hongryul Ahn
- Bioinformatics Institute, Seoul National University, Seoul, South Korea
| | - Kyuri Jo
- Bioinformatics Institute, Seoul National University, Seoul, South Korea
| | - Dabin Jeong
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea
| | - Minwoo Pak
- Department of Computer Science and Engineering, Seoul National University, Seoul, South Korea
| | - Jihye Hur
- Department of Crop Science, Konkuk University, Seoul, South Korea
| | - Woosuk Jung
- Department of Crop Science, Konkuk University, Seoul, South Korea
| | - Sun Kim
- Bioinformatics Institute, Seoul National University, Seoul, South Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea
- Department of Computer Science and Engineering, Seoul National University, Seoul, South Korea
| |
Collapse
|
20
|
King D, Glynn M, Cindric S, Kernan D, O'Connell T, Hakimjavadi R, Kearney S, Ackermann T, Berbel XM, Llobera A, Simonsen U, Laursen BE, Redmond EM, Cahill PA, Ducrée J. Label-Free Multi Parameter Optical Interrogation of Endothelial Activation in Single Cells using a Lab on a Disc Platform. Sci Rep 2019; 9:4157. [PMID: 30858536 PMCID: PMC6411894 DOI: 10.1038/s41598-019-40612-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 01/31/2019] [Indexed: 12/31/2022] Open
Abstract
Cellular activation and inflammation leading to endothelial dysfunction is associated with cardiovascular disease (CVD). We investigated whether a single cell label-free multi parameter optical interrogation system can detect endothelial cell and endothelial progenitor cell (EPC) activation in vitro and ex vivo, respectively. Cultured human endothelial cells were exposed to increasing concentrations of tumour necrosis factor alpha (TNF-α) or lipopolysaccharide (LPS) before endothelial activation was validated using fluorescence-activated cell sorting (FACS) analysis of inflammatory marker expression (PECAM-1, E-selectin and ICAM-1). A centrifugal microfluidic system and V-cup array was used to capture individual cells before optical measurement of light scattering, immunocytofluorescence, auto-fluorescence (AF) and cell morphology was determined. In vitro, TNF-α promoted specific changes to the refractive index and cell morphology of individual cells concomitant with enhanced photon activity of fluorescently labelled inflammatory markers and increased auto-fluorescence (AF) intensity at three different wavelengths, an effect blocked by inhibition of downstream signalling with Iκβ. Ex vivo, there was a significant increase in EPC number and AF intensity of individual EPCs from CVD patients concomitant with enhanced PECAM-1 expression when compared to normal controls. This novel label-free 'lab on a disc' (LoaD) platform can successfully detect endothelial activation in response to inflammatory stimuli in vitro and ex vivo.
Collapse
Affiliation(s)
- Damien King
- Dublin City University, School of Physical Sciences, National Centre for Sensor Research, Dublin, Ireland
| | - MacDara Glynn
- Dublin City University, School of Physical Sciences, National Centre for Sensor Research, Dublin, Ireland
| | - Sandra Cindric
- Dublin City University, School of Physical Sciences, National Centre for Sensor Research, Dublin, Ireland
| | - David Kernan
- Dublin City University, School of Physical Sciences, National Centre for Sensor Research, Dublin, Ireland
| | - Tríona O'Connell
- Dublin City University, School of Biotechnology, Irish Science Separation Cluster, Dublin, Ireland
| | - Roya Hakimjavadi
- Dublin City University, School of Biotechnology, Vascular Biology & Therapeutics, Dublin, Ireland
| | - Sinéad Kearney
- Dublin City University, School of Physical Sciences, National Centre for Sensor Research, Dublin, Ireland
| | - Tobias Ackermann
- Dublin City University, School of Biotechnology, Vascular Biology & Therapeutics, Dublin, Ireland
| | | | - Andreu Llobera
- Centre Nacional de Microelectronica, Campus UAB, Barcelona, Spain
| | - Ulf Simonsen
- Aarhus University, Department of Biomedicine, Aarhus, Denmark
| | - Britt E Laursen
- Aarhus University, Department of Biomedicine, Aarhus, Denmark
| | - Eileen M Redmond
- University of Rochester, Dept Surgery Rochester, New York, United States
| | - Paul A Cahill
- Dublin City University, School of Biotechnology, Vascular Biology & Therapeutics, Dublin, Ireland
| | - Jens Ducrée
- Dublin City University, School of Physical Sciences, National Centre for Sensor Research, Dublin, Ireland.
| |
Collapse
|
21
|
Zhou Y, Zhu W, Zhang L, Zeng Y, Xu C, Tian Q, Deng HW. Transcriptomic Data Identified Key Transcription Factors for Osteoporosis in Caucasian Women. Calcif Tissue Int 2018; 103:581-588. [PMID: 30056508 PMCID: PMC6343666 DOI: 10.1007/s00223-018-0457-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 07/14/2018] [Indexed: 12/27/2022]
Abstract
Osteoporosis is a prevalent bone metabolic disease, mainly caused by excessive bone resorption (by osteoclasts) over bone formation (by osteoblasts). Identifying the key transcription factors and understanding the regulatory network influencing osteoclastogenesis will be helpful to explore the potential biological mechanism for osteoporosis. In our study, peripheral blood monocyte (PBM) was used as a cell model for bone mineral density (BMD) research. PBMs serve as progenitors of osteoclasts and produce important cytokines for osteoclastogenesis. In our study, via exon arrays, gene expression profiles of PBMs were analyzed between high versus low hip BMD groups. Transcription factors for differentially expressed genes were then predicted based on the enrichment analysis. We found that 591 genes were differentially expressed between the two BMD groups (nominally significant, raw p value < 0.05). For high BMD subjects, 482 genes were up-regulated and 109 genes were down-regulated. We then found 29 potential transcription factors for up-regulated genes and nine transcription factors for down-regulated genes. Among these transcription factors, HMGA1 and NFKB2 were differentially expressed between high versus low BMD groups. In addition, their regulation types with their target genes were consistent with the information from public databases. Our findings of key transcription factors and their target genes for osteoporosis were further validated by GWAS analysis. Overall, we predicted important transcription factors for osteoporosis. We were also able to infer the regulatory mechanism that exists between transcription factors and target genes in bone metabolism.
Collapse
Affiliation(s)
- Yu Zhou
- Center of Genomics and Bioinformatics, Tulane University, New Orleans, LA, 70112, USA
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA, 70118, USA
| | - Wei Zhu
- Center of Genomics and Bioinformatics, Tulane University, New Orleans, LA, 70112, USA
- Department of Biostatistics and Bioinformatics, Tulane University, New Orleans, LA, 70112, USA
| | - Lan Zhang
- Center of Genomics and Bioinformatics, Tulane University, New Orleans, LA, 70112, USA
- Department of Biostatistics and Bioinformatics, Tulane University, New Orleans, LA, 70112, USA
| | - Yong Zeng
- Center of Genomics and Bioinformatics, Tulane University, New Orleans, LA, 70112, USA
- Department of Biostatistics and Bioinformatics, Tulane University, New Orleans, LA, 70112, USA
| | - Chao Xu
- Center of Genomics and Bioinformatics, Tulane University, New Orleans, LA, 70112, USA
- Department of Biostatistics and Bioinformatics, Tulane University, New Orleans, LA, 70112, USA
| | - Qing Tian
- Center of Genomics and Bioinformatics, Tulane University, New Orleans, LA, 70112, USA
- Department of Biostatistics and Bioinformatics, Tulane University, New Orleans, LA, 70112, USA
| | - Hong-Wen Deng
- Center of Genomics and Bioinformatics, Tulane University, New Orleans, LA, 70112, USA.
- Department of Biostatistics and Bioinformatics, Tulane University, New Orleans, LA, 70112, USA.
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal St., RM 1619F, New Orleans, LA, 70112, USA.
| |
Collapse
|
22
|
Liu S, Yao X, Zhang D, Sheng J, Wen X, Wang Q, Chen G, Li Z, Du Z, Zhang X. Analysis of Transcription Factor-Related Regulatory Networks Based on Bioinformatics Analysis and Validation in Hepatocellular Carcinoma. BIOMED RESEARCH INTERNATIONAL 2018; 2018:1431396. [PMID: 30228980 PMCID: PMC6136478 DOI: 10.1155/2018/1431396] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 07/03/2018] [Accepted: 07/25/2018] [Indexed: 02/07/2023]
Abstract
Hepatocellular carcinoma (HCC) accounts for a significant proportion of liver cancer, which has become the second most common cause of cancer-related mortality worldwide. To investigate the potential mechanisms of invasion and progression of HCC, bioinformatics analysis and validation by qRT-PCR were performed. We found 237 differentially expressed genes (DEGs) including EGR1, FOS, and FOSB, which were three cancer-related transcription factors. Subsequently, we constructed TF-gene network and miRNA-TF-mRNA network based on data obtained from mRNA and miRNA expression profiles for analysis of HCC. We found that 42 key genes from the TF-gene network including EGR1, FOS, and FOSB were most enriched in the p53 signaling pathway. The qRT-PCR data confirmed that mRNA levels of EGR1, FOS, and FOSB all were decreased in HCC tissues. In addition, we confirmed that the mRNA levels of CCNB1, CCNB2, and CHEK1, three key markers of the p53 signaling pathway, were all increased in HCC tissues by bioinformatics analysis and qRT-PCR validation. Therefore, we speculated that miR-181a-5p, which was upregulated in HCC tissues, could regulate FOS and EGR1 to promote the invasion and progression of HCC by p53 signaling pathway. Overall, the study provides support for the possible mechanisms of progression in HCC.
Collapse
Affiliation(s)
- Shui Liu
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun 130041, China
- Jilin Engineering Laboratory for Translational Medicine of Hepatobiliary and Pancreatic Diseases, The Second Hospital of Jilin University, Changchun 130041, China
| | - Xiaoxiao Yao
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun 130041, China
- Jilin Engineering Laboratory for Translational Medicine of Hepatobiliary and Pancreatic Diseases, The Second Hospital of Jilin University, Changchun 130041, China
| | - Dan Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun 130041, China
- Jilin Engineering Laboratory for Translational Medicine of Hepatobiliary and Pancreatic Diseases, The Second Hospital of Jilin University, Changchun 130041, China
| | - Jiyao Sheng
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun 130041, China
- Jilin Engineering Laboratory for Translational Medicine of Hepatobiliary and Pancreatic Diseases, The Second Hospital of Jilin University, Changchun 130041, China
| | - Xin Wen
- The Second Hospital of Jilin University, Changchun 130041, China
| | - Qingyu Wang
- Department of Orthopedics, The Second Hospital of Jilin University, Changchun 130041, China
| | - Gaoyang Chen
- Department of Orthopedics, The Second Hospital of Jilin University, Changchun 130041, China
| | - Zhaoyan Li
- Department of Orthopedics, The Second Hospital of Jilin University, Changchun 130041, China
| | - Zhenwu Du
- Department of Orthopedics, The Second Hospital of Jilin University, Changchun 130041, China
- Research Center of Second Clinical College, Jilin University, Changchun 130041, China
| | - Xuewen Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun 130041, China
- Jilin Engineering Laboratory for Translational Medicine of Hepatobiliary and Pancreatic Diseases, The Second Hospital of Jilin University, Changchun 130041, China
| |
Collapse
|
23
|
Do D, Bozdag S. Cancerin: A computational pipeline to infer cancer-associated ceRNA interaction networks. PLoS Comput Biol 2018; 14:e1006318. [PMID: 30011266 PMCID: PMC6072113 DOI: 10.1371/journal.pcbi.1006318] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 08/02/2018] [Accepted: 06/17/2018] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRNAs) inhibit expression of target genes by binding to their RNA transcripts. It has been recently shown that RNA transcripts targeted by the same miRNA could “compete” for the miRNA molecules and thereby indirectly regulate each other. Experimental evidence has suggested that the aberration of such miRNA-mediated interaction between RNAs—called competing endogenous RNA (ceRNA) interaction—can play important roles in tumorigenesis. Given the difficulty of deciphering context-specific miRNA binding, and the existence of various gene regulatory factors such as DNA methylation and copy number alteration, inferring context-specific ceRNA interactions accurately is a computationally challenging task. Here we propose a computational method called Cancerin to identify cancer-associated ceRNA interactions. Cancerin incorporates DNA methylation, copy number alteration, gene and miRNA expression datasets to construct cancer-specific ceRNA networks. We applied Cancerin to three cancer datasets from the Cancer Genome Atlas (TCGA) project. Our results indicated that ceRNAs were enriched with cancer-related genes, and ceRNA modules in the inferred ceRNA networks were involved in cancer-associated biological processes. Using LINCS-L1000 shRNA-mediated gene knockdown experiment in breast cancer cell line to assess accuracy, Cancerin was able to predict expression outcome of ceRNA genes with high accuracy. CeRNA interaction is a post-transcriptional gene regulation that involves interactions between RNAs competing for common miRNA regulators. Dysregulation of ceRNA interactions have been implicated in multiple diseases including cancer. Here we propose a computational pipeline called Cancerin that infers genome-wide ceRNA interactions in cancer. Unlike existing ceRNA inference tools that consider miRNAs as the only factor that regulate gene expression, Cancerin considers other types of gene regulators besides miRNAs, namely transcription factors, copy number alteration, and DNA methylation. To identify miRNA regulators for each gene, Cancerin incorporates a LASSO-based variable selection procedure that leverages both sequence-based and gene expression information. Then multiple expression-based filtering conditions are employed to select ceRNA interactions. Cancerin was applied to three cancer datasets from TCGA. Functional analysis indicated that the inferred ceRNAs were enriched with cancer-related genes, and ceRNAs within ceRNA modules (densely-connected ceRNAs) were involved in cancer-associated biological processes. Survival analysis showed that compared to non-ceRNAs, ceRNAs hold better prognostic power to predict survival outcomes. Our results showed that Cancerin can be used to identify genome-wide and functionally important ceRNA interactions, which makes it a valuable tool to better understand this recently discovered gene regulation mechanism and its role in cancer biology.
Collapse
Affiliation(s)
- Duc Do
- Department of Mathematics, Statistics, and Computer Science, Marquette University, Milwaukee, Wisconsin, United States of America
| | - Serdar Bozdag
- Department of Mathematics, Statistics, and Computer Science, Marquette University, Milwaukee, Wisconsin, United States of America
- * E-mail:
| |
Collapse
|
24
|
Arsenic-induced apoptosis in the p53-proficient and p53-deficient cells through differential modulation of NFkB pathway. Food Chem Toxicol 2018; 118:849-860. [PMID: 29944914 DOI: 10.1016/j.fct.2018.06.053] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 06/21/2018] [Accepted: 06/22/2018] [Indexed: 12/31/2022]
Abstract
Arsenic is a well-known environmental carcinogen and an effective chemotherapeutic agent. The underlying mechanism of this dual-effect, however, is not fully understood. In this study, we applied mouse p53+/+ and p53-/- cells to examine the NFκB pathway and proinflammatory cytokines after arsenic treatment. Arsenic reduced cell viability and increased more apoptosis in the p53-/- cells as compared to p53+/+ cells, which was correlated with activation of SAPK/JNK, p38 MAPK, and AKT pathways. A transcriptional regulatory network analysis revealed that arsenic activated transcription regulatory elements E2F, Egr1, Trp53, Stat6, Bcl6, Creb2 and ATF4 in the p53+/+ cells, while in the p53-/- cells, arsenic treatment altered transcription factors NFκB, Pparg, Creb2, ATF4, and Egr1. We observed dynamic changes in phosphorylated NFκB p65 (p-NFκB p65) and phosphorylated IKKαβ (p-IKKαβ) in both genotypes from 4 h to 24 h after treatment, significant decreases of p-NFκB p65 and p-IKKαβ in the p53-/- cells, whereas increases of p-NFκB p65 and p-IKKαβ were observed in the p53+/+ cells. Our study confirmed the differential modulation of NFκB pathway by arsenic in the p53+/+ or p53-/- cells and this observation of the differential mechanism of cell death between the p53+/+ and p53-/- cells might be linked to the unique ability of arsenic to act as both a carcinogen and a chemotherapeutic agent.
Collapse
|
25
|
Zhang S, Li M, Ji H, Fang Z. Landscape of transcriptional deregulation in lung cancer. BMC Genomics 2018; 19:435. [PMID: 29866045 PMCID: PMC5987572 DOI: 10.1186/s12864-018-4828-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 05/25/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Lung cancer is a very heterogeneous disease that can be pathologically classified into different subtypes including small-cell lung carcinoma (SCLC), lung adenocarcinoma (LUAD), lung squamous cell carcinoma (LUSC) and large-cell carcinoma (LCC). Although much progress has been made towards the oncogenic mechanism of each subtype, transcriptional circuits mediating the upstream signaling pathways and downstream functional consequences remain to be systematically studied. RESULTS Here we trained a one-class support vector machine (OC-SVM) model to establish a general transcription factor (TF) regulatory network containing 325 TFs and 18724 target genes. We then applied this network to lung cancer subtypes and identified those deregulated TFs and downstream targets. We found that the TP63/SOX2/DMRT3 module was specific to LUSC, corresponding to squamous epithelial differentiation and/or survival. Moreover, the LEF1/MSC module was specifically activated in LUAD and likely to confer epithelial-to-mesenchymal transition, known important for cancer malignant progression and metastasis. The proneural factor, ASCL1, was specifically up-regulated in SCLC which is known to have a neuroendocrine phenotype. Also, ID2 was differentially regulated between SCLC and LUSC, with its up-regulation in SCLC linking to energy supply for fast mitosis and its down-regulation in LUSC linking to the attenuation of immune response. We further described the landscape of TF regulation among the three major subtypes of lung cancer, highlighting their functional commonalities and specificities. CONCLUSIONS Our approach uncovered the landscape of transcriptional deregulation in lung cancer, and provided a useful resource of TF regulatory network for future studies.
Collapse
Affiliation(s)
- Shu Zhang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 People’s Republic of China
- State Key Laboratory of Cell Biology, Shanghai, China
- CAS Center for Excellence in Molecular Cell Science, Shanghai, China
- Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai, 200031 China
| | - Mingfa Li
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 People’s Republic of China
| | - Hongbin Ji
- State Key Laboratory of Cell Biology, Shanghai, China
- CAS Center for Excellence in Molecular Cell Science, Shanghai, China
- Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai, 200031 China
- School of Life Science and Technology, Shanghai Tech University, Shanghai, 200120 China
| | - Zhaoyuan Fang
- State Key Laboratory of Cell Biology, Shanghai, China
- CAS Center for Excellence in Molecular Cell Science, Shanghai, China
- Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai, 200031 China
- Shanghai Institutes for Biological Sciences, Chinese Academy of Science, Shanghai, 200031 China
| |
Collapse
|
26
|
Amalraj T, Dravid AA, Tripathi R, Lulu SS. Database of transcription factors in lung cancer (DBTFLC): A novel resource for exploring transcription factors associated with lung cancer. J Cell Biochem 2018; 119:5253-5261. [DOI: 10.1002/jcb.26603] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 12/04/2017] [Indexed: 01/13/2023]
Affiliation(s)
- Thabitha Amalraj
- Department of BiotechnologySchool of Bio Sciences and TechnologyVIT UniversityVelloreTamilnaduIndia
| | - Ameya A. Dravid
- Department of BiotechnologySchool of Bio Sciences and TechnologyVIT UniversityVelloreTamilnaduIndia
| | - Riya Tripathi
- Department of BiotechnologySchool of Bio Sciences and TechnologyVIT UniversityVelloreTamilnaduIndia
| | - S. Sajitha Lulu
- Department of BiotechnologySchool of Bio Sciences and TechnologyVIT UniversityVelloreTamilnaduIndia
| |
Collapse
|
27
|
Data Mining Mycobacterium tuberculosis Pathogenic Gene Transcription Factors and Their Regulatory Network Nodes. Int J Genomics 2018; 2018:3079730. [PMID: 29725597 PMCID: PMC5872665 DOI: 10.1155/2018/3079730] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 11/06/2017] [Accepted: 12/05/2017] [Indexed: 02/06/2023] Open
Abstract
Tuberculosis (TB) is one of the deadliest infectious diseases worldwide. In Mycobacterium tuberculosis, changes in gene expression are highly variable and involve many genes, so traditional single-gene screening of M. tuberculosis targets has been unable to meet the needs of clinical diagnosis. In this study, using the National Center for Biotechnology Information (NCBI) GEO Datasets, whole blood gene expression profile data were obtained in patients with active pulmonary tuberculosis. Linear model-experience Bayesian statistics using the Limma package in R combined with t-tests were applied for nonspecific filtration of the expression profile data, and the differentially expressed human genes were determined. Using DAVID and KEGG, the functional analysis of differentially expressed genes (GO analysis) and the analysis of signaling pathways were performed. Based on the differentially expressed gene, the transcriptional regulatory element databases (TRED) were integrated to construct the M. tuberculosis pathogenic gene regulatory network, and the correlation of the network genes with disease was analyzed with the DAVID online annotation tool. It was predicted that IL-6, JUN, and TP53, along with transcription factors SRC, TNF, and MAPK14, could regulate the immune response, with their function being extracellular region activity and protein binding during infection with M. tuberculosis.
Collapse
|
28
|
Xu G, Xu J, Han X, Li H, Yuan G, An L, Du P. mRNA chip-based analysis on transcription factor regulatory network central nodes of protection targets of Deproteinized Extract of Calf Blood on acute liver injury in mice. Int Immunopharmacol 2018; 56:212-216. [PMID: 29414653 DOI: 10.1016/j.intimp.2018.01.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/18/2018] [Accepted: 01/18/2018] [Indexed: 02/06/2023]
Abstract
Our previous study found that Deproteinized Extract of Calf Blood (DECB) could protect the acute liver injury induced by carbon tetrachloride in mice, but the target-related transcription factors and their regulatory networks were not comprehensively studied. Based on the mRNA expression microarray data obtained in the previous study, the mRNA transcription factor regulatory networks were constructed by screening the transcription factors of differentially expressed genes and their corresponding target proteins, and the analysis on the functions and pathways of the regulatory network central nodes was performed. Eight genes Ltf, Tnf, Il6, Jun, Il12b, Stat3, Rel and Crem could regulate the inflammatory factors, and TNF signaling pathway and Jak-STAT signaling pathway might play an important role in the mechanism through which DECB protected the liver of mice. DECB can not only inhibit the apoptosis of hepatocytes, but also inhibit the inflammatory cytokines.
Collapse
Affiliation(s)
- Guangyu Xu
- College of Pharmacy, Beihua University, Jilin, Jilin 132013, China
| | - Jinhe Xu
- College of Pharmacy, Beihua University, Jilin, Jilin 132013, China
| | - Xiao Han
- College of Pharmacy, Beihua University, Jilin, Jilin 132013, China
| | - Hongyu Li
- College of Pharmacy, Beihua University, Jilin, Jilin 132013, China
| | - Guangxin Yuan
- College of Pharmacy, Beihua University, Jilin, Jilin 132013, China
| | - Liping An
- College of Pharmacy, Beihua University, Jilin, Jilin 132013, China.
| | - Peige Du
- College of Pharmacy, Beihua University, Jilin, Jilin 132013, China.
| |
Collapse
|
29
|
Han H, Cho JW, Lee S, Yun A, Kim H, Bae D, Yang S, Kim CY, Lee M, Kim E, Lee S, Kang B, Jeong D, Kim Y, Jeon HN, Jung H, Nam S, Chung M, Kim JH, Lee I. TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions. Nucleic Acids Res 2018; 46:D380-D386. [PMID: 29087512 PMCID: PMC5753191 DOI: 10.1093/nar/gkx1013] [Citation(s) in RCA: 1026] [Impact Index Per Article: 171.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 10/02/2017] [Accepted: 10/13/2017] [Indexed: 02/07/2023] Open
Abstract
Transcription factors (TFs) are major trans-acting factors in transcriptional regulation. Therefore, elucidating TF-target interactions is a key step toward understanding the regulatory circuitry underlying complex traits such as human diseases. We previously published a reference TF-target interaction database for humans-TRRUST (Transcriptional Regulatory Relationships Unraveled by Sentence-based Text mining)-which was constructed using sentence-based text mining, followed by manual curation. Here, we present TRRUST v2 (www.grnpedia.org/trrust) with a significant improvement from the previous version, including a significantly increased size of the database consisting of 8444 regulatory interactions for 800 TFs in humans. More importantly, TRRUST v2 also contains a database for TF-target interactions in mice, including 6552 TF-target interactions for 828 mouse TFs. TRRUST v2 is also substantially more comprehensive and less biased than other TF-target interaction databases. We also improved the web interface, which now enables prioritization of key TFs for a physiological condition depicted by a set of user-input transcriptional responsive genes. With the significant expansion in the database size and inclusion of the new web tool for TF prioritization, we believe that TRRUST v2 will be a versatile database for the study of the transcriptional regulation involved in human diseases.
Collapse
Affiliation(s)
- Heonjong Han
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Jae-Won Cho
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Sangyoung Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Ayoung Yun
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Hyojin Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Dasom Bae
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Sunmo Yang
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Chan Yeong Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Muyoung Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Eunbeen Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Sungho Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Byunghee Kang
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Dabin Jeong
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Yaeji Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Hyeon-Nae Jeon
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Haein Jung
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Sunhwee Nam
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Michael Chung
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Jong-Hoon Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Korea University, Seoul 02841, Korea
| | - Insuk Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| |
Collapse
|
30
|
Soliman M, Andreeva K, Nasraoui O, Cooper NGF. A causal mediation model of ischemia reperfusion injury in the retina. PLoS One 2017; 12:e0187426. [PMID: 29121052 PMCID: PMC5679526 DOI: 10.1371/journal.pone.0187426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 10/19/2017] [Indexed: 11/30/2022] Open
Abstract
The goal of this study is to develop a model that explains the relationship between microRNAs, transcription factors, and their co-target genes. This relationship was previously reported in gene regulatory loops associated with 24 hour (24h) and 7 day (7d) time periods following ischemia-reperfusion injury in a rat's retina. Using a model system of retinal ischemia-reperfusion injury, we propose that microRNAs first influence transcription factors, which in turn act as mediators to influence transcription of genes via triadic regulatory loops. Analysis of the relative contributions of direct and indirect regulatory influences on genes revealed that a substantial fraction of the regulatory loops (69% for 24 hours and 77% for 7 days) could be explained by causal mediation. Over 40% of the mediated loops in both time points were regulated by transcription factors only, while about 20% of the loops were regulated entirely by microRNAs. The remaining fractions of the mediated regulatory loops were cooperatively mediated by both microRNAs and transcription factors. The results from these analyses were supported by the patterns of expression of the genes, transcription factors, and microRNAs involved in the mediated loops in both post-ischemic time points. Additionally, network motif detection for the mediated loops showed a handful of time specific motifs related to ischemia-reperfusion injury in a rat's retina. In summary, the effects of microRNAs on genes are mediated, in large part, via transcription factors.
Collapse
Affiliation(s)
- Maha Soliman
- Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, KY, United States of America
| | - Kalina Andreeva
- Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, KY, United States of America
| | - Olfa Nasraoui
- Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY, United States of America
| | - Nigel G. F. Cooper
- Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, KY, United States of America
| |
Collapse
|
31
|
Majewska M, Wysokińska H, Kuźma Ł, Szymczyk P. Eukaryotic and prokaryotic promoter databases as valuable tools in exploring the regulation of gene transcription: a comprehensive overview. Gene 2017; 644:38-48. [PMID: 29104165 DOI: 10.1016/j.gene.2017.10.079] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 07/26/2017] [Accepted: 10/27/2017] [Indexed: 01/02/2023]
Abstract
The complete exploration of the regulation of gene expression remains one of the top-priority goals for researchers. As the regulation is mainly controlled at the level of transcription by promoters, study on promoters and findings are of great importance. This review summarizes forty selected databases that centralize experimental and theoretical knowledge regarding the organization of promoters, interacting transcription factors (TFs) and microRNAs (miRNAs) in many eukaryotic and prokaryotic species. The presented databases offer researchers valuable support in elucidating the regulation of gene transcription.
Collapse
Affiliation(s)
- Małgorzata Majewska
- Department of Biology and Pharmaceutical Botany, Medical University of Lodz, 90-151 Lodz, Poland.
| | - Halina Wysokińska
- Department of Biology and Pharmaceutical Botany, Medical University of Lodz, 90-151 Lodz, Poland
| | - Łukasz Kuźma
- Department of Biology and Pharmaceutical Botany, Medical University of Lodz, 90-151 Lodz, Poland
| | - Piotr Szymczyk
- Department of Pharmaceutical Biotechnology, Medical University of Lodz, 90-151 Lodz, Poland
| |
Collapse
|
32
|
Transcriptome analysis of inflammation-related gene expression in endothelial cells activated by complement MASP-1. Sci Rep 2017; 7:10462. [PMID: 28874747 PMCID: PMC5585174 DOI: 10.1038/s41598-017-09058-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 07/19/2017] [Indexed: 01/15/2023] Open
Abstract
Mannan-binding lectin-associated serine protease 1 (MASP-1), the most abundant enzyme of the complement lectin pathway, is able to stimulate human umbilical vein endothelial cells (HUVECs) to alter the expression of several cytokines and adhesion molecules. This study has assessed to what extent MASP-1 is able to modify the transcriptional pattern of inflammation-related (IR) genes in HUVECs. We utilized Agilent microarray to analyse the effects of recombinant MASP-1 (rMASP-1) in HUVECs, on a set of 884 IR genes. Gene Set Enrichment Analysis showed an overall activation of inflammation-related genes in response to rMASP-1. rMASP-1 treatment up- and down-regulated 19 and 11 IR genes, respectively. Most of them were previously unidentified, such as genes of chemokines (CXCL1, CXCL2, CXCL3), inflammatory receptors (TLR2, BDKRB2) and other inflammatory factors (F3, LBP). Expression of IR genes changed early, during the first 2 hours of activation. Both p38-MAPK inhibitor and NFκB inhibitor efficiently suppressed the effect of rMASP-1. We delineated 12 transcriptional factors as possible regulators of rMASP-1-induced IR genes. Our microarray-based data are in line with the hypothesis that complement lectin pathway activation, generating active MASP-1, directly regulates inflammatory processes by shifting the phenotype of endothelial cells towards a more pro-inflammatory type.
Collapse
|
33
|
Howe V, Sharpe LJ, Prabhu AV, Brown AJ. New insights into cellular cholesterol acquisition: promoter analysis of human HMGCR and SQLE , two key control enzymes in cholesterol synthesis. Biochim Biophys Acta Mol Cell Biol Lipids 2017; 1862:647-657. [DOI: 10.1016/j.bbalip.2017.03.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 03/22/2017] [Indexed: 01/06/2023]
|
34
|
Khot VV, Yadav DK, Shrestha S, Kaur L, Sundrani DP, Chavan-Gautam PM, Mehendale SS, Chandak GR, Joshi SR. Hypermethylated CpG sites in the MTR gene promoter in preterm placenta. Epigenomics 2017; 9:985-996. [PMID: 28617183 DOI: 10.2217/epi-2016-0173] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM Altered maternal one-carbon metabolism influences placental DNA methylation patterns and 'programs' the fetus for noncommunicable diseases in adult life. EXPERIMENTAL PROCEDURES Levels of plasma folate, vitamin B12, homocysteine, mRNA and protein levels of MTHFR and MTR enzymes in placenta were compared among women delivering preterm (n = 83) and term (n = 75). MTR promoter CpG methylation was undertaken. RESULTS MTHFR and MTR mRNA levels were higher while protein levels were lower, and MTR CpG sites were hypermethylated in the preterm group, as compared with the term group. Methylated CpG sites were negatively associated with maternal plasma vitamin B12 levels. CONCLUSION Study suggests a dysregulation of enzyme genes in remethylation arm of the one-carbon metabolism in placenta of women delivering preterm.
Collapse
Affiliation(s)
- Vinita V Khot
- Departments of Nutritional Medicine, Interactive Research School for Health Affairs, Bharati Vidyapeeth University, Pune 411043, Maharashtra, India
| | - Dilip K Yadav
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular & Molecular Biology (CSIR-CCMB), Habsiguda, Uppal Road, Hyderabad 500007, Telangana, India
| | - Smeeta Shrestha
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular & Molecular Biology (CSIR-CCMB), Habsiguda, Uppal Road, Hyderabad 500007, Telangana, India
| | - Lovejeet Kaur
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular & Molecular Biology (CSIR-CCMB), Habsiguda, Uppal Road, Hyderabad 500007, Telangana, India
| | - Deepali P Sundrani
- Departments of Nutritional Medicine, Interactive Research School for Health Affairs, Bharati Vidyapeeth University, Pune 411043, Maharashtra, India
| | - Preeti M Chavan-Gautam
- Departments of Nutritional Medicine, Interactive Research School for Health Affairs, Bharati Vidyapeeth University, Pune 411043, Maharashtra, India
| | - Savita S Mehendale
- Obstetrics & Gynecology, Bharati Medical College & Hospital, Bharati Vidyapeeth University, Pune 411043, Maharashtra, India
| | - Giriraj R Chandak
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular & Molecular Biology (CSIR-CCMB), Habsiguda, Uppal Road, Hyderabad 500007, Telangana, India
| | - Sadhana R Joshi
- Departments of Nutritional Medicine, Interactive Research School for Health Affairs, Bharati Vidyapeeth University, Pune 411043, Maharashtra, India
| |
Collapse
|
35
|
Juhnke M, Heumann A, Chirico V, Höflmayer D, Menz A, Hinsch A, Hube-Magg C, Kluth M, Lang DS, Möller-Koop C, Sauter G, Simon R, Beyer B, Pompe R, Thederan I, Schlomm T, Luebke AM. Apurinic/apyrimidinic endonuclease 1 (APE1/Ref-1) overexpression is an independent prognostic marker in prostate cancer withoutTMPRSS2:ERGfusion. Mol Carcinog 2017; 56:2135-2145. [DOI: 10.1002/mc.22670] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 04/19/2017] [Accepted: 05/01/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Manuela Juhnke
- Institute of Pathology; University Medical Center Hamburg-Eppendorf; Hamburg Germany
| | - Asmus Heumann
- Department of General, Visceral and Thoracic Surgery; University Medical Center Hamburg-Eppendorf; Hamburg Germany
| | - Viktoria Chirico
- Institute of Pathology; University Medical Center Hamburg-Eppendorf; Hamburg Germany
| | - Doris Höflmayer
- Institute of Pathology; University Medical Center Hamburg-Eppendorf; Hamburg Germany
| | - Anne Menz
- Institute of Pathology; University Medical Center Hamburg-Eppendorf; Hamburg Germany
| | - Andrea Hinsch
- Institute of Pathology; University Medical Center Hamburg-Eppendorf; Hamburg Germany
| | - Claudia Hube-Magg
- Institute of Pathology; University Medical Center Hamburg-Eppendorf; Hamburg Germany
| | - Martina Kluth
- Institute of Pathology; University Medical Center Hamburg-Eppendorf; Hamburg Germany
| | - Dagmar S. Lang
- Institute of Pathology; University Medical Center Hamburg-Eppendorf; Hamburg Germany
| | - Christina Möller-Koop
- Institute of Pathology; University Medical Center Hamburg-Eppendorf; Hamburg Germany
| | - Guido Sauter
- Institute of Pathology; University Medical Center Hamburg-Eppendorf; Hamburg Germany
| | - Ronald Simon
- Institute of Pathology; University Medical Center Hamburg-Eppendorf; Hamburg Germany
| | - Burkhard Beyer
- Martini-Clinic, Prostate Cancer Center; University Medical Center Hamburg-Eppendorf; Germany
| | - Raisa Pompe
- Martini-Clinic, Prostate Cancer Center; University Medical Center Hamburg-Eppendorf; Germany
| | - Imke Thederan
- Martini-Clinic, Prostate Cancer Center; University Medical Center Hamburg-Eppendorf; Germany
| | - Thorsten Schlomm
- Martini-Clinic, Prostate Cancer Center; University Medical Center Hamburg-Eppendorf; Germany
- Department of Urology, Section for Translational Prostate Cancer Research; University Medical Center Hamburg-Eppendorf; Germany
| | - Andreas M. Luebke
- Institute of Pathology; University Medical Center Hamburg-Eppendorf; Hamburg Germany
| |
Collapse
|
36
|
In silico analyses and global transcriptional profiling reveal novel putative targets for Pea3 transcription factor related to its function in neurons. PLoS One 2017; 12:e0170585. [PMID: 28158215 PMCID: PMC5291419 DOI: 10.1371/journal.pone.0170585] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 01/08/2017] [Indexed: 01/05/2023] Open
Abstract
Pea3 transcription factor belongs to the PEA3 subfamily within the ETS domain transcription factor superfamily, and has been largely studied in relation to its role in breast cancer metastasis. Nonetheless, Pea3 plays a role not only in breast tumor, but also in other tissues with branching morphogenesis, including kidneys, blood vasculature, bronchi and the developing nervous system. Identification of Pea3 target promoters in these systems are important for a thorough understanding of how Pea3 functions. Present study particularly focuses on the identification of novel neuronal targets of Pea3 in a combinatorial approach, through curation, computational analysis and microarray studies in a neuronal model system, SH-SY5Y neuroblastoma cells. We not only show that quite a number of genes in cancer, immune system and cell cycle pathways, among many others, are either up- or down-regulated by Pea3, but also identify novel targets including ephrins and ephrin receptors, semaphorins, cell adhesion molecules, as well as metalloproteases such as kallikreins, to be among potential target promoters in neuronal systems. Our overall results indicate that rather than early stages of neurite extension and axonal guidance, Pea3 is more involved in target identification and synaptic maturation.
Collapse
|
37
|
Donakonda S, Sinha S, Dighe SN, Rao MRS. System analysis identifies distinct and common functional networks governed by transcription factor ASCL1, in glioma and small cell lung cancer. MOLECULAR BIOSYSTEMS 2017; 13:1481-1494. [DOI: 10.1039/c6mb00851h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Systematic functional network analysis of ASCL1 revealed that it regulates mitosis and cell proliferation pathways and has distinct functions in glioma and SCLC.
Collapse
Affiliation(s)
- Sainitin Donakonda
- Chromatin Biology Laboratory
- Molecular Biology and Genetics Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bangalore-560064
- India
| | - Swati Sinha
- Chromatin Biology Laboratory
- Molecular Biology and Genetics Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bangalore-560064
- India
| | - Shrinivas Nivrutti Dighe
- Chromatin Biology Laboratory
- Molecular Biology and Genetics Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bangalore-560064
- India
| | - Manchanahalli R Satyanarayana Rao
- Chromatin Biology Laboratory
- Molecular Biology and Genetics Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bangalore-560064
- India
| |
Collapse
|
38
|
Heidkamp GF, Sander J, Lehmann CHK, Heger L, Eissing N, Baranska A, Lu hr JJ, Hoffmann A, Reimer KC, Lux A, So der S, Hartmann A, Zenk J, Ulas T, McGovern N, Alexiou C, Spriewald B, Mackensen A, Schuler G, Schauf B, Forster A, Repp R, Fasching PA, Purbojo A, Cesnjevar R, Ullrich E, Ginhoux F, Schlitzer A, Nimmerjahn F, Schultze JL, Dudziak D. Human lymphoid organ dendritic cell identity is predominantly dictated by ontogeny, not tissue microenvironment. Sci Immunol 2016; 1:1/6/eaai7677. [DOI: 10.1126/sciimmunol.aai7677] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 11/14/2016] [Indexed: 11/02/2022]
|
39
|
An Integrative Analysis of Preeclampsia Based on the Construction of an Extended Composite Network Featuring Protein-Protein Physical Interactions and Transcriptional Relationships. PLoS One 2016; 11:e0165849. [PMID: 27802351 PMCID: PMC5089765 DOI: 10.1371/journal.pone.0165849] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 10/18/2016] [Indexed: 11/19/2022] Open
Abstract
Preeclampsia (PE) is a pregnancy disorder defined by hypertension and proteinuria. This disease remains a major cause of maternal and fetal morbidity and mortality. Defective placentation is generally described as being at the root of the disease. The characterization of the transcriptome signature of the preeclamptic placenta has allowed to identify differentially expressed genes (DEGs). However, we still lack a detailed knowledge on how these DEGs impact the function of the placenta. The tools of network biology offer a methodology to explore complex diseases at a systems level. In this study we performed a cross-platform meta-analysis of seven publically available gene expression datasets comparing non-pathological and preeclamptic placentas. Using the rank product algorithm we identified a total of 369 DEGs consistently modified in PE. The DEGs were used as seeds to build both an extended physical protein-protein interactions network and a transcription factors regulatory network. Topological and clustering analysis was conducted to analyze the connectivity properties of the networks. Finally both networks were merged into a composite network which presents an integrated view of the regulatory pathways involved in preeclampsia and the crosstalk between them. This network is a useful tool to explore the relationship between the DEGs and enable hypothesis generation for functional experimentation.
Collapse
|
40
|
Liu Y, Zhang R, Zhao N, Zhang Q, Yan Z, Chang Z, Wei Y, Wu C, Xu J, Xu Y. A comparative analysis reveals the dosage sensitivity and regulatory patterns of lncRNA in prostate cancer. MOLECULAR BIOSYSTEMS 2016; 12:3176-85. [PMID: 27507663 DOI: 10.1039/c6mb00359a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Although the key roles of long non-coding RNAs (lncRNAs) in multiple diseases are well documented, the relationship between the lncRNA copy number and expression is unknown. Here, we present a comprehensive study that demonstrates the impact of miRNA-TF co-regulatory motifs on the dosage effects of protein-coding genes (PCGs) and lncRNAs in prostate cancer. By integrating copy number profiles, expression profiles and regulatory relationships with miRNAs and transcription factors, we reveal that lncRNAs and PCGs correlate with distinct dosage sensitivity and regulatory pattern characteristics. We also show that lncRNAs from different genomic regions have different features. Using a custom-built framework, we identified 24 candidate prostate cancer-related lncRNAs based on the known properties of established prostate-related lncRNAs. Our method will enable the identification of cancer-related lncRNAs, which will provide new insights into cancer lncRNA biology.
Collapse
Affiliation(s)
- Yongjing Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Vafaee F, Krycer JR, Ma X, Burykin T, James DE, Kuncic Z. ORTI: An Open-Access Repository of Transcriptional Interactions for Interrogating Mammalian Gene Expression Data. PLoS One 2016; 11:e0164535. [PMID: 27723773 PMCID: PMC5056720 DOI: 10.1371/journal.pone.0164535] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 09/27/2016] [Indexed: 12/11/2022] Open
Abstract
Transcription factors (TFs) play a fundamental role in coordinating biological processes in response to stimuli. Consequently, we often seek to determine the key TFs and their regulated target genes (TGs) amidst gene expression data. This requires a knowledge-base of TF-TG interactions, which would enable us to determine the topology of the transcriptional network and predict novel regulatory interactions. To address this, we generated an Open-access Repository of Transcriptional Interactions, ORTI, by integrating available TF-TG interaction databases. These databases rely on different types of experimental evidence, including low-throughput assays, high-throughput screens, and bioinformatics predictions. We have subsequently categorised TF-TG interactions in ORTI according to the quality of this evidence. To demonstrate its capabilities, we applied ORTI to gene expression data and identified modulated TFs using an enrichment analysis. Combining this with pairwise TF-TG interactions enabled us to visualise temporal regulation of a transcriptional network. Additionally, ORTI enables the prediction of novel TF-TG interactions, based on how well candidate genes co-express with known TGs of the target TF. By filtering out known TF-TG interactions that are unlikely to occur within the experimental context, this analysis predicts context-specific TF-TG interactions. We show that this can be applied to experimental designs of varying complexities. In conclusion, ORTI is a rich and publicly available database of experimentally validated mammalian transcriptional interactions which is accompanied with tools that can identify and predict transcriptional interactions, serving as a useful resource for unravelling the topology of transcriptional networks.
Collapse
Affiliation(s)
- Fatemeh Vafaee
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, Australia
- * E-mail: (FV); (ZK)
| | - James R. Krycer
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Xiuquan Ma
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
- Diabetes and Metabolism Division, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia
| | - Timur Burykin
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - David E. James
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
- Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Zdenka Kuncic
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
- School of Physics, The University of Sydney, Sydney, NSW, Australia
- * E-mail: (FV); (ZK)
| |
Collapse
|
42
|
Chen J, Cui X, Qian Z, Li Y, Kang K, Qu J, Li L, Gou D. Multi-omics analysis reveals regulators of the response to PDGF-BB treatment in pulmonary artery smooth muscle cells. BMC Genomics 2016; 17:781. [PMID: 27716141 PMCID: PMC5053085 DOI: 10.1186/s12864-016-3122-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 09/26/2016] [Indexed: 12/18/2022] Open
Abstract
Background Pulmonary arterial hypertension (PAH) is a lethal disease with pronounced narrowing of pulmonary vessels due to abnormal cell proliferation. The platelet-derived growth factor BB (PDGF-BB) is well known as a potent mitogen for smooth muscle cell proliferation. To better understand how this growth factor regulates pulmonary arterial smooth muscle cells (PASMCs) proliferation, we sought to characterize the response to PDGF-BB stimulation at system-wide levels, including the transcriptome and proteome. Results In this study, we identified 1611 mRNAs (transcriptome), 207 proteins (proteome) differentially expressed in response to PDGF-BB stimulation in PASMCs based on RNA-sequencing and isobaric tags for relative and absolute quantification (iTRAQ) assay. Transcription factor (TF)-target network analysis revealed that PDGF-BB regulated gene expression potentially via TFs including HIF1A, JUN, EST1, ETS1, SMAD1, FOS, SP1, STAT1, LEF1 and CEBPB. Among them, SMAD1-involved BMPR2/SMADs axis plays a significant role in PAH development. Interestingly, we observed that the expression of BMPR2 was decreased in both mRNA and protein level in response to PDGF-BB. Further study revealed that BMPR2 is the direct target of miR-376b that is up-regulated upon PDGF-BB treatment. Finally, EdU incorporation assay showed that miR-376b promoted proliferation of PASMCs. Conclusion This integrated analysis of PDGF-BB-regulated transcriptome and proteome was performed for the first time in normal PASMCs, which revealed a crosstalk between PDGF signaling and BMPR2/SMADs axis. Further study demonstrated that PDGF-BB-induced miR-376b upregulation mediated the downregulation of BMPR2, which led to expression change of its downstream targets and promoted proliferation of PASMCs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3122-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jidong Chen
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Nanhai Ave 3688, Shenzhen, Guangdong, 518060, China.,Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Xiaolei Cui
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Nanhai Ave 3688, Shenzhen, Guangdong, 518060, China
| | - Zhengjiang Qian
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Nanhai Ave 3688, Shenzhen, Guangdong, 518060, China.,Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Yanjiao Li
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Nanhai Ave 3688, Shenzhen, Guangdong, 518060, China.,Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Kang Kang
- Department of Physiology, Shenzhen University Health Science Center, Shenzhen, Guangdong, 518060, China
| | - Junle Qu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Li Li
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Nanhai Ave 3688, Shenzhen, Guangdong, 518060, China.
| | - Deming Gou
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Nanhai Ave 3688, Shenzhen, Guangdong, 518060, China.
| |
Collapse
|
43
|
Ung MH, Liu CC, Cheng C. Integrative analysis of cancer genes in a functional interactome. Sci Rep 2016; 6:29228. [PMID: 27356765 PMCID: PMC4928112 DOI: 10.1038/srep29228] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 06/16/2016] [Indexed: 11/09/2022] Open
Abstract
The post-genomic era has resulted in the accumulation of high-throughput cancer data from a vast array of genomic technologies including next-generation sequencing and microarray. As such, the large amounts of germline variant and somatic mutation data that have been generated from GWAS and sequencing projects, respectively, show great promise in providing a systems-level view of these genetic aberrations. In this study, we analyze publicly available GWAS, somatic mutation, and drug target data derived from large databanks using a network-based approach that incorporates directed edge information under a randomized network hypothesis testing procedure. We show that these three classes of disease-associated nodes exhibit non-random topological characteristics in the context of a functional interactome. Specifically, we show that drug targets tend to lie upstream of somatic mutations and disease susceptibility germline variants. In addition, we introduce a new approach to measuring hierarchy between drug targets, somatic mutants, and disease susceptibility genes by utilizing directionality and path length information. Overall, our results provide new insight into the intrinsic relationships between these node classes that broaden our understanding of cancer. In addition, our results align with current knowledge on the therapeutic actionability of GWAS and somatic mutant nodes, while demonstrating relationships between node classes from a global network perspective.
Collapse
Affiliation(s)
- Matthew H Ung
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, 03755 USA.,Program in Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, 03755 USA
| | - Chun-Chi Liu
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taiwan
| | - Chao Cheng
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, 03755 USA.,Program in Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, 03755 USA.,Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, 03766 USA
| |
Collapse
|
44
|
Liu ZP. Identifying network-based biomarkers of complex diseases from high-throughput data. Biomark Med 2016; 10:633-50. [DOI: 10.2217/bmm-2015-0035] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In this work, we review the main available computational methods of identifying biomarkers of complex diseases from high-throughput data. The emerging omics techniques provide powerful alternatives to measure thousands of molecules in cells in parallel manners. The generated genomic, transcriptomic, proteomic, metabolomic and phenomic data provide comprehensive molecular and cellular information for detecting critical signals served as biomarkers by classifying disease phenotypic states. Networks are often employed to organize these profiles in the identification of biomarkers to deal with complex diseases in diagnosis, prognosis and therapy as well as mechanism deciphering from systematic perspectives. Here, we summarize some representative network-based bioinformatics methods in order to highlight the importance of computational strategies in biomarker discovery.
Collapse
Affiliation(s)
- Zhi-Ping Liu
- Department of Biomedical Engineering, School of Control Science & Engineering, Shandong University, Jinan, Shandong 250061, China
| |
Collapse
|
45
|
Kann M, Bae E, Lenz MO, Li L, Trannguyen B, Schumacher VA, Taglienti ME, Bordeianou L, Hartwig S, Rinschen MM, Schermer B, Benzing T, Fan CM, Kreidberg JA. WT1 targets Gas1 to maintain nephron progenitor cells by modulating FGF signals. Development 2016; 142:1254-66. [PMID: 25804736 DOI: 10.1242/dev.119735] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Development of the metanephric kidney depends on tightly regulated interplay between self-renewal and differentiation of a nephron progenitor cell (NPC) pool. Several key factors required for the survival of NPCs have been identified, including fibroblast growth factor (FGF) signaling and the transcription factor Wilms' tumor suppressor 1 (WT1). Here, we present evidence that WT1 modulates FGF signaling by activating the expression of growth arrest-specific 1 (Gas1), a novel WT1 target gene and novel modulator of FGF signaling. We show that WT1 directly binds to a conserved DNA binding motif within the Gas1 promoter and activates Gas1 mRNA transcription in NPCs. We confirm that WT1 is required for Gas1 expression in kidneys in vivo. Loss of function of GAS1 in vivo results in hypoplastic kidneys with reduced nephron mass due to premature depletion of NPCs. Although kidney development in Gas1 knockout mice progresses normally until E15.5, NPCs show decreased rates of proliferation at this stage and are depleted as of E17.5. Lastly, we show that Gas1 is selectively required for FGF-stimulated AKT signaling in vitro. In summary, our data suggest a model in which WT1 modulates receptor tyrosine kinase signaling in NPCs by directing the expression of Gas1.
Collapse
Affiliation(s)
- Martin Kann
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA Department II of Medicine and Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
| | - Eunnyung Bae
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Maximilian O Lenz
- Department II of Medicine and Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
| | - Liangji Li
- Department of Embryology, Carnegie Institution of Washington, Baltimore, MD 21218, USA
| | - BaoTran Trannguyen
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Valerie A Schumacher
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Mary E Taglienti
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Liliana Bordeianou
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Sunny Hartwig
- Department of Biomedical Sciences, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada C1A 4P3
| | - Markus M Rinschen
- Department II of Medicine and Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
| | - Bernhard Schermer
- Department II of Medicine and Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany Cluster of Excellence on Cellular Stress Responses in Ageing-Associated Diseases (CECAD) and Systems Biology of Ageing Cologne, University of Cologne, 50931 Cologne, Germany
| | - Thomas Benzing
- Department II of Medicine and Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany Cluster of Excellence on Cellular Stress Responses in Ageing-Associated Diseases (CECAD) and Systems Biology of Ageing Cologne, University of Cologne, 50931 Cologne, Germany
| | - Chen-Ming Fan
- Department of Embryology, Carnegie Institution of Washington, Baltimore, MD 21218, USA
| | - Jordan A Kreidberg
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| |
Collapse
|
46
|
Ansari-Pour N, Razaghi-Moghadam Z, Barneh F, Jafari M. Testis-Specific Y-Centric Protein-Protein Interaction Network Provides Clues to the Etiology of Severe Spermatogenic Failure. J Proteome Res 2016; 15:1011-22. [PMID: 26794825 DOI: 10.1021/acs.jproteome.5b01080] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Pinpointing causal genes for spermatogenic failure (SpF) on the Y chromosome has been an ever daunting challenge with setbacks during the past decade. Since complex diseases result from the interaction of multiple genes and also display considerable missing heritability, network analysis is more likely to explicate an etiological molecular basis. We therefore took a network medicine approach by integrating interactome (protein-protein interaction (PPI)) and transcriptome data to reconstruct a Y-centric SpF network. Two sets of seed genes (Y genes and SpF-implicated genes (SIGs)) were used for network reconstruction. Since no PPI was observed among Y genes, we identified their common immediate interactors. Interestingly, 81% (N = 175) of these interactors not only interacted directly with SIGs, but also they were enriched for differentially expressed genes (89.6%; N = 43). The SpF network, formed mainly by the dys-regulated interactors and the two seed gene sets, comprised three modules enriched for ribosomal proteins and nuclear receptors for sex hormones. Ribosomal proteins generally showed significant dys-regulation with RPL39L, thought to be expressed at the onset of spermatogenesis, strongly down-regulated. This network is the first global PPI network pertaining to severe SpF and if experimentally validated on independent data sets can lead to more accurate diagnosis and potential fertility recovery of patients.
Collapse
Affiliation(s)
- Naser Ansari-Pour
- Faculty of New Sciences and Technology, University of Tehran , North Kargar Street, Tehran 143995-7131, Iran.,School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM) , Tehran 19395-5531, Iran
| | - Zahra Razaghi-Moghadam
- Faculty of New Sciences and Technology, University of Tehran , North Kargar Street, Tehran 143995-7131, Iran.,School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM) , Tehran 19395-5531, Iran
| | - Farnaz Barneh
- Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences , Tehran 198396-3113, Iran
| | - Mohieddin Jafari
- Drug Design and Bioinformatics Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran , Tehran 131694-3551, Iran.,School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM) , Tehran 19395-5531, Iran
| |
Collapse
|
47
|
Baur B, Bozdag S. A canonical correlation analysis-based dynamic bayesian network prior to infer gene regulatory networks from multiple types of biological data. J Comput Biol 2016; 22:289-99. [PMID: 25844668 DOI: 10.1089/cmb.2014.0296] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
One of the challenging and important computational problems in systems biology is to infer gene regulatory networks (GRNs) of biological systems. Several methods that exploit gene expression data have been developed to tackle this problem. In this study, we propose the use of copy number and DNA methylation data to infer GRNs. We developed an algorithm that scores regulatory interactions between genes based on canonical correlation analysis. In this algorithm, copy number or DNA methylation variables are treated as potential regulator variables, and expression variables are treated as potential target variables. We first validated that the canonical correlation analysis method is able to infer true interactions in high accuracy. We showed that the use of DNA methylation or copy number datasets leads to improved inference over steady-state expression. Our results also showed that epigenetic and structural information could be used to infer directionality of regulatory interactions. Additional improvements in GRN inference can be gleaned from incorporating the result in an informative prior in a dynamic Bayesian algorithm. This is the first study that incorporates copy number and DNA methylation into an informative prior in dynamic Bayesian framework. By closely examining top-scoring interactions with different sources of epigenetic or structural information, we also identified potential novel regulatory interactions.
Collapse
Affiliation(s)
- Brittany Baur
- Department of Math, Statistics and Computer Science, Marquette University , Milwaukee, Wisconsin
| | | |
Collapse
|
48
|
Long Noncoding RNA MEG3 Interacts with p53 Protein and Regulates Partial p53 Target Genes in Hepatoma Cells. PLoS One 2015; 10:e0139790. [PMID: 26444285 PMCID: PMC4596861 DOI: 10.1371/journal.pone.0139790] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 09/17/2015] [Indexed: 12/13/2022] Open
Abstract
Maternally Expressed Gene 3 (MEG3) encodes a lncRNA which is suggested to function as a tumor suppressor. Previous studies suggested that MEG3 functioned through activation of p53, however, the functional properties of MEG3 remain obscure and their relevance to human diseases is under continuous investigation. Here, we try to illuminate the relationship of MEG3 and p53, and the consequence in hepatoma cells. We find that transfection of expression construct of MEG3 enhances stability and transcriptional activity of p53. Deletion analysis of MEG3 confirms that full length and intact structure of MEG3 are critical for it to activate p53-mediated transactivation. Interestingly, our results demonstrate for the first time that MEG3 can interact with p53 DNA binding domain and various p53 target genes are deregulated after overexpression of MEG3 in hepatoma cells. Furthermore, results of qRT-PCR have shown that MEG3 RNA is lost or reduced in the majority of HCC samples compared with adjacent non-tumorous samples. Ectopic expression of MEG3 in hepatoma cells significantly inhibits proliferation and induces apoptosis. In conclusion, our data demonstrates that MEG3 functions as a tumor suppressor in hepatoma cells through interacting with p53 protein to activate p53-mediated transcriptional activity and influence the expression of partial p53 target genes.
Collapse
|
49
|
Liu ZP, Wu C, Miao H, Wu H. RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav095. [PMID: 26424082 PMCID: PMC4589691 DOI: 10.1093/database/bav095] [Citation(s) in RCA: 256] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 09/04/2015] [Indexed: 01/01/2023]
Abstract
Transcriptional and post-transcriptional regulation of gene expression is of fundamental importance to numerous biological processes. Nowadays, an increasing amount of gene regulatory relationships have been documented in various databases and literature. However, to more efficiently exploit such knowledge for biomedical research and applications, it is necessary to construct a genome-wide regulatory network database to integrate the information on gene regulatory relationships that are widely scattered in many different places. Therefore, in this work, we build a knowledge-based database, named ‘RegNetwork’, of gene regulatory networks for human and mouse by collecting and integrating the documented regulatory interactions among transcription factors (TFs), microRNAs (miRNAs) and target genes from 25 selected databases. Moreover, we also inferred and incorporated potential regulatory relationships based on transcription factor binding site (TFBS) motifs into RegNetwork. As a result, RegNetwork contains a comprehensive set of experimentally observed or predicted transcriptional and post-transcriptional regulatory relationships, and the database framework is flexibly designed for potential extensions to include gene regulatory networks for other organisms in the future. Based on RegNetwork, we characterized the statistical and topological properties of genome-wide regulatory networks for human and mouse, we also extracted and interpreted simple yet important network motifs that involve the interplays between TF-miRNA and their targets. In summary, RegNetwork provides an integrated resource on the prior information for gene regulatory relationships, and it enables us to further investigate context-specific transcriptional and post-transcriptional regulatory interactions based on domain-specific experimental data. Database URL: http://www.regnetworkweb.org
Collapse
Affiliation(s)
- Zhi-Ping Liu
- Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan, Shandong 250061, China and
| | - Canglin Wu
- Department of Biostatistics, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Hongyu Miao
- Department of Biostatistics, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Hulin Wu
- Department of Biostatistics, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| |
Collapse
|
50
|
Zhao N, Liu Y, Chang Z, Li K, Zhang R, Zhou Y, Qiu F, Han X, Xu Y. Identification of Biomarker and Co-Regulatory Motifs in Lung Adenocarcinoma Based on Differential Interactions. PLoS One 2015; 10:e0139165. [PMID: 26402252 PMCID: PMC4581687 DOI: 10.1371/journal.pone.0139165] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 09/08/2015] [Indexed: 01/01/2023] Open
Abstract
Changes in intermolecular interactions (differential interactions) may influence the progression of cancer. Specific genes and their regulatory networks may be more closely associated with cancer when taking their transcriptional and post-transcriptional levels and dynamic and static interactions into account simultaneously. In this paper, a differential interaction analysis was performed to detect lung adenocarcinoma-related genes. Furthermore, a miRNA-TF (transcription factor) synergistic regulation network was constructed to identify three kinds of co-regulated motifs, namely, triplet, crosstalk and joint. Not only were the known cancer-related miRNAs and TFs (let-7, miR-15a, miR-17, TP53, ETS1, and so on) were detected in the motifs, but also the miR-15, let-7 and miR-17 families showed a tendency to regulate the triplet, crosstalk and joint motifs, respectively. Moreover, several biological functions (i.e., cell cycle, signaling pathways and hemopoiesis) associated with the three motifs were found to be frequently targeted by the drugs for lung adenocarcinoma. Specifically, the two 4-node motifs (crosstalk and joint) based on co-expression and interaction had a closer relationship to lung adenocarcinoma, and so further research was performed on them. A 10-gene biomarker (UBC, SRC, SP1, MYC, STAT3, JUN, NR3C1, RB1, GRB2 and MAPK1) was selected from the joint motif, and a survival analysis indicated its significant association with survival. Among the ten genes, JUN, NR3C1 and GRB2 are our newly detected candidate lung adenocarcinoma-related genes. The genes, regulators and regulatory motifs detected in this work will provide potential drug targets and new strategies for individual therapy.
Collapse
Affiliation(s)
- Ning Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yongjing Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Zhiqiang Chang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Kening Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Rui Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yuanshuai Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Fujun Qiu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Xiaole Han
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
- * E-mail:
| |
Collapse
|