101
|
Li H, Sun X, Yu F, Xu L, Miu J, Xiao P. In Silico Investigation of the Pharmacological Mechanisms of Beneficial Effects of Ginkgo biloba L. on Alzheimer's Disease. Nutrients 2018; 10:nu10050589. [PMID: 29747475 PMCID: PMC5986469 DOI: 10.3390/nu10050589] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 05/01/2018] [Accepted: 05/08/2018] [Indexed: 11/21/2022] Open
Abstract
Based on compelling experimental and clinical evidence, Ginkgo biloba L. exerts a beneficial effect in ameliorating mild to moderate dementia in patients with Alzheimer’s disease (AD) and other neurological disorders, although the pharmacological mechanisms remain unknown. In the present study, compounds, their putative target proteins identified using an inverse docking approach, and clinically tested AD-related target proteins were systematically integrated together with applicable bioinformatics methods in silico. The results suggested that the beneficial effects of G. biloba on AD may be contributed by the regulation of hormone sensitivity, improvements in endocrine homeostasis, maintenance of endothelial microvascular integrity, and proteolysis of tau proteins, particularly prior to amyloid β-protein (Aβ) plaque formation. Moreover, we identified six putative protein targets that are significantly related to AD, but have not been researched or have had only preliminary studies conducted on the anti-AD effects of G. biloba. These mechanisms and protein targets are very significant for future scientific research. In addition, the existing mechanisms were also verified, such as the reduction of oxidative stress, anti-apoptotic effects, and protective effects against amyloidogenesis and Aβ aggregation. The discoveries summarized here may provide a macroscopic perspective that will improve our understanding of the molecular mechanism of medicinal plants or dietary supplements, as well as new clues for the future development of therapeutic strategies for AD.
Collapse
Affiliation(s)
- Hongxiang Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, 151 Malianwa North Road, Beijing 100193, China.
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, 151 Malianwa North Road, Beijing 100193, China.
| | - Xiaoyuan Sun
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, 151 Malianwa North Road, Beijing 100193, China.
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, 151 Malianwa North Road, Beijing 100193, China.
| | - Fan Yu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, 151 Malianwa North Road, Beijing 100193, China.
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, 151 Malianwa North Road, Beijing 100193, China.
| | - Lijia Xu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, 151 Malianwa North Road, Beijing 100193, China.
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, 151 Malianwa North Road, Beijing 100193, China.
| | - Jianhua Miu
- Guangxi Institute of Medicinal Plant Development, Nanning, 189 Changgang Road, Nanning 520023, China.
| | - Peigen Xiao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, 151 Malianwa North Road, Beijing 100193, China.
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, 151 Malianwa North Road, Beijing 100193, China.
| |
Collapse
|
102
|
Sagers JE, Brown AS, Vasilijic S, Lewis RM, Sahin MI, Landegger LD, Perlis RH, Kohane IS, Welling DB, Patel CJ, Stankovic KM. Computational repositioning and preclinical validation of mifepristone for human vestibular schwannoma. Sci Rep 2018; 8:5437. [PMID: 29615643 PMCID: PMC5882888 DOI: 10.1038/s41598-018-23609-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 03/14/2018] [Indexed: 12/30/2022] Open
Abstract
The computational repositioning of existing drugs represents an appealing avenue for identifying effective compounds to treat diseases with no FDA-approved pharmacotherapies. Here we present the largest meta-analysis to date of differential gene expression in human vestibular schwannoma (VS), a debilitating intracranial tumor, and use these data to inform the first application of algorithm-based drug repositioning for this tumor class. We apply an open-source computational drug repositioning platform to gene expression data from 80 patient tumors and identify eight promising FDA-approved drugs with potential for repurposing in VS. Of these eight, mifepristone, a progesterone and glucocorticoid receptor antagonist, consistently and adversely affects the morphology, metabolic activity, and proliferation of primary human VS cells and HEI-193 human schwannoma cells. Mifepristone treatment reduces VS cell viability more significantly than cells derived from patient meningiomas, while healthy human Schwann cells remain unaffected. Our data recommend a Phase II clinical trial of mifepristone in VS.
Collapse
Affiliation(s)
- Jessica E Sagers
- Eaton-Peabody Laboratories, Department of Otolaryngology, Massachusetts Eye and Ear, Boston, MA, 02114, USA
- Program in Speech and Hearing Bioscience and Technology, Harvard Medical School, Boston, MA, 02115, USA
- Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, 02115, USA
| | - Adam S Brown
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, 02115, USA
| | - Sasa Vasilijic
- Eaton-Peabody Laboratories, Department of Otolaryngology, Massachusetts Eye and Ear, Boston, MA, 02114, USA
- Department of Otolaryngology, Harvard Medical School, Boston, MA, 02114, USA
| | - Rebecca M Lewis
- Eaton-Peabody Laboratories, Department of Otolaryngology, Massachusetts Eye and Ear, Boston, MA, 02114, USA
- Department of Otolaryngology, Harvard Medical School, Boston, MA, 02114, USA
| | - Mehmet I Sahin
- Eaton-Peabody Laboratories, Department of Otolaryngology, Massachusetts Eye and Ear, Boston, MA, 02114, USA
- Department of Otolaryngology, Harvard Medical School, Boston, MA, 02114, USA
| | - Lukas D Landegger
- Eaton-Peabody Laboratories, Department of Otolaryngology, Massachusetts Eye and Ear, Boston, MA, 02114, USA
- Department of Otolaryngology, Harvard Medical School, Boston, MA, 02114, USA
- Department of Otolaryngology, Vienna General Hospital, Medical University of Vienna, Vienna, 1090, Austria
| | - Roy H Perlis
- Center for Experimental Drugs and Diagnostics, Department of Psychiatry and Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Isaac S Kohane
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - D Bradley Welling
- Eaton-Peabody Laboratories, Department of Otolaryngology, Massachusetts Eye and Ear, Boston, MA, 02114, USA
- Department of Otolaryngology, Harvard Medical School, Boston, MA, 02114, USA
| | - Chirag J Patel
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Konstantina M Stankovic
- Eaton-Peabody Laboratories, Department of Otolaryngology, Massachusetts Eye and Ear, Boston, MA, 02114, USA.
- Program in Speech and Hearing Bioscience and Technology, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Otolaryngology, Harvard Medical School, Boston, MA, 02114, USA.
| |
Collapse
|
103
|
Jang G, Lee T, Lee BM, Yoon Y. Literature-based prediction of novel drug indications considering relationships between entities. MOLECULAR BIOSYSTEMS 2018; 13:1399-1405. [PMID: 28581007 DOI: 10.1039/c7mb00020k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
There have been many attempts to identify and develop new uses for existing drugs, which is known as drug repositioning. Among these efforts, text mining is an effective means of discovering novel knowledge from a large amount of literature data. We identify a gene regulation by a drug and a phenotype based on the biomedical literature. Drugs or phenotypes can activate or inhibit gene regulation. We calculate the therapeutic possibility that a drug acts on a phenotype by means of these two types of regulation. We assume that a drug treats a phenotype if the genes regulated by the phenotype are inversely correlated with the genes regulated by the drug. Based on this hypothesis, we identify drug-phenotype associations with therapeutic possibility. To validate the drug-phenotype associations predicted by our method, we make an enrichment comparison with known drug-phenotype associations. We also identify candidate drugs for drug repositioning from novel associations and thus reveal that our method is a novel approach to drug repositioning.
Collapse
Affiliation(s)
- Giup Jang
- Dept. of IT Convergence Engineering, Gachon University, Korea.
| | | | | | | |
Collapse
|
104
|
Neely MG, Morey JS, Anderson P, Balmer BC, Ylitalo GM, Zolman ES, Speakman TR, Sinclair C, Bachman MJ, Huncik K, Kucklick J, Rosel PE, Mullin KD, Rowles TK, Schwacke LH, Van Dolah FM. Skin Transcriptomes of common bottlenose dolphins (Tursiops truncatus) from the northern Gulf of Mexico and southeastern U.S. Atlantic coasts. Mar Genomics 2018; 38:45-58. [DOI: 10.1016/j.margen.2017.08.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 07/08/2017] [Accepted: 08/04/2017] [Indexed: 11/16/2022]
|
105
|
Hörtenhuber M, Toledo EM, Smedler E, Arenas E, Malmersjö S, Louhivuori L, Uhlén P. Mapping genes for calcium signaling and their associated human genetic disorders. Bioinformatics 2018; 33:2547-2554. [PMID: 28430858 PMCID: PMC5870714 DOI: 10.1093/bioinformatics/btx225] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 04/18/2017] [Indexed: 01/21/2023] Open
Abstract
Motivation Signal transduction via calcium ions (Ca2+) represents a fundamental signaling pathway in all eukaryotic cells. A large portion of the human genome encodes proteins used to assemble signaling systems that can transduce signals with diverse spatial and temporal dynamics. Results Here, we provide a map of all of the genes involved in Ca2+ signaling and link these genes to human genetic disorders. Using Gene Ontology terms and genome databases, 1805 genes were identified as regulators or targets of intracellular Ca2+ signals. Associating these 1805 genes with human genetic disorders uncovered 1470 diseases with mutated ‘Ca2+ genes’. A network with scale-free properties appeared when the Ca2+ genes were mapped to their associated genetic disorders. Availability and Implementation The Ca2+ genome database is freely available at http://cagedb.uhlenlab.org and will foster studies of gene functions and genetic disorders associated with Ca2+ signaling. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Matthias Hörtenhuber
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Enrique M Toledo
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Erik Smedler
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Ernest Arenas
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Seth Malmersjö
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lauri Louhivuori
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Per Uhlén
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| |
Collapse
|
106
|
Lou Y, Zhang Y, Qian T, Li F, Xiong S, Ji D. A transition-based joint model for disease named entity recognition and normalization. Bioinformatics 2018; 33:2363-2371. [PMID: 28369171 DOI: 10.1093/bioinformatics/btx172] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 03/23/2017] [Indexed: 11/13/2022] Open
Abstract
Motivation Disease named entities play a central role in many areas of biomedical research, and automatic recognition and normalization of such entities have received increasing attention in biomedical research communities. Existing methods typically used pipeline models with two independent phases: (i) a disease named entity recognition (DER) system is used to find the boundaries of mentions in text and (ii) a disease named entity normalization (DEN) system is used to connect the mentions recognized to concepts in a controlled vocabulary. The main problems of such models are: (i) there is error propagation from DER to DEN and (ii) DEN is useful for DER, but pipeline models cannot utilize this. Methods We propose a transition-based model to jointly perform disease named entity recognition and normalization, casting the output construction process into an incremental state transition process, learning sequences of transition actions globally, which correspond to joint structural outputs. Beam search and online structured learning are used, with learning being designed to guide search. Compared with the only existing method for joint DEN and DER, our method allows non-local features to be used, which significantly improves the accuracies. Results We evaluate our model on two corpora: the BioCreative V Chemical Disease Relation (CDR) corpus and the NCBI disease corpus. Experiments show that our joint framework achieves significantly higher performances compared to competitive pipeline baselines. Our method compares favourably to other state-of-the-art approaches. Availability and Implementation Data and code are available at https://github.com/louyinxia/jointRN. Contact dhji@whu.edu.cn.
Collapse
Affiliation(s)
- Yinxia Lou
- Computer School, Wuhan University, Wuhan, 430072, China.,School of Computer and Information Technology, Shangqiu Normal University, Shangqiu, 476000, China
| | - Yue Zhang
- Singapore University of Technology and Design
| | - Tao Qian
- College of Computer Science and Technology,Hubei University of Science and Technology, Xianning, 437000, China
| | - Fei Li
- Computer School, Wuhan University, Wuhan, 430072, China
| | - Shufeng Xiong
- Pingdingshan University, Pingdingshan, 467000, China
| | - Donghong Ji
- Computer School, Wuhan University, Wuhan, 430072, China
| |
Collapse
|
107
|
Vachon J, Pagé-Larivière F, Sirard MA, Rodriguez MJ, Levallois P, Campagna C. Availability, Quality, and Relevance of Toxicogenomics Data for Human Health Risk Assessment: A Scoping Review of the Literature on Trihalomethanes. Toxicol Sci 2018. [DOI: 10.1093/toxsci/kfy050] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Julien Vachon
- Direction de la Santé Environnementale et de la Toxicologie, Institut National de Santé Publique du Québec (INSPQ), Québec, Québec, Canada G1V 5B3
| | - Florence Pagé-Larivière
- Département des Sciences Animales, Faculté des Sciences de l’Agriculture et de l’Alimentation, Université Laval, Québec, Québec, Canada G1V 0A6
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle (CRDSI), Québec, Québec, Canada G1V 0A6
| | - Marc-André Sirard
- Département des Sciences Animales, Faculté des Sciences de l’Agriculture et de l’Alimentation, Université Laval, Québec, Québec, Canada G1V 0A6
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle (CRDSI), Québec, Québec, Canada G1V 0A6
| | - Manuel J Rodriguez
- École Supérieure d’Aménagement du Territoire et de Développement Régional, Université Laval, Québec, Québec, Canada G1V 0A6
- Chaire de Recherche CRSNG en Eau Potable, Université Laval, Québec, Québec, Canada G1V 0A6
| | - Patrick Levallois
- Direction de la Santé Environnementale et de la Toxicologie, Institut National de Santé Publique du Québec (INSPQ), Québec, Québec, Canada G1V 5B3
- Département de Médecine Sociale et Préventive, Faculté de Médecine, Université Laval, Québec, Québec, Canada G1V 0A6
- Axe Santé des Populations et Pratiques Optimales en Santé, Centre de Recherche du Centre Hospitalier Universitaire de Québec (CRCHUQ), Québec, Québec, Canada G1S 4L8
| | - Céline Campagna
- Direction de la Santé Environnementale et de la Toxicologie, Institut National de Santé Publique du Québec (INSPQ), Québec, Québec, Canada G1V 5B3
- Département de Médecine Sociale et Préventive, Faculté de Médecine, Université Laval, Québec, Québec, Canada G1V 0A6
| |
Collapse
|
108
|
Mao Y, Hao J, Jin ZQ, Niu YY, Yang X, Liu D, Cao R, Wu XZ. Network pharmacology-based and clinically relevant prediction of the active ingredients and potential targets of Chinese herbs in metastatic breast cancer patients. Oncotarget 2018; 8:27007-27021. [PMID: 28212580 PMCID: PMC5432314 DOI: 10.18632/oncotarget.15351] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 01/22/2017] [Indexed: 01/24/2023] Open
Abstract
Chinese Herbal Medicine (CHM) plays a significant role in breast cancer treatment. We conduct the study to ascertain the relative molecular targets of effective Chinese herbs in treating stage IV breast cancer.Survival benefit of CHM was verified by Kaplan-Meier method and Cox regression analysis. A bivariate correlation analysis was used to find and establish the effect of herbs in complex CHM formulas. A network pharmacological approach was adopted to explore the potential mechanisms of CHM.Patients in the CHM group had a median survival time of 55 months, which was longer than the 23 months of patients in the non-CHM group. Cox regression analysis indicated that CHM was an independent protective factor. Correlation analysis showed that 10 herbs were strongly correlated with favorable survival outcomes (P<0.01). Bioinformatics analyses suggested that the 10 herbs might achieve anti-breast cancer activity primarily through inhibiting HSP90, ERα and TOP-II related pathways.
Collapse
Affiliation(s)
- Yu Mao
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
| | - Jian Hao
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
| | - Zi-Qi Jin
- Tianjin Medical University, Tianjin, 300070, China
| | | | - Xue Yang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
| | - Dan Liu
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
| | - Rui Cao
- Zhong-Shan-Men Inpatient Department, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China
| | - Xiong-Zhi Wu
- Zhong-Shan-Men Inpatient Department, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China
| |
Collapse
|
109
|
Sialana FJ, Wang AL, Fazari B, Kristofova M, Smidak R, Trossbach SV, Korth C, Huston JP, de Souza Silva MA, Lubec G. Quantitative Proteomics of Synaptosomal Fractions in a Rat Overexpressing Human DISC1 Gene Indicates Profound Synaptic Dysregulation in the Dorsal Striatum. Front Mol Neurosci 2018; 11:26. [PMID: 29467617 PMCID: PMC5808171 DOI: 10.3389/fnmol.2018.00026] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 01/18/2018] [Indexed: 12/12/2022] Open
Abstract
Disrupted-in-schizophrenia 1 (DISC1) is a key protein involved in behavioral processes and various mental disorders, including schizophrenia and major depression. A transgenic rat overexpressing non-mutant human DISC1, modeling aberrant proteostasis of the DISC1 protein, displays behavioral, biochemical and anatomical deficits consistent with aspects of mental disorders, including changes in the dorsal striatum, an anatomical region critical in the development of behavioral disorders. Herein, dorsal striatum of 10 transgenic DISC1 (tgDISC1) and 10 wild type (WT) littermate control rats was used for synaptosomal preparations and for performing liquid chromatography-tandem mass spectrometry (LC-MS)-based quantitative proteomics, using isobaric labeling (TMT10plex). Functional enrichment analysis was generated from proteins with level changes. The increase in DISC1 expression leads to changes in proteins and synaptic-associated processes including membrane trafficking, ion transport, synaptic organization and neurodevelopment. Canonical pathway analysis assigned proteins with level changes to actin cytoskeleton, Gαq, Rho family GTPase and Rho GDI, axonal guidance, ephrin receptor and dopamine-DARPP32 feedback in cAMP signaling. DISC1-regulated proteins proposed in the current study are also highly associated with neurodevelopmental and mental disorders. Bioinformatics analyses from the current study predicted that the following biological processes may be activated by overexpression of DISC1, i.e., regulation of cell quantities, neuronal and axonal extension and long term potentiation. Our findings demonstrate that the effects of overexpression of non-mutant DISC1 or its misassembly has profound consequences on protein networks essential for behavioral control. These results are also relevant for the interpretation of previous as well as for the design of future studies on DISC1.
Collapse
Affiliation(s)
- Fernando J Sialana
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
| | - An-Li Wang
- Center for Behavioral Neuroscience, University of Düsseldorf, Düsseldorf, Germany
| | - Benedetta Fazari
- Center for Behavioral Neuroscience, University of Düsseldorf, Düsseldorf, Germany
| | - Martina Kristofova
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
| | - Roman Smidak
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
| | - Svenja V Trossbach
- Department of Neuropathology, Heinrich-Heine University of Düsseldorf, Düsseldorf, Germany
| | - Carsten Korth
- Department of Neuropathology, Heinrich-Heine University of Düsseldorf, Düsseldorf, Germany
| | - Joseph P Huston
- Center for Behavioral Neuroscience, University of Düsseldorf, Düsseldorf, Germany
| | | | - Gert Lubec
- Department of Neuroproteomics, Paracelsus Private Medical University, Salzburg, Austria
| |
Collapse
|
110
|
Darde TA, Gaudriault P, Beranger R, Lancien C, Caillarec-Joly A, Sallou O, Bonvallot N, Chevrier C, Mazaud-Guittot S, Jégou B, Collin O, Becker E, Rolland AD, Chalmel F. TOXsIgN: a cross-species repository for toxicogenomic signatures. Bioinformatics 2018; 34:2116-2122. [DOI: 10.1093/bioinformatics/bty040] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/24/2018] [Indexed: 02/02/2023] Open
Affiliation(s)
- Thomas A Darde
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S1085, F-35000 Rennes, France
- Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA/INRIA) – GenOuest Platform, Université de Rennes 1, F-35042 Rennes, France
| | - Pierre Gaudriault
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S1085, F-35000 Rennes, France
| | - Rémi Beranger
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S1085, F-35000 Rennes, France
| | - Clément Lancien
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S1085, F-35000 Rennes, France
| | - Annaëlle Caillarec-Joly
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S1085, F-35000 Rennes, France
| | - Olivier Sallou
- Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA/INRIA) – GenOuest Platform, Université de Rennes 1, F-35042 Rennes, France
| | - Nathalie Bonvallot
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S1085, F-35000 Rennes, France
| | - Cécile Chevrier
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S1085, F-35000 Rennes, France
| | - Séverine Mazaud-Guittot
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S1085, F-35000 Rennes, France
| | - Bernard Jégou
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S1085, F-35000 Rennes, France
| | - Olivier Collin
- Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA/INRIA) – GenOuest Platform, Université de Rennes 1, F-35042 Rennes, France
| | - Emmanuelle Becker
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S1085, F-35000 Rennes, France
| | - Antoine D Rolland
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S1085, F-35000 Rennes, France
| | - Frédéric Chalmel
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S1085, F-35000 Rennes, France
| |
Collapse
|
111
|
Chen X, Sun YZ, Zhang DH, Li JQ, Yan GY, An JY, You ZH. NRDTD: a database for clinically or experimentally supported non-coding RNAs and drug targets associations. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2017:4027556. [PMID: 29220444 PMCID: PMC5527270 DOI: 10.1093/database/bax057] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 06/30/2017] [Indexed: 11/14/2022]
Abstract
In recent years, more and more non-coding RNAs (ncRNAs) have been identified and increasing evidences have shown that ncRNAs may affect gene expression and disease progression, making them a new class of targets for drug discovery. It thus becomes important to understand the relationship between ncRNAs and drug targets. For this purpose, an ncRNAs and drug targets association database would be extremely beneficial. Here, we developed ncRNA Drug Targets Database (NRDTD) that collected 165 entries of clinically or experimentally supported ncRNAs as drug targets, including 97 ncRNAs and 96 drugs. Moreover, we annotated ncRNA-drug target associations with drug information from KEGG, PubChem, DrugBank, CTD or Wikipedia, GenBank sequence links, OMIM disease ID, pathway and function annotation for ncRNAs, detailed description of associations between ncRNAs and diseases from HMDD or LncRNADisease and the publication PubMed ID. Additionally, we provided users a link to submit novel disease-ncRNA-drug associations and corresponding supporting evidences into the database. We hope NRDTD will be a useful resource for investigating the roles of ncRNAs in drug target identification, drug discovery and disease treatment. Database URL:http://chengroup.cumt.edu.cn/NRDTD
Collapse
Affiliation(s)
- Xing Chen
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou 221116, China
| | - Ya-Zhou Sun
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen 518060, China
| | - De-Hong Zhang
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou 221116, China
| | - Jian-Qiang Li
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen 518060, China
| | - Gui-Ying Yan
- Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China
| | - Ji-Yong An
- School of Computer Science and Technology, China University of Mining and Technology, Xuzhou 21116, China
| | - Zhu-Hong You
- Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Science, Urumqi 830011, China
| |
Collapse
|
112
|
Haynes WA, Tomczak A, Khatri P. Gene annotation bias impedes biomedical research. Sci Rep 2018; 8:1362. [PMID: 29358745 PMCID: PMC5778030 DOI: 10.1038/s41598-018-19333-x] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 12/28/2017] [Indexed: 12/21/2022] Open
Abstract
We found tremendous inequality across gene and protein annotation resources. We observed that this bias leads biomedical researchers to focus on richly annotated genes instead of those with the strongest molecular data. We advocate that researchers reduce these biases by pursuing data-driven hypotheses.
Collapse
Affiliation(s)
- Winston A Haynes
- Stanford Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, California, USA
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, California, USA
- Biomedical Informatics Training Program, Stanford University, Stanford, California, USA
| | - Aurelie Tomczak
- Stanford Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, California, USA
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, California, USA
| | - Purvesh Khatri
- Stanford Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, California, USA.
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, California, USA.
| |
Collapse
|
113
|
Grondin CJ, Davis AP, Wiegers TC, Wiegers JA, Mattingly CJ. Accessing an Expanded Exposure Science Module at the Comparative Toxicogenomics Database. ENVIRONMENTAL HEALTH PERSPECTIVES 2018; 126:014501. [PMID: 29351546 PMCID: PMC6014688 DOI: 10.1289/ehp2873] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 11/17/2017] [Indexed: 05/22/2023]
Abstract
The Comparative Toxicogenomics Database (CTD; http://ctdbase.org) is a free resource that provides manually curated information on chemical, gene, phenotype, and disease relationships to advance understanding of the effect of environmental exposures on human health. Four core content areas are independently curated: chemical-gene interactions, chemical-disease and gene-disease associations, chemical-phenotype interactions, and environmental exposure data (e.g., effects of chemical stressors on humans). Since releasing exposure data in 2015, we have vastly increased our coverage of chemicals and disease/phenotype outcomes; greatly expanded access to exposure content; added search capability by stressors, cohorts, population demographics, and measured outcomes; and created user-specified displays of content. These enhancements aim to facilitate human studies by allowing comparisons among experimental parameters and across studies involving specified chemicals, populations, or outcomes. Integration of data among CTD's four content areas and external data sets, such as Gene Ontology annotations and pathway information, links exposure data with over 1.8 million chemical-gene, chemical-disease and gene-disease interactions. Our analysis tools reveal direct and inferred relationships among the data and provide opportunities to generate predictive connections between environmental exposures and population-level health outcomes. https://doi.org/10.1289/EHP2873.
Collapse
Affiliation(s)
- Cynthia J Grondin
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Allan Peter Davis
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Thomas C Wiegers
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Jolene A Wiegers
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Carolyn J Mattingly
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
- Center for Human Health and the Environment, North Carolina State University , Raleigh, North Carolina, USA
| |
Collapse
|
114
|
Warikoo N, Chang YC, Hsu WL. LPTK: a linguistic pattern-aware dependency tree kernel approach for the BioCreative VI CHEMPROT task. Database (Oxford) 2018; 2018:5139652. [PMID: 30346607 PMCID: PMC6196310 DOI: 10.1093/database/bay108] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 08/30/2018] [Accepted: 09/24/2018] [Indexed: 11/14/2022]
Abstract
Identifying the interactions between chemical compounds and genes from biomedical literatures is one of the frequently discussed topics of text mining in the life science field. In this paper, we describe Linguistic Pattern-Aware Dependency Tree Kernel, a linguistic interaction pattern learning method developed for CHEMPROT task-BioCreative VI, to capture chemical-protein interaction (CPI) patterns within biomedical literatures. We also introduce a framework to integrate these linguistic patterns with smooth partial tree kernel to extract the CPIs. This new method of feature representation models aspects of linguistic probability in geometric representation, which not only optimizes the sufficiency of feature dimension for classification, but also defines features as interpretable contexts rather than long vectors of numbers. In order to test the robustness and efficiency of our system in identifying different kinds of biological interactions, we evaluated our framework on three separate data sets, i.e. CHEMPROT corpus, Chemical-Disease Relation corpus and Protein-Protein Interaction corpus. Corresponding experiment results demonstrate that our method is effective and outperforms several compared systems for each data set.
Collapse
Affiliation(s)
- Neha Warikoo
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan
- Institute of Information Science, Academia Sinica, Taipei, Taiwan
| | - Yung-Chun Chang
- Graduate Institute of Data Science, Taipei Medical University, Taipei, Taiwan
| | - Wen-Lian Hsu
- Institute of Information Science, Academia Sinica, Taipei, Taiwan
| |
Collapse
|
115
|
Zhu X, Wang Z, Zhao Y, Jiang C. Investigation of candidate genes and mechanisms underlying postmenopausal osteoporosis using bioinformatics analysis. Mol Med Rep 2018; 17:1561-1572. [PMID: 29138843 PMCID: PMC5780095 DOI: 10.3892/mmr.2017.8045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 10/06/2017] [Indexed: 12/28/2022] Open
Abstract
The present study aimed to determine candidate genes, chemicals and mechanisms underlying postmenopausal osteoporosis (PMOP). A gene expression profile (accession no. GSE68303), which included 12 tissue samples from ovariectomized mice (OVX group) and 11 normal tissue samples from sham surgery mice (control group), was downloaded from the Gene Expression Omnibus database. The identification of differentially expressed genes (DEGs), and Gene Ontology functional enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses, was performed, followed by an investigation of protein‑protein interactions (PPI), PPI modules, transcription factors (TFs) and chemicals. A total of 784 upregulated and 729 downregulated DEGs between the two groups were identified. Furthermore, 2 upregulated modules and 6 downregulated modules were determined. The upregulated DEGs in modules were enriched in 'sensory perception of smell' function and 'olfactory transduction' pathway, and a number of genes belonging to the olfactory receptor (OLFR) family were identified in upregulated modules. The downregulated DEGs in modules were enriched in 'DNA replication initiation' function and 'cell cycle' pathway. A total of 8 TFs, including SP1 TF (SP1) and protein C‑ets‑1 (ETS1), were associated with PMOP. Furthermore, estradiol and resveratrol were identified as key chemicals in the chemical‑gene interaction network. Therefore, TFs, including SP1 and ETS1, in addition to members of the OLFR gene family, may be employed as novel targets for treatment of PMOP. Furthermore, functions including 'sensory perception of smell' and 'replication initiation', and 'olfactory transduction' and 'cell cycle' pathways, may serve roles in PMOP. In addition, based on the chemical‑gene interaction network, estradiol and resveratrol may also be considered for the treatment PMOP.
Collapse
Affiliation(s)
- Xiaozhong Zhu
- Department of Orthopedic Surgery, Tongji Hospital, Tongji University, Shanghai 200065, P.R. China
| | - Zhiyuan Wang
- Department of Orthopedic Surgery, Tongji Hospital, Tongji University, Shanghai 200065, P.R. China
| | - Yanxun Zhao
- Department of Orthopedic Surgery, Tongji Hospital, Tongji University, Shanghai 200065, P.R. China
| | - Chao Jiang
- Department of Orthopedic Surgery, Tongji Hospital, Tongji University, Shanghai 200065, P.R. China
| |
Collapse
|
116
|
Espín-Pérez A, Font-Ribera L, van Veldhoven K, Krauskopf J, Portengen L, Chadeau-Hyam M, Vermeulen R, Grimalt JO, Villanueva CM, Vineis P, Kogevinas M, Kleinjans JC, de Kok TM. Blood transcriptional and microRNA responses to short-term exposure to disinfection by-products in a swimming pool. ENVIRONMENT INTERNATIONAL 2018; 110:42-50. [PMID: 29122314 DOI: 10.1016/j.envint.2017.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 09/08/2017] [Accepted: 10/11/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Swimming in a chlorinated pool results in high exposure levels to disinfection by-products (DBPs), which have been associated with an increased risk of bladder cancer. OBJECTIVES By studying molecular responses at the blood transcriptome level we examined the biological processes associated with exposure to these compounds. METHODS Whole-genome gene expression and microRNA analysis was performed on blood samples collected from 43 volunteers before and 2h after 40min swimming in an indoor chlorinated pool (PISCINAII study). Exposure to THMs was measured in exhaled breath. Heart rate and kcal expenditure were measured as proxies for physical activity. Associations between exposure levels and gene expression were assessed using multivariate normal models (MVN), correcting for age, body mass index and sex. A Bonferroni threshold at 5% was applied. RESULTS MVN-models for the individual exposures identified 1778 genes and 23 microRNAs that were significantly associated with exposure to at least one DBP. Due to co-linearity it was not possible to statistically disentangle responses to DBP exposure from those related to physical activity. However, after eliminating previously reported transcripts associated with physical activity a large number of hits remained associated with DBP exposure. Among those, 9 were linked with bladder and 31 with colon cancer. Concordant microRNA/mRNA expressions were identified in association with DBP exposure for hsa-mir-22-3p and hsa-miR-146a-5p and their targets RCOR1 and TLR4, both related to colon cancer in association with DBP exposure. CONCLUSIONS Short-term exposure to low levels of DBPs shows genomics responses that may be indicative of increased cancer risk.
Collapse
Affiliation(s)
- Almudena Espín-Pérez
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands.
| | - Laia Font-Ribera
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
| | - Karin van Veldhoven
- MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Julian Krauskopf
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Lutzen Portengen
- Institute for Risk Assessment Sciences, Utrecht, The Netherlands
| | - Marc Chadeau-Hyam
- MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Roel Vermeulen
- Institute for Risk Assessment Sciences, Utrecht, The Netherlands
| | - Joan O Grimalt
- Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Barcelona, Catalonia, Spain
| | | | - Paolo Vineis
- MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | | | - Jos C Kleinjans
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Theo M de Kok
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| |
Collapse
|
117
|
He A, Wang W, Prakash NT, Tinkov AA, Skalny AV, Wen Y, Hao J, Guo X, Zhang F. Integrating genome-wide association study summaries and element-gene interaction datasets identified multiple associations between elements and complex diseases. Genet Epidemiol 2017; 42:168-173. [PMID: 29265413 DOI: 10.1002/gepi.22106] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 11/08/2017] [Accepted: 11/08/2017] [Indexed: 12/17/2022]
Abstract
Chemical elements are closely related to human health. Extensive genomic profile data of complex diseases offer us a good opportunity to systemically investigate the relationships between elements and complex diseases/traits. In this study, we applied gene set enrichment analysis (GSEA) approach to detect the associations between elements and complex diseases/traits though integrating element-gene interaction datasets and genome-wide association study (GWAS) data of complex diseases/traits. To illustrate the performance of GSEA, the element-gene interaction datasets of 24 elements were extracted from the comparative toxicogenomics database (CTD). GWAS summary datasets of 24 complex diseases or traits were downloaded from the dbGaP or GEFOS websites. We observed significant associations between 7 elements and 13 complex diseases or traits (all false discovery rate (FDR) < 0.05), including reported relationships such as aluminum vs. Alzheimer's disease (FDR = 0.042), calcium vs. bone mineral density (FDR = 0.031), magnesium vs. systemic lupus erythematosus (FDR = 0.012) as well as novel associations, such as nickel vs. hypertriglyceridemia (FDR = 0.002) and bipolar disorder (FDR = 0.027). Our study results are consistent with previous biological studies, supporting the good performance of GSEA. Our analyzing results based on GSEA framework provide novel clues for discovering causal relationships between elements and complex diseases.
Collapse
Affiliation(s)
- Awen He
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Wenyu Wang
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | | | - Alexey A Tinkov
- Peoples' Friendship University of Russia (RUDN University), Moscow, Russia.,Yaroslavl State University, Yaroslavl, Russia
| | - Anatoly V Skalny
- Peoples' Friendship University of Russia (RUDN University), Moscow, Russia.,Yaroslavl State University, Yaroslavl, Russia.,Orenburg State University, Orenburg, Russia.,Trace Element Institute for UNESCO, Lyon, France
| | - Yan Wen
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Jingcan Hao
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Xiong Guo
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Feng Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, P. R. China
| |
Collapse
|
118
|
Shimoyama M, Laulederkind SJF, De Pons J, Nigam R, Smith JR, Tutaj M, Petri V, Hayman GT, Wang SJ, Ghiasvand O, Thota J, Dwinell MR. Exploring human disease using the Rat Genome Database. Dis Model Mech 2017; 9:1089-1095. [PMID: 27736745 PMCID: PMC5087824 DOI: 10.1242/dmm.026021] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Rattus norvegicus, the laboratory rat, has been a crucial model for studies of the environmental and genetic factors associated with human diseases for over 150 years. It is the primary model organism for toxicology and pharmacology studies, and has features that make it the model of choice in many complex-disease studies. Since 1999, the Rat Genome Database (RGD; http://rgd.mcw.edu) has been the premier resource for genomic, genetic, phenotype and strain data for the laboratory rat. The primary role of RGD is to curate rat data and validate orthologous relationships with human and mouse genes, and make these data available for incorporation into other major databases such as NCBI, Ensembl and UniProt. RGD also provides official nomenclature for rat genes, quantitative trait loci, strains and genetic markers, as well as unique identifiers. The RGD team adds enormous value to these basic data elements through functional and disease annotations, the analysis and visual presentation of pathways, and the integration of phenotype measurement data for strains used as disease models. Because much of the rat research community focuses on understanding human diseases, RGD provides a number of datasets and software tools that allow users to easily explore and make disease-related connections among these datasets. RGD also provides comprehensive human and mouse data for comparative purposes, illustrating the value of the rat in translational research. This article introduces RGD and its suite of tools and datasets to researchers - within and beyond the rat community - who are particularly interested in leveraging rat-based insights to understand human diseases.
Collapse
Affiliation(s)
- Mary Shimoyama
- Medical College of Wisconsin, Department of Surgery, Milwaukee, WI 53226, USA
| | | | - Jeff De Pons
- Medical College of Wisconsin, Department of Surgery, Milwaukee, WI 53226, USA
| | - Rajni Nigam
- Medical College of Wisconsin, Department of Surgery, Milwaukee, WI 53226, USA
| | - Jennifer R Smith
- Medical College of Wisconsin, Department of Surgery, Milwaukee, WI 53226, USA
| | - Marek Tutaj
- Medical College of Wisconsin, Department of Surgery, Milwaukee, WI 53226, USA
| | - Victoria Petri
- Medical College of Wisconsin, Department of Surgery, Milwaukee, WI 53226, USA
| | - G Thomas Hayman
- Medical College of Wisconsin, Department of Surgery, Milwaukee, WI 53226, USA
| | - Shur-Jen Wang
- Medical College of Wisconsin, Department of Surgery, Milwaukee, WI 53226, USA
| | - Omid Ghiasvand
- Medical College of Wisconsin, Department of Surgery, Milwaukee, WI 53226, USA
| | - Jyothi Thota
- Medical College of Wisconsin, Department of Surgery, Milwaukee, WI 53226, USA
| | - Melinda R Dwinell
- Medical College of Wisconsin, Department of Physiology, Milwaukee, WI 53226, USA
| |
Collapse
|
119
|
Shi G, Wang Y, Zhang C, Zhao Z, Sun X, Zhang S, Fan J, Zhou C, Zhang J, Zhang H, Liu J. Identification of genes involved in the four stages of colorectal cancer: Gene expression profiling. Mol Cell Probes 2017; 37:39-47. [PMID: 29179987 DOI: 10.1016/j.mcp.2017.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 10/09/2017] [Accepted: 11/13/2017] [Indexed: 02/05/2023]
Abstract
BACKGROUND Colorectal cancer (CRC) is a common cancer with high morbidity and mortality. However, its molecular mechanism is not clear, nor the genes related to CRC stages. METHODS Gene expression data in CRC and healthy colorectal tissues were obtained from gene expression omnibus. Limma package was used to identify the differentially expressed genes (DEGs) between control and CRC (stage I, II, III, and IV), obtaining 4 DEG sets. VennPlex was utilized to find all DEGs and intersection DEGs. Functional interactions between all DEGs and protein-protein interactions (PPIs) between intersection DEGs were analyzed using ReactomeFIViz and STRING, respectively, and networks were visualized. Known CRC-related genes were down-loaded from Comparative Toxicogenomics Database and mapped to PPI network. RESULTS Totally, 851, 760, 729, and 878 DEGs were found between control and CRC stage I, II, III, and IV, respectively. Taken together, 1235 DEGs were found, as well as 128 up-regulated intersection DEGs, 365 down-regulated intersection DEGs, and 0 contra-regulated DEG. A functional interaction network of all DEGs and a PPI network of intersection DEGs were constructed, in which CDC20, PTTG1, and MAD2L1 interacted with BUB1B; UGT2B17 interacted with ADH1B; MCM7 interacted with MCM2. BUB1B, ADH1B, and MCM2 were known CRC-related genes. Gradually upregulated expressions of CDC20, PTTG1, MAD2L1, UGT2B17, and MCM7 in stage I, II, III, and IV CRC were confirmed by using quantitative PCR. Besides, up-regulated intersection DEGs enriched in pathways about Cell cycle, DNA replication, and p53 signaling. CONCLUSION CDC20, PTTG1, MAD2L1, UGT2B17, and MCM7 might be CRC stage-related genes.
Collapse
Affiliation(s)
- Guiling Shi
- Tianjin Union Medical Center, 190 Jieyuan Road, Hongqiao District, Tianjin 300121, PR China
| | - Yijia Wang
- Tianjin Union Medical Center, 190 Jieyuan Road, Hongqiao District, Tianjin 300121, PR China
| | - Chunze Zhang
- Tianjin Union Medical Center, 190 Jieyuan Road, Hongqiao District, Tianjin 300121, PR China
| | - Zhenying Zhao
- Tianjin Union Medical Center, 190 Jieyuan Road, Hongqiao District, Tianjin 300121, PR China; School of Chemical Engineering and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, PR China
| | - Xiuying Sun
- Tianjin Union Medical Center, 190 Jieyuan Road, Hongqiao District, Tianjin 300121, PR China
| | - Shiwu Zhang
- Tianjin Union Medical Center, 190 Jieyuan Road, Hongqiao District, Tianjin 300121, PR China
| | - Jinling Fan
- Tianjin Union Medical Center, 190 Jieyuan Road, Hongqiao District, Tianjin 300121, PR China
| | - Cunxia Zhou
- Tianjin Union Medical Center, 190 Jieyuan Road, Hongqiao District, Tianjin 300121, PR China
| | - Jihong Zhang
- Tianjin Union Medical Center, 190 Jieyuan Road, Hongqiao District, Tianjin 300121, PR China
| | - Huijuan Zhang
- Tianjin Union Medical Center, 190 Jieyuan Road, Hongqiao District, Tianjin 300121, PR China.
| | - Jun Liu
- Tianjin Union Medical Center, 190 Jieyuan Road, Hongqiao District, Tianjin 300121, PR China.
| |
Collapse
|
120
|
Penberthy KK, Rival C, Shankman LS, Raymond MH, Zhang J, Perry JSA, Lee CS, Han CZ, Onengut-Gumuscu S, Palczewski K, Lysiak JJ, Ravichandran KS. Context-dependent compensation among phosphatidylserine-recognition receptors. Sci Rep 2017; 7:14623. [PMID: 29116131 PMCID: PMC5676788 DOI: 10.1038/s41598-017-15191-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 10/19/2017] [Indexed: 12/03/2022] Open
Abstract
Phagocytes express multiple phosphatidylserine (PtdSer) receptors that recognize apoptotic cells. It is unknown whether these receptors are interchangeable or if they play unique roles during cell clearance. Loss of the PtdSer receptor Mertk is associated with apoptotic corpse accumulation in the testes and degeneration of photoreceptors in the eye. Both phenotypes are linked to impaired phagocytosis by specialized phagocytes: Sertoli cells and the retinal pigmented epithelium (RPE). Here, we overexpressed the PtdSer receptor BAI1 in mice lacking MerTK (Mertk -/- Bai1 Tg ) to evaluate PtdSer receptor compensation in vivo. While Bai1 overexpression rescues clearance of apoptotic germ cells in the testes of Mertk -/- mice it fails to enhance RPE phagocytosis or prevent photoreceptor degeneration. To determine why MerTK is critical to RPE function, we examined visual cycle intermediates and performed unbiased RNAseq analysis of RPE from Mertk +/+ and Mertk -/- mice. Prior to the onset of photoreceptor degeneration, Mertk -/- mice had less accumulation of retinyl esters and dysregulation of a striking array of genes, including genes related to phagocytosis, metabolism, and retinal disease in humans. Collectively, these experiments establish that not all phagocytic receptors are functionally equal, and that compensation among specific engulfment receptors is context and tissue dependent.
Collapse
Affiliation(s)
- Kristen K Penberthy
- Center for Cell Clearance, University of Virginia, Charlottesville, VA, USA
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, USA
| | - Claudia Rival
- Center for Cell Clearance, University of Virginia, Charlottesville, VA, USA
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, USA
- Department of Urology, University of Virginia, Charlottesville, VA, USA
| | - Laura S Shankman
- Center for Cell Clearance, University of Virginia, Charlottesville, VA, USA
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, USA
| | - Michael H Raymond
- Center for Cell Clearance, University of Virginia, Charlottesville, VA, USA
- Department of Neuroscience, University of Virginia, Charlottesville, VA, USA
| | - Jianye Zhang
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Justin S A Perry
- Center for Cell Clearance, University of Virginia, Charlottesville, VA, USA
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, USA
| | - Chang Sup Lee
- Center for Cell Clearance, University of Virginia, Charlottesville, VA, USA
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, USA
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Gyeongsang National University, 501 Jinju-daero, Jinju, Gyeongnam, 52828, Korea
| | - Claudia Z Han
- Center for Cell Clearance, University of Virginia, Charlottesville, VA, USA
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, USA
| | - Suna Onengut-Gumuscu
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Krzysztof Palczewski
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Jeffrey J Lysiak
- Center for Cell Clearance, University of Virginia, Charlottesville, VA, USA
- Department of Urology, University of Virginia, Charlottesville, VA, USA
| | - Kodi S Ravichandran
- Center for Cell Clearance, University of Virginia, Charlottesville, VA, USA.
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, USA.
- Inflammation Research Center, VIB, and the Department of Biomedical molecular Biology, Ghent University, Ghent, Belgium.
| |
Collapse
|
121
|
Huang R, He Y, Sun B, Liu B. Bioinformatic Analysis Identifies Three Potentially Key Differentially Expressed Genes in Peripheral Blood Mononuclear Cells of Patients with Takayasu's Arteritis. CELL JOURNAL 2017; 19:647-653. [PMID: 29105401 PMCID: PMC5672105 DOI: 10.22074/cellj.2018.4991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 05/09/2017] [Indexed: 11/29/2022]
Abstract
Objective This study aimed to identify several potentially key genes associated with the pathogenesis of Takayasu’s
arteritis (TA). This identification may lead to a deeper mechanistic understanding of TA etiology and pave the way for
potential therapeutic approaches.
Materials and Methods In this experimental study, the microarray dataset GSE33910, which includes expression
data for peripheral blood mononuclear cell (PBMC) samples isolated from TA patients and normal volunteers, was
downloaded from the publicly accessible Gene Expression Omnibus (GEO) database. Differentially expressed genes
(DEGs) were identified in PBMCs of TA patients compared with normal controls. Gene ontology (GO) enrichment
analysis of DEGs and analysis of protein-protein interaction (PPI) network were carried out. Several hub proteins were
extracted from the PPI network based on node degrees and random walk algorithm. Additionally, transcription factors
(TFs) were predicted and the corresponding regulatory network was constructed.
Results A total of 932 DEGs (372 up- and 560 down-regulated genes) were identified in PBMCs from TA patients.
Interestingly, up-regulated and down-regulated genes were involved in different GO terms and pathways. A PPI network
of proteins encoded by DEGs was constructed and RHOA, FOS, EGR1, and GNB1 were considered to be hub proteins
with both higher random walk score and node degree. A total of 13 TFs were predicted to be differentially expressed. A
total of 49 DEGs had been reported to be associated with TA in the Comparative Toxicogenomics Database (CTD). The
only TA marker gene in the CTD database was NOS2, confirmed by three studies. However, NOS2 was not significantly
altered in the analyzed microarray dataset. Nevertheless,NOS3 was a significantly down-regulated gene and was
involved in the platelet activation pathway.
Conclusion RHOA, FOS, and EGR1 are potential candidate genes for the diagnosis and therapy of TA.
Collapse
Affiliation(s)
- Renping Huang
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yang He
- Department of Anesthesiology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Bei Sun
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Bing Liu
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.
| |
Collapse
|
122
|
Li S, Kumar T P, Joshee S, Kirschstein T, Subburaju S, Khalili JS, Kloepper J, Du C, Elkhal A, Szabó G, Jain RK, Köhling R, Vasudevan A. Endothelial cell-derived GABA signaling modulates neuronal migration and postnatal behavior. Cell Res 2017; 28:221-248. [PMID: 29086765 PMCID: PMC5799810 DOI: 10.1038/cr.2017.135] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 08/06/2017] [Accepted: 09/07/2017] [Indexed: 01/27/2023] Open
Abstract
The cerebral cortex is essential for integration and processing of information
that is required for most behaviors. The exquisitely precise laminar
organization of the cerebral cortex arises during embryonic development when
neurons migrate successively from ventricular zones to coalesce into specific
cortical layers. While radial glia act as guide rails for projection neuron
migration, pre-formed vascular networks provide support and guidance cues for
GABAergic interneuron migration. This study provides novel conceptual and
mechanistic insights into this paradigm of vascular-neuronal interactions,
revealing new mechanisms of GABA and its receptor-mediated signaling via
embryonic forebrain endothelial cells. With the use of two new endothelial cell
specific conditional mouse models of the GABA pathway
(Gabrb3ΔTie2-Cre and
VgatΔTie2-Cre), we show that partial or
complete loss of GABA release from endothelial cells during embryogenesis
results in vascular defects and impairs long-distance migration and positioning
of cortical interneurons. The downstream effects of perturbed endothelial
cell-derived GABA signaling are critical, leading to lasting changes to cortical
circuits and persistent behavioral deficits. Furthermore, we illustrate new
mechanisms of activation of GABA signaling in forebrain endothelial cells that
promotes their migration, angiogenesis and acquisition of blood-brain barrier
properties. Our findings uncover and elucidate a novel endothelial GABA
signaling pathway in the CNS that is distinct from the classical neuronal GABA
signaling pathway and shed new light on the etiology and pathophysiology of
neuropsychiatric diseases, such as autism spectrum disorders, epilepsy, anxiety,
depression and schizophrenia.
Collapse
Affiliation(s)
- Suyan Li
- Department of Psychiatry, Harvard Medical School, Boston, MA 02215, USA.,Angiogenesis and Brain Development Laboratory, Division of Basic Neuroscience, McLean Hospital, 115 Mill Street, Belmont, MA 02478, USA
| | - Peeyush Kumar T
- Department of Psychiatry, Harvard Medical School, Boston, MA 02215, USA.,Angiogenesis and Brain Development Laboratory, Division of Basic Neuroscience, McLean Hospital, 115 Mill Street, Belmont, MA 02478, USA
| | - Sampada Joshee
- Angiogenesis and Brain Development Laboratory, Division of Basic Neuroscience, McLean Hospital, 115 Mill Street, Belmont, MA 02478, USA
| | - Timo Kirschstein
- Oscar-Langendorff-Institute of Physiology, Rostock University Medical Center, Gertrudenstrasse 9, 18057 Rostock, Germany
| | - Sivan Subburaju
- Department of Psychiatry, Harvard Medical School, Boston, MA 02215, USA.,Program in Structural and Molecular Neuroscience, McLean Hospital, 115 Mill Street, Belmont, MA 02478, USA
| | | | - Jonas Kloepper
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Chuang Du
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA 02148, USA
| | - Abdallah Elkhal
- Department of Surgery, Harvard Medical School, Boston, MA 02115, USA.,Division of Transplantation, Brigham and Women's Hospital, 221 Longwood Avenue, EBRC 309, Boston, MA 02115, USA
| | - Gábor Szabó
- Laboratory of Molecular Biology and Genetics, Department of Gene Technology and Developmental Neurobiology, Institute of Experimental Medicine, 1083 Budapest, Hungary
| | - Rakesh K Jain
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Rüdiger Köhling
- Oscar-Langendorff-Institute of Physiology, Rostock University Medical Center, Gertrudenstrasse 9, 18057 Rostock, Germany
| | - Anju Vasudevan
- Department of Psychiatry, Harvard Medical School, Boston, MA 02215, USA.,Angiogenesis and Brain Development Laboratory, Division of Basic Neuroscience, McLean Hospital, 115 Mill Street, Belmont, MA 02478, USA
| |
Collapse
|
123
|
McAllister K, Mechanic LE, Amos C, Aschard H, Blair IA, Chatterjee N, Conti D, Gauderman WJ, Hsu L, Hutter CM, Jankowska MM, Kerr J, Kraft P, Montgomery SB, Mukherjee B, Papanicolaou GJ, Patel CJ, Ritchie MD, Ritz BR, Thomas DC, Wei P, Witte JS. Current Challenges and New Opportunities for Gene-Environment Interaction Studies of Complex Diseases. Am J Epidemiol 2017; 186:753-761. [PMID: 28978193 PMCID: PMC5860428 DOI: 10.1093/aje/kwx227] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 03/14/2017] [Accepted: 03/16/2017] [Indexed: 12/25/2022] Open
Abstract
Recently, many new approaches, study designs, and statistical and analytical methods have emerged for studying gene-environment interactions (G×Es) in large-scale studies of human populations. There are opportunities in this field, particularly with respect to the incorporation of -omics and next-generation sequencing data and continual improvement in measures of environmental exposures implicated in complex disease outcomes. In a workshop called "Current Challenges and New Opportunities for Gene-Environment Interaction Studies of Complex Diseases," held October 17-18, 2014, by the National Institute of Environmental Health Sciences and the National Cancer Institute in conjunction with the annual American Society of Human Genetics meeting, participants explored new approaches and tools that have been developed in recent years for G×E discovery. This paper highlights current and critical issues and themes in G×E research that need additional consideration, including the improved data analytical methods, environmental exposure assessment, and incorporation of functional data and annotations.
Collapse
Affiliation(s)
| | - Leah E. Mechanic
- Correspondence to Dr. Leah E. Mechanic, Genomic Epidemiology Branch, Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, 9609 Medical Center Drive, Room 4E104, MSC 9763, Bethesda, MD 20892 (e-mail: )
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
124
|
Chen C, He J, Bliss N, Tong H. Towards Optimal Connectivity on Multi-layered Networks. IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING 2017; 29:2332-2346. [PMID: 29755246 PMCID: PMC5945354 DOI: 10.1109/tkde.2017.2719026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Networks are prevalent in many high impact domains. Moreover, cross-domain interactions are frequently observed in many applications, which naturally form the dependencies between different networks. Such kind of highly coupled network systems are referred to as multi-layered networks, and have been used to characterize various complex systems, including critical infrastructure networks, cyber-physical systems, collaboration platforms, biological systems and many more. Different from single-layered networks where the functionality of their nodes is mainly affected by within-layer connections, multi-layered networks are more vulnerable to disturbance as the impact can be amplified through cross-layer dependencies, leading to the cascade failure to the entire system. To manipulate the connectivity in multi-layered networks, some recent methods have been proposed based on two-layered networks with specific types of connectivity measures. In this paper, we address the above challenges in multiple dimensions. First, we propose a family of connectivity measures (SUBLINE) that unifies a wide range of classic network connectivity measures. Third, we reveal that the connectivity measures in SUBLINE family enjoy diminishing returns property, which guarantees a near-optimal solution with linear complexity for the connectivity optimization problem. Finally, we evaluate our proposed algorithm on real data sets to demonstrate its effectiveness and efficiency.
Collapse
Affiliation(s)
- Chen Chen
- Arizona State University, Tempe, AZ, 85281, USA
| | - Jingrui He
- Arizona State University, Tempe, AZ, 85281, USA
| | - Nadya Bliss
- Arizona State University, Tempe, AZ, 85281, USA
| | | |
Collapse
|
125
|
Wang YY, Bai H, Zhang RZ, Yan H, Ning K, Zhao XM. Predicting new indications of compounds with a network pharmacology approach: Liuwei Dihuang Wan as a case study. Oncotarget 2017; 8:93957-93968. [PMID: 29212201 PMCID: PMC5706847 DOI: 10.18632/oncotarget.21398] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 09/05/2017] [Indexed: 01/15/2023] Open
Abstract
With the ever increasing cost and time required for drug development, new strategies for drug development are highly demanded, whereas repurposing old drugs has attracted much attention in drug discovery. In this paper, we introduce a new network pharmacology approach, namely PINA, to predict potential novel indications of old drugs based on the molecular networks affected by drugs and associated with diseases. Benchmark results on FDA approved drugs have shown the superiority of PINA over traditional computational approaches in identifying new indications of old drugs. We further extend PINA to predict the novel indications of Traditional Chinese Medicines (TCMs) with Liuwei Dihuang Wan (LDW) as a case study. The predicted indications, including immune system disorders and tumor, are validated by expert knowledge and evidences from literature, demonstrating the effectiveness of our proposed computational approach.
Collapse
Affiliation(s)
- Yin-Ying Wang
- Institute of Science and Technology for Brain-Inspired Intelligence (ISTBI), Fudan University, Shanghai 200433, China.,Department of Computer Science and Technology, Tongji University, Shanghai 201804, China.,Department of Electronic Engineering, City University of Hong Kong, Kowloon 999077, Hong Kong
| | - Hong Bai
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Run-Zhi Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Hong Yan
- Department of Electronic Engineering, City University of Hong Kong, Kowloon 999077, Hong Kong
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xing-Ming Zhao
- Institute of Science and Technology for Brain-Inspired Intelligence (ISTBI), Fudan University, Shanghai 200433, China
| |
Collapse
|
126
|
Xu Y, Wang J, Xu Y, Xiao H, Li J, Wang Z. Screening critical genes associated with malignant glioma using bioinformatics analysis. Mol Med Rep 2017; 16:6580-6589. [PMID: 28901452 PMCID: PMC5865802 DOI: 10.3892/mmr.2017.7471] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 07/05/2017] [Indexed: 11/06/2022] Open
Abstract
Malignant gliomas are high‑grade gliomas, which are derived from glial cells in the spine or brain. To examine the mechanisms underlying malignant gliomas in the present study, the expression profile of GSE54004, which included 12 grade II astrocytomas, 33 grade III astrocytomas and 98 grade IV astrocytomas, was downloaded from the Gene Expression Omnibus. Using the Limma package in R, the differentially expressed genes (DEGs) in grade III, vs. grade II astrocytoma, grade IV, vs. grade II astrocytoma, and grade IV, vs. grade III astrocytoma were analyzed. Venn diagram analysis and enrichment analyses were performed separately for the DEGs using VennPlex software and the Database for Annotation, Visualization and Integrated Discovery. Protein‑protein interaction (PPI) networks were visualized using Cytoscape software, and subsequent module analysis of the PPI networks was performed using the ClusterONE tool. Finally, glioma‑associated genes and glioma marker genes among the DEGs were identified using the CTD database. A total of 27, 1,446 and 776 DEGs were screened for the grade III, vs. grade II, grade IV, vs. grade II, and grade IV, vs. grade III astrocytoma comparison groups, respectively. Functional enrichment analyses showed that matrix metalloproteinase 9 (MMP9) and chitinase 3‑like 1 (CHI3L1) were enriched in the extracellular matrix and extracellular matrix structural constituent, respectively. In the PPI networks, annexin A1 (ANXA1) had a higher degree and MMP9 had interactions with vascular endothelial growth factor A (VEGFA). There were 10 common glioma marker genes between the grade IV, vs. grade II and the grade IV, vs. grade III comparison groups, including MMP9, CHI3L1, VEGFA and S100 calcium binding protein A4 (S100A4). This suggested that MMP9, CHI3L1, VEGFA, S100A4 and ANXA1 may be involved in the progression of malignant gliomas.
Collapse
Affiliation(s)
- Yonggang Xu
- Department of Minimally Invasive Neurosurgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Jie Wang
- Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150001, P.R. China
| | - Yanbin Xu
- Department of Minimally Invasive Neurosurgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Hong Xiao
- Department of Minimally Invasive Neurosurgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Jianhua Li
- Department of Minimally Invasive Neurosurgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Zhi Wang
- Department of Minimally Invasive Neurosurgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| |
Collapse
|
127
|
Abstract
Motivation: The rapid growth of diverse biological data allows us to consider interactions between a variety of objects, such as genes, chemicals, molecular signatures, diseases, pathways and environmental exposures. Often, any pair of objects—such as a gene and a disease—can be related in different ways, for example, directly via gene–disease associations or indirectly via functional annotations, chemicals and pathways. Different ways of relating these objects carry different semantic meanings. However, traditional methods disregard these semantics and thus cannot fully exploit their value in data modeling. Results: We present Medusa, an approach to detect size-k modules of objects that, taken together, appear most significant to another set of objects. Medusa operates on large-scale collections of heterogeneous datasets and explicitly distinguishes between diverse data semantics. It advances research along two dimensions: it builds on collective matrix factorization to derive different semantics, and it formulates the growing of the modules as a submodular optimization program. Medusa is flexible in choosing or combining semantic meanings and provides theoretical guarantees about detection quality. In a systematic study on 310 complex diseases, we show the effectiveness of Medusa in associating genes with diseases and detecting disease modules. We demonstrate that in predicting gene–disease associations Medusa compares favorably to methods that ignore diverse semantic meanings. We find that the utility of different semantics depends on disease categories and that, overall, Medusa recovers disease modules more accurately when combining different semantics. Availability and implementation: Source code is at http://github.com/marinkaz/medusa Contact:marinka@cs.stanford.edu, blaz.zupan@fri.uni-lj.si
Collapse
Affiliation(s)
- Marinka Zitnik
- Department of Computer Science, Stanford University, CA 94305, USA Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia 1000
| | - Blaz Zupan
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia 1000 Department of Molecular and Human Genetics, Baylor College of Medicine, TX 77030, USA
| |
Collapse
|
128
|
Wang CC, Lin YC, Lin YC, Jhang SR, Tung CW. Identification of informative features for predicting proinflammatory potentials of engine exhausts. Biomed Eng Online 2017; 16:66. [PMID: 28830522 PMCID: PMC5568601 DOI: 10.1186/s12938-017-0355-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND The immunotoxicity of engine exhausts is of high concern to human health due to the increasing prevalence of immune-related diseases. However, the evaluation of immunotoxicity of engine exhausts is currently based on expensive and time-consuming experiments. It is desirable to develop efficient methods for immunotoxicity assessment. METHODS To accelerate the development of safe alternative fuels, this study proposed a computational method for identifying informative features for predicting proinflammatory potentials of engine exhausts. A principal component regression (PCR) algorithm was applied to develop prediction models. The informative features were identified by a sequential backward feature elimination (SBFE) algorithm. RESULTS A total of 19 informative chemical and biological features were successfully identified by SBFE algorithm. The informative features were utilized to develop a computational method named FS-CBM for predicting proinflammatory potentials of engine exhausts. FS-CBM model achieved a high performance with correlation coefficient values of 0.997 and 0.943 obtained from training and independent test sets, respectively. CONCLUSIONS The FS-CBM model was developed for predicting proinflammatory potentials of engine exhausts with a large improvement on prediction performance compared with our previous CBM model. The proposed method could be further applied to construct models for bioactivities of mixtures.
Collapse
Affiliation(s)
- Chia-Chi Wang
- School of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan
- Ph.D. Program in Toxicology, Kaohsiung Medical University, Kaohsiung, Taiwan
- Institute of Environmental Engineering, National Sun Yat-sen University, Kaohsiung, Taiwan
- National Institute of Environmental Health Sciences, National Health Research Institutes, Miaoli County, Taiwan
| | - Ying-Chi Lin
- School of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan
- Ph.D. Program in Toxicology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yuan-Chung Lin
- Ph.D. Program in Toxicology, Kaohsiung Medical University, Kaohsiung, Taiwan
- Institute of Environmental Engineering, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Syu-Ruei Jhang
- Institute of Environmental Engineering, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Chun-Wei Tung
- School of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan
- Ph.D. Program in Toxicology, Kaohsiung Medical University, Kaohsiung, Taiwan
- National Institute of Environmental Health Sciences, National Health Research Institutes, Miaoli County, Taiwan
| |
Collapse
|
129
|
Witt KL, Hsieh JH, Smith-Roe SL, Xia M, Huang R, Auerbach SS, Hur J, Tice RR. Assessment of the DNA damaging potential of environmental chemicals using a quantitative high-throughput screening approach to measure p53 activation. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2017; 58:494-507. [PMID: 28714573 PMCID: PMC5555817 DOI: 10.1002/em.22112] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 06/16/2017] [Accepted: 06/19/2017] [Indexed: 05/08/2023]
Abstract
Genotoxicity potential is a critical component of any comprehensive toxicological profile. Compounds that induce DNA or chromosomal damage often activate p53, a transcription factor essential to cell cycle regulation. Thus, within the US Tox21 Program, we screened a library of ∼10,000 (∼8,300 unique) environmental compounds and drugs for activation of the p53-signaling pathway using a quantitative high-throughput screening assay employing HCT-116 cells (p53+/+ ) containing a stably integrated β-lactamase reporter gene under control of the p53 response element (p53RE). Cells were exposed (-S9) for 16 hr at 15 concentrations (generally 1.2 nM to 92 μM) three times, independently. Excluding compounds that failed analytical chemistry analysis or were suspected of inducing assay interference, 365 (4.7%) of 7,849 unique compounds were concluded to activate p53. As part of an in-depth characterization of our results, we first compared them with results from traditional in vitro genotoxicity assays (bacterial mutation, chromosomal aberration); ∼15% of known, direct-acting genotoxicants in our library activated the p53RE. Mining the Comparative Toxicogenomics Database revealed that these p53 actives were significantly associated with increased expression of p53 downstream genes involved in DNA damage responses. Furthermore, 53 chemical substructures associated with genotoxicity were enriched in certain classes of p53 actives, for example, anthracyclines (antineoplastics) and vinca alkaloids (tubulin disruptors). Interestingly, the tubulin disruptors manifested unusual nonmonotonic concentration response curves suggesting activity through a unique p53 regulatory mechanism. Through the analysis of our results, we aim to define a role for this assay as one component of a comprehensive toxicological characterization of large compound libraries. Environ. Mol. Mutagen. 58:494-507, 2017. © 2017 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Kristine L. Witt
- National Institute of Environmental Health Sciences, Division of the National Toxicology Program, Research Triangle Park, NC
- Corresponding author: Kristine L. Witt, NIEHS/DNTP, 919-541-2761,
| | | | - Stephanie L. Smith-Roe
- National Institute of Environmental Health Sciences, Division of the National Toxicology Program, Research Triangle Park, NC
| | - Menghang Xia
- National Institutes of Health Center for Advancing Translational Sciences, Bethesda, MD
| | - Ruili Huang
- National Institutes of Health Center for Advancing Translational Sciences, Bethesda, MD
| | - Scott S. Auerbach
- National Institute of Environmental Health Sciences, Division of the National Toxicology Program, Research Triangle Park, NC
| | - Junguk Hur
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND
| | - Raymond R. Tice
- National Institute of Environmental Health Sciences, Division of the National Toxicology Program, Research Triangle Park, NC
| |
Collapse
|
130
|
Perkins EJ, Habib T, Escalon BL, Cavallin JE, Thomas L, Weberg M, Hughes MN, Jensen KM, Kahl MD, Villeneuve DL, Ankley GT, Garcia-Reyero N. Prioritization of Contaminants of Emerging Concern in Wastewater Treatment Plant Discharges Using Chemical:Gene Interactions in Caged Fish. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51. [PMID: 28651047 PMCID: PMC6126926 DOI: 10.1021/acs.est.7b01567] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
We examined whether contaminants present in surface waters could be prioritized for further assessment by linking the presence of specific chemicals to gene expression changes in exposed fish. Fathead minnows were deployed in cages for 2, 4, or 8 days at three locations near two different wastewater treatment plant discharge sites in the Saint Louis Bay, Duluth, MN and one upstream reference site. The biological impact of 51 chemicals detected in the surface water of 133 targeted chemicals was determined using biochemical endpoints, exposure activity ratios for biological and estrogenic responses, known chemical:gene interactions from biological pathways and knowledge bases, and analysis of the covariance of ovary gene expression with surface water chemistry. Thirty-two chemicals were significantly linked by covariance with expressed genes. No estrogenic impact on biochemical endpoints was observed in male or female minnows. However, bisphenol A (BPA) was identified by chemical:gene covariation as the most impactful estrogenic chemical across all exposure sites. This was consistent with identification of estrogenic effects on gene expression, high BPA exposure activity ratios across all test sites, and historical analysis of the study area. Gene expression analysis also indicated the presence of nontargeted chemicals including chemotherapeutics consistent with a local hospital waste stream. Overall impacts on gene expression appeared to be related to changes in treatment plant function during rain events. This approach appears useful in examining the impacts of complex mixtures on fish and offers a potential route in linking chemical exposure to adverse outcomes that may reduce population sustainability.
Collapse
Affiliation(s)
- Edward J. Perkins
- U.S. Army Engineer Research and Development Center, Environmental Laboratory, 3909 Halls Ferry Road, Vicksburg, MS, USA
- Corresponding author: ; ERDC, 3909 Halls Ferry Rd,Vicksburg, MS 39180; phone: +1-601-634-2872
| | - Tanwir Habib
- Badger Technical Services, 3909 Halls Ferry Road, Vicksburg, MS, USA
| | - Barbara L. Escalon
- U.S. Army Engineer Research and Development Center, Environmental Laboratory, 3909 Halls Ferry Road, Vicksburg, MS, USA
| | - Jenna E. Cavallin
- U.S. EPA, National Health and Environmental Effects Research Laboratory, Duluth, MN, USA
| | - Linnea Thomas
- U.S. EPA, National Health and Environmental Effects Research Laboratory, Duluth, MN, USA
| | - Matthew Weberg
- U.S. EPA, National Health and Environmental Effects Research Laboratory, Duluth, MN, USA
| | - Megan N. Hughes
- U.S. EPA, National Health and Environmental Effects Research Laboratory, Duluth, MN, USA
| | - Kathleen M. Jensen
- U.S. EPA, National Health and Environmental Effects Research Laboratory, Duluth, MN, USA
| | - Michael D. Kahl
- U.S. EPA, National Health and Environmental Effects Research Laboratory, Duluth, MN, USA
| | - Daniel L. Villeneuve
- U.S. EPA, National Health and Environmental Effects Research Laboratory, Duluth, MN, USA
| | - Gerald T. Ankley
- U.S. EPA, National Health and Environmental Effects Research Laboratory, Duluth, MN, USA
| | - Natàlia Garcia-Reyero
- U.S. Army Engineer Research and Development Center, Environmental Laboratory, 3909 Halls Ferry Road, Vicksburg, MS, USA
| |
Collapse
|
131
|
Chen C, Tong H, Xie L, Ying L, He Q. Cross-Dependency Inference in Multi-Layered Networks: A Collaborative Filtering Perspective. ACM TRANSACTIONS ON KNOWLEDGE DISCOVERY FROM DATA 2017; 11:42. [PMID: 29204108 PMCID: PMC5711486 DOI: 10.1145/3056562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The increasingly connected world has catalyzed the fusion of networks from different domains, which facilitates the emergence of a new network model-multi-layered networks. Examples of such kind of network systems include critical infrastructure networks, biological systems, organization-level collaborations, cross-platform e-commerce, and so forth. One crucial structure that distances multi-layered network from other network models is its cross-layer dependency, which describes the associations between the nodes from different layers. Needless to say, the cross-layer dependency in the network plays an essential role in many data mining applications like system robustness analysis and complex network control. However, it remains a daunting task to know the exact dependency relationships due to noise, limited accessibility, and so forth. In this article, we tackle the cross-layer dependency inference problem by modeling it as a collective collaborative filtering problem. Based on this idea, we propose an effective algorithm Fascinate that can reveal unobserved dependencies with linear complexity. Moreover, we derive Fascinate-ZERO, an online variant of Fascinate that can respond to a newly added node timely by checking its neighborhood dependencies. We perform extensive evaluations on real datasets to substantiate the superiority of our proposed approaches.
Collapse
|
132
|
Park J, Hescott BJ, Slonim DK. Towards a more molecular taxonomy of disease. J Biomed Semantics 2017; 8:25. [PMID: 28750648 PMCID: PMC5530939 DOI: 10.1186/s13326-017-0134-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 07/17/2017] [Indexed: 02/05/2023] Open
Abstract
Background Disease taxonomies have been designed for many applications, but they tend not to fully incorporate the growing amount of molecular-level knowledge of disease processes, inhibiting research efforts. Understanding the degree to which we can infer disease relationships from molecular data alone may yield insights into how to ultimately construct more modern taxonomies that integrate both physiological and molecular information. Results We introduce a new technique we call Parent Promotion to infer hierarchical relationships between disease terms using disease-gene data. We compare this technique with both an established ontology inference method (CliXO) and a minimum weight spanning tree approach. Because there is no gold standard molecular disease taxonomy available, we compare our inferred hierarchies to both the Medical Subject Headings (MeSH) category C forest of diseases and to subnetworks of the Disease Ontology (DO). This comparison provides insights about the inference algorithms, choices of evaluation metrics, and the existing molecular content of various subnetworks of MeSH and the DO. Our results suggest that the Parent Promotion method performs well in most cases. Performance across MeSH trees is also correlated between inference methods. Specifically, inferred relationships are more consistent with those in smaller MeSH disease trees than larger ones, but there are some notable exceptions that may correlate with higher molecular content in MeSH. Conclusions Our experiments provide insights about learning relationships between diseases from disease genes alone. Future work should explore the prospect of disease term discovery from molecular data and how best to integrate molecular data with anatomical and clinical knowledge. This study nonetheless suggests that disease gene information has the potential to form an important part of the foundation for future representations of the disease landscape. Electronic supplementary material The online version of this article (doi:10.1186/s13326-017-0134-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jisoo Park
- Department of Computer Science, Tufts University, 161 College Avenue, Medford, 02155, MA, USA.
| | - Benjamin J Hescott
- Department of Computer Science, Tufts University, 161 College Avenue, Medford, 02155, MA, USA
| | - Donna K Slonim
- Department of Computer Science, Tufts University, 161 College Avenue, Medford, 02155, MA, USA.,Department of Integrative Physiology and Pathobiology, Tufts University School of Medicine, 145 Harrison Avenue, Boston, 02111, MA, USA
| |
Collapse
|
133
|
A review of drug-induced liver injury databases. Arch Toxicol 2017; 91:3039-3049. [DOI: 10.1007/s00204-017-2024-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 06/28/2017] [Indexed: 01/23/2023]
|
134
|
Rager JE, Ring CL, Fry RC, Suh M, Proctor DM, Haws LC, Harris MA, Thompson CM. High-Throughput Screening Data Interpretation in the Context of In Vivo Transcriptomic Responses to Oral Cr(VI) Exposure. Toxicol Sci 2017; 158:199-212. [PMID: 28472532 PMCID: PMC5837509 DOI: 10.1093/toxsci/kfx085] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The toxicity of hexavalent chromium [Cr(VI)] in drinking water has been studied extensively, and available in vivo and in vitro studies provide a robust dataset for application of advanced toxicological tools to inform the mode of action (MOA). This study aimed to contribute to the understanding of Cr(VI) MOA by evaluating high-throughput screening (HTS) data and other in vitro data relevant to Cr(VI), and comparing these findings to robust in vivo data, including transcriptomic profiles in target tissues. Evaluation of Tox21 HTS data for Cr(VI) identified 11 active assay endpoints relevant to the Ten Key Characteristics of Carcinogens (TKCCs) that have been proposed by other investigators. Four of these endpoints were related to TP53 (tumor protein 53) activation mapping to genotoxicity (KCC#2), and four were related to cell death/proliferation (KCC#10). HTS results were consistent with other in vitro data from the Comparative Toxicogenomics Database. In vitro responses were compared to in vivo transcriptomic responses in the most sensitive target tissue, the duodenum, of mice exposed to ≤ 180 ppm Cr(VI) for 7 and 90 days. Pathways that were altered both in vitro and in vivo included those relevant to cell death/proliferation. In contrast, pathways relevant to p53/DNA damage were identified in vitro but not in vivo. Benchmark dose modeling and phenotypic anchoring of in vivo transcriptomic responses strengthened the finding that Cr(VI) causes cell stress/injury followed by proliferation in the mouse duodenum at high doses. These findings contribute to the body of evidence supporting a non-mutagenic MOA for Cr(VI)-induced intestinal cancer.
Collapse
Affiliation(s)
| | | | - Rebecca C. Fry
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health
- Curriculum in Toxicology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27516
| | - Mina Suh
- ToxStrategies Inc, Mission Viejo, California 92692
| | | | | | | | | |
Collapse
|
135
|
Lazzarini N, Bacardit J. RGIFE: a ranked guided iterative feature elimination heuristic for the identification of biomarkers. BMC Bioinformatics 2017; 18:322. [PMID: 28666416 PMCID: PMC5493069 DOI: 10.1186/s12859-017-1729-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 06/13/2017] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Current -omics technologies are able to sense the state of a biological sample in a very wide variety of ways. Given the high dimensionality that typically characterises these data, relevant knowledge is often hidden and hard to identify. Machine learning methods, and particularly feature selection algorithms, have proven very effective over the years at identifying small but relevant subsets of variables from a variety of application domains, including -omics data. Many methods exist with varying trade-off between the size of the identified variable subsets and the predictive power of such subsets. In this paper we focus on an heuristic for the identification of biomarkers called RGIFE: Rank Guided Iterative Feature Elimination. RGIFE is guided in its biomarker identification process by the information extracted from machine learning models and incorporates several mechanisms to ensure that it creates minimal and highly predictive features sets. RESULTS We compare RGIFE against five well-known feature selection algorithms using both synthetic and real (cancer-related transcriptomics) datasets. First, we assess the ability of the methods to identify relevant and highly predictive features. Then, using a prostate cancer dataset as a case study, we look at the biological relevance of the identified biomarkers. CONCLUSIONS We propose RGIFE, a heuristic for the inference of reduced panels of biomarkers that obtains similar predictive performance to widely adopted feature selection methods while selecting significantly fewer feature. Furthermore, focusing on the case study, we show the higher biological relevance of the biomarkers selected by our approach. The RGIFE source code is available at: http://ico2s.org/software/rgife.html .
Collapse
Affiliation(s)
- Nicola Lazzarini
- ICOS research group, School of Computing Science, Newcastle-upon-Tyne, UK
| | - Jaume Bacardit
- ICOS research group, School of Computing Science, Newcastle-upon-Tyne, UK.
| |
Collapse
|
136
|
Raja K, Patrick M, Elder JT, Tsoi LC. Machine learning workflow to enhance predictions of Adverse Drug Reactions (ADRs) through drug-gene interactions: application to drugs for cutaneous diseases. Sci Rep 2017. [PMID: 28623363 PMCID: PMC5473874 DOI: 10.1038/s41598-017-03914-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Adverse drug reactions (ADRs) pose critical public health issues, affecting over 6% of hospitalized patients. While knowledge of potential drug-drug interactions (DDI) is necessary to prevent ADR, the rapid pace of drug discovery makes it challenging to maintain a strong insight into DDIs. In this study, we present a novel literature-mining framework for enhancing the predictions of DDIs and ADR types by integrating drug-gene interactions (DGIs). The ADR types were adapted from a DDI corpus, including i) adverse effect; ii) effect at molecular level; iii) effect related to pharmacokinetics; and iv) DDIs without known ADRs. By using random forest classifier our approach achieves an F-score of 0.87 across the ADRs classification using only the DDI features. We then enhanced the performance of the classifier by including DGIs (F-score = 0.90), and applied the classification model trained with the DDI corpus to identify the drugs that might interact with the drugs for cutaneous diseases. We successfully predict previously known ADRs for drugs prescribed to cutaneous diseases, and are also able to identify promising new ADRs.
Collapse
Affiliation(s)
- Kalpana Raja
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Matthew Patrick
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - James T Elder
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Lam C Tsoi
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA. .,Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA. .,Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA.
| |
Collapse
|
137
|
Li L, Wang G, Li N, Yu H, Si J, Wang J. Identification of key genes and pathways associated with obesity in children. Exp Ther Med 2017; 14:1065-1073. [PMID: 28810559 PMCID: PMC5525596 DOI: 10.3892/etm.2017.4597] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 02/24/2017] [Indexed: 01/22/2023] Open
Abstract
The present study aimed to identify potential key genes and pathways in obese children in order to explore possible molecular mechanisms associated with child obesity. The array dataset GSE29718 was downloaded from the Gene Expression Omnibus database. Subcutaneous adipose tissue samples derived from 7 obese children and 8 lean children were selected for the analysis. Differentially expressed genes (DEGs) in samples from obese children compared with those from lean children were analyzed by the limma package. Gene ontology (GO) annotation, Kyoto Encyclopedia of Genes and Genomes and Reactome pathway enrichment analyses for up and downregulated genes were performed. A protein-protein interaction (PPI) network was constructed with Cytoscape software and important genes associated with obesity were determined using IRegulon. A total of 199 DEGs (79 up and 120 downregulated genes) were identified in the samples of obese children compared with those from lean children. The PPI network was established with 103 nodes and 147 protein pairs. Matrix metalloproteinase 9 (MMP9) and acetyl-CoA carboxylase β (ACACB) were identified as hub genes in the PPI network and may therefore be marker genes for child obesity. In addition, upregulated DEGs were enriched in Reactome pathways associated with the immune system. Besides, MMP9 was upregulated in immune system processes as a GO term in the category Biological Processes. The results of the present study indicated that MMP9, ACACB and immune system pathways may have a significant role in child obesity.
Collapse
Affiliation(s)
- Ling Li
- Department of Paediatrics, Jinan Children's Hospital, Jinan, Shandong 250022, P.R. China
| | - Guangyu Wang
- Department of Paediatrics, Jinan Children's Hospital, Jinan, Shandong 250022, P.R. China
| | - Ning Li
- Department of Paediatrics, Jinan Children's Hospital, Jinan, Shandong 250022, P.R. China
| | - Haiyan Yu
- Department of Paediatrics, The Fifth People's Hospital of Jinan, Jinan, Shandong 250022, P.R. China
| | - Jianping Si
- Department of Pediatrics, The People's Hospital of Guangrao, Dongying, Shandong 257300, P.R. China
| | - Jiwen Wang
- Department of Neurology, Children's Medical Center, Qilu Hospital of Shandong University, Jinan, Shandong 250012, P.R. China.,Brain Science Research Institute, Shandong University, Jinan, Shandong 250012, P.R. China.,Department of Neurology, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai 200240, P.R. China
| |
Collapse
|
138
|
Genetic background influences susceptibility to chemotherapy-induced hematotoxicity. THE PHARMACOGENOMICS JOURNAL 2017; 18:319-330. [PMID: 28607509 PMCID: PMC5729066 DOI: 10.1038/tpj.2017.23] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 04/26/2017] [Accepted: 05/01/2017] [Indexed: 12/23/2022]
Abstract
Hematotoxicity is a life-threatening side effect of many chemotherapy regimens. While clinical factors influence patient responses, genetic factors may also play an important role. We sought to identify genomic loci that influence chemotherapy-induced hematotoxicity by dosing Diversity Outbred mice with one of three chemotherapy drugs; doxorubicin, cyclophosphamide or docetaxel. We observed that each drug had a distinct effect on both the changes in blood cell sub-populations and the underlying genetic architecture of hematotoxicity. For doxorubicin, we mapped the change in cell counts before and after dosing and found that alleles of ATP-binding cassette B1B (Abcb1b) on chromosome 5 influence all cell populations. For cyclophosphamide and docetaxel, we found that each cell population was influenced by distinct loci, none of which overlapped between drugs. These results suggest that susceptibility to chemotherapy-induced hematotoxicity is influenced by different genes for different chemotherapy drugs.
Collapse
|
139
|
Wang P, Hao T, Yan J, Jin L. Large-scale extraction of drug-disease pairs from the medical literature. J Assoc Inf Sci Technol 2017. [DOI: 10.1002/asi.23876] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Pengwei Wang
- School of Electronic and Information Engineering; South China University of Technology; Guangzhou China
| | - Tianyong Hao
- Cisco School of Informatics; Guangdong University of Foreign Studies; Guangzhou China
| | - Jun Yan
- Microsoft Research Asia; Beijing China
| | - Lianwen Jin
- School of Electronic and Information Engineering; South China University of Technology; Guangzhou China
| |
Collapse
|
140
|
Comparative analysis of microRNA and mRNA expression profiles in cells and exosomes under toluene exposure. Toxicol In Vitro 2017; 41:92-101. [DOI: 10.1016/j.tiv.2017.02.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 01/26/2017] [Accepted: 02/23/2017] [Indexed: 12/12/2022]
|
141
|
Wu H, Huang J, Zhong Y, Huang Q. DrugSig: A resource for computational drug repositioning utilizing gene expression signatures. PLoS One 2017; 12:e0177743. [PMID: 28562632 PMCID: PMC5451001 DOI: 10.1371/journal.pone.0177743] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 05/02/2017] [Indexed: 12/12/2022] Open
Abstract
Computational drug repositioning has been proved as an effective approach to develop new drug uses. However, currently existing strategies strongly rely on drug response gene signatures which scattered in separated or individual experimental data, and resulted in low efficient outputs. So, a fully drug response gene signatures database will be very helpful to these methods. We collected drug response microarray data and annotated related drug and targets information from public databases and scientific literature. By selecting top 500 up-regulated and down-regulated genes as drug signatures, we manually established the DrugSig database. Currently DrugSig contains more than 1300 drugs, 7000 microarray and 800 targets. Moreover, we developed the signature based and target based functions to aid drug repositioning. The constructed database can serve as a resource to quicken computational drug repositioning. Database URL: http://biotechlab.fudan.edu.cn/database/drugsig/.
Collapse
Affiliation(s)
- Hongyu Wu
- School of Life Sciences, Fudan University, Shanghai, China
- Shanghai High-Tech United Bio-Technological R&D Co., Ltd., Shanghai, China
| | - Jinjiang Huang
- School of Life Sciences, Fudan University, Shanghai, China
| | - Yang Zhong
- School of Life Sciences, Fudan University, Shanghai, China
| | - Qingshan Huang
- School of Life Sciences, Fudan University, Shanghai, China
- Shanghai High-Tech United Bio-Technological R&D Co., Ltd., Shanghai, China
- * E-mail:
| |
Collapse
|
142
|
Iyer PM, Karthikeyan S, Sanjay Kumar P, Krishnan Namboori PK. Comprehensive strategy for the design of precision drugs and identification of genetic signature behind proneness of the disease-a pharmacogenomic approach. Funct Integr Genomics 2017; 17:375-385. [PMID: 28470340 DOI: 10.1007/s10142-017-0559-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 04/05/2017] [Indexed: 12/20/2022]
Abstract
The proneness of diseases and susceptibility towards drugs vary from person to person. At present, there is a strong demand for the personalization of drugs. The genetic signature behind proneness of the disease has been studied through a comprehensive 'octopodial approach'. All the genetic variants included in the approach have been introduced. The breast cancer associated with BRCA1 mutation has been taken as the illustrative example to introduce all these factors. The genetic variants associated with the drug action of tamoxifen have been fully illustrated in the manuscript. The design of a new personalized anti-breast cancer drug has been explained in the third phase. For the design of new personalized drugs, a metabolite of anti-cancer drug chlorambucil has been taken as the template. The design of drug has been made with respect to the protein 1T15 of BRCA1 gene corresponding to the genetic signature of rs28897696.
Collapse
Affiliation(s)
- Preethi M Iyer
- Department of Electronics and Communication Engineering, M.Tech-Biomedical Engineering Amrita School of Engineering, AMRITA Vishwa Vidyapeetham Amrita University, Amritanagar, Ettimadai, Coimbatore, Tamil Nadu, 641112, India
| | - S Karthikeyan
- Amrita School of Engineering, AMRITA Vishwa Vidyapeetham Amrita University, Amritanagar, Ettimadai, Coimbatore, Tamil Nadu, 641112, India
| | - P Sanjay Kumar
- Amrita School of Engineering, AMRITA Vishwa Vidyapeetham Amrita University, Amritanagar, Ettimadai, Coimbatore, Tamil Nadu, 641112, India
| | - P K Krishnan Namboori
- Amrita School of Engineering, AMRITA Vishwa Vidyapeetham Amrita University, Amritanagar, Ettimadai, Coimbatore, Tamil Nadu, 641112, India.
| |
Collapse
|
143
|
Chen CHS, Yuan TH, Shie RH, Wu KY, Chan CC. Linking sources to early effects by profiling urine metabolome of residents living near oil refineries and coal-fired power plants. ENVIRONMENT INTERNATIONAL 2017; 102:87-96. [PMID: 28238459 DOI: 10.1016/j.envint.2017.02.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 02/09/2017] [Accepted: 02/10/2017] [Indexed: 06/06/2023]
Abstract
BACKGROUND This study aims at identifying metabolic changes linking external exposure to industrial air toxics with oxidative stress biomarkers. METHODS We classified 252 study subjects as 111 high vs. 141 low exposure subjects by the distance from their homes to the two main emission sources, oil refineries and coal-fired power plants. We estimated individual's external exposure to heavy metals and polycyclic aromatic hydrocarbons (PAHs) by dispersion and kriging models, respectively. We measured urinary levels of heavy metals and 1-hydroxypyrene (1-OHP) as biomarkers of internal exposure, and 8-OHdG, HNE-MA, 8-isoPGF2α, and 8-NO2Gua as biomarkers of early health effects. We used two-dimensional gas chromatography time-of-flight mass spectrometry to identify urine metabolomics. We applied "meet-in-the-middle" approach to identify potential metabolites as putative intermediate biomarkers linking multiple air toxics exposures to oxidative stress with plausible exposures-related pathways. RESULTS High exposure subjects showed elevated ambient concentrations of vanadium and PAHs, increased urine concentrations of 1-OHP, vanadium, nickel, copper, arsenic, strontium, cadmium, mercury, and thallium, and higher urine concentrations of all four urine oxidative stress biomarkers compared to low exposure subjects. We identified a profile of putative intermediate biomarkers that were associated with both exposures and oxidative stress biomarkers in participants. Urine metabolomics identified age-dependent biological pathways, including tryptophan metabolism and phenylalanine metabolism in children subjects (aged 9-11), and glycine, serine, and threonine metabolism in elderly subjects (aged>55), that could associate multiple exposures with oxidative stress. CONCLUSION By profiling urine biomarkers and metabolomics in children and elderly residents living near a petrochemical complex, we can link their internal exposure to oxidative stress biomarkers through biological pathways associated with common complex chronic diseases and allergic respiratory diseases. The internal exposure may possibly be traced to multiple air toxics emitted from specific sources of oil refineries and coal-fired power plants.
Collapse
Affiliation(s)
- Chi-Hsin Sally Chen
- Institute of Occupational Medicine and Industrial Hygiene, College of Public Health, National Taiwan University, Taiwan
| | - Tzu-Hsuen Yuan
- Institute of Occupational Medicine and Industrial Hygiene, College of Public Health, National Taiwan University, Taiwan
| | - Ruei-Hao Shie
- Green Energy and Environment Research Laboratories, Industrial Technology Research Institute of Taiwan, Taiwan
| | - Kuen-Yuh Wu
- Institute of Occupational Medicine and Industrial Hygiene, College of Public Health, National Taiwan University, Taiwan
| | - Chang-Chuan Chan
- Institute of Occupational Medicine and Industrial Hygiene, College of Public Health, National Taiwan University, Taiwan.
| |
Collapse
|
144
|
Sun P, Guo J, Winnenburg R, Baumbach J. Drug repurposing by integrated literature mining and drug–gene–disease triangulation. Drug Discov Today 2017; 22:615-619. [DOI: 10.1016/j.drudis.2016.10.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 09/26/2016] [Accepted: 10/18/2016] [Indexed: 01/18/2023]
|
145
|
Sundarrajan S, Arumugam M. A systems pharmacology perspective to decipher the mechanism of action of Parangichakkai chooranam , a Siddha formulation for the treatment of psoriasis. Biomed Pharmacother 2017; 88:74-86. [DOI: 10.1016/j.biopha.2016.12.135] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 12/29/2016] [Accepted: 12/29/2016] [Indexed: 10/20/2022] Open
|
146
|
Leung MCK, Procter AC, Goldstone JV, Foox J, DeSalle R, Mattingly CJ, Siddall ME, Timme-Laragy AR. Applying evolutionary genetics to developmental toxicology and risk assessment. Reprod Toxicol 2017; 69:174-186. [PMID: 28267574 PMCID: PMC5829367 DOI: 10.1016/j.reprotox.2017.03.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 02/27/2017] [Accepted: 03/02/2017] [Indexed: 12/26/2022]
Abstract
Evolutionary thinking continues to challenge our views on health and disease. Yet, there is a communication gap between evolutionary biologists and toxicologists in recognizing the connections among developmental pathways, high-throughput screening, and birth defects in humans. To increase our capability in identifying potential developmental toxicants in humans, we propose to apply evolutionary genetics to improve the experimental design and data interpretation with various in vitro and whole-organism models. We review five molecular systems of stress response and update 18 consensual cell-cell signaling pathways that are the hallmark for early development, organogenesis, and differentiation; and revisit the principles of teratology in light of recent advances in high-throughput screening, big data techniques, and systems toxicology. Multiscale systems modeling plays an integral role in the evolutionary approach to cross-species extrapolation. Phylogenetic analysis and comparative bioinformatics are both valuable tools in identifying and validating the molecular initiating events that account for adverse developmental outcomes in humans. The discordance of susceptibility between test species and humans (ontogeny) reflects their differences in evolutionary history (phylogeny). This synthesis not only can lead to novel applications in developmental toxicity and risk assessment, but also can pave the way for applying an evo-devo perspective to the study of developmental origins of health and disease.
Collapse
Affiliation(s)
- Maxwell C K Leung
- Nicholas School of the Environment, Duke University, Durham, NC, United States.
| | - Andrew C Procter
- Institute for Advanced Analytics, North Carolina State University, Raleigh, NC, United States
| | - Jared V Goldstone
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Jonathan Foox
- Department of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States
| | - Robert DeSalle
- Department of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States
| | - Carolyn J Mattingly
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States
| | - Mark E Siddall
- Department of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States
| | - Alicia R Timme-Laragy
- Department of Environmental Health Sciences, University of Massachusetts, Amherst, MA, United States
| |
Collapse
|
147
|
Marlatt VL, Martyniuk CJ. Biological responses to phenylurea herbicides in fish and amphibians: New directions for characterizing mechanisms of toxicity. Comp Biochem Physiol C Toxicol Pharmacol 2017; 194:9-21. [PMID: 28109972 DOI: 10.1016/j.cbpc.2017.01.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 01/11/2017] [Accepted: 01/13/2017] [Indexed: 12/19/2022]
Abstract
Urea-based herbicides are applied in agriculture to control broadleaf and grassy weeds, acting to either inhibit photosynthesis at photosystem II (phenylureas) or to inhibit acetolactate synthase acetohydroxyacid synthase (sulfonylureas). While there are different chemical formulas for urea-based herbicides, the phenylureas are a widely used class in North America and have been detected in aquatic environments due to agricultural run-off. Here, we summarize the current state of the literature, synthesizing data on phenylureas and their biological effects in two non-target animals, fish and amphibians, with a primary focus on diuron and linuron. In fish, although the acutely lethal effects of diuron in early life stages appear to be >1mg/L, recent studies measuring sub-lethal behavioural and developmental endpoints suggest that diuron causes adverse effects at lower concentrations (i.e. <0.1mg/L). Considerably less toxicity data exist for amphibians, and this is a knowledge gap in the literature. In terms of sub-lethal effects and mode of action (MOA), linuron is well documented to have anti-androgenic effects in vertebrates, including fish. However, there are other MOAs that are not adequately assessed in toxicology studies. In order to identify additional potential MOAs, we conducted in silico analyses for linuron and diuron that were based upon transcriptome studies and chemical structure-function relationships (i.e. ToxCast™, Prediction of Activity Spectra of Substances). Based upon these analyses, we suggest that steroid biosynthesis, cholesterol metabolism and pregnane X receptor activation are common targets, and offer some new endpoints for future investigations of phenylurea herbicides in non-target animals.
Collapse
Affiliation(s)
- Vicki L Marlatt
- Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, Canada.
| | - Christopher J Martyniuk
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, UF Genetics Institute, College of Veterinary Medicine, University of Florida, Gainesville, FL 326111, USA; Canadian Rivers Institute, Canada
| |
Collapse
|
148
|
Martinović-Weigelt D, Mehinto AC, Ankley GT, Berninger JP, Collette TW, Davis JM, Denslow ND, Durhan EJ, Eid E, Ekman DR, Jensen KM, Kahl MD, LaLone CA, Teng Q, Villeneuve DL. Derivation and Evaluation of Putative Adverse Outcome Pathways for the Effects of Cyclooxygenase Inhibitors on Reproductive Processes in Female Fish. Toxicol Sci 2017; 156:344-361. [PMID: 28201806 PMCID: PMC11017233 DOI: 10.1093/toxsci/kfw257] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Cyclooxygenase (COX) inhibitors are ubiquitous in aquatic systems and have been detected in fish tissues. The exposure of fish to these pharmaceuticals is concerning because COX inhibitors disrupt the synthesis of prostaglandins (PGs), which modulate a variety of essential biological functions, including reproduction. In this study, we investigated the effects of well-characterized mammalian COX inhibitors on female fathead minnow reproductive health. Fish (n = 8) were exposed for 96 h to water containing indomethacin (IN; 100 µg/l), ibuprofen (IB; 200 µg/l) or celecoxib (CX; 20 µg/l), and evaluated for effects on liver metabolome and ovarian gene expression. Metabolomic profiles of IN, IB and CX were not significantly different from control or one another. Exposure to IB and CX resulted in differential expression of comparable numbers of genes (IB = 433, CX = 545). In contrast, 2558 genes were differentially expressed in IN-treated fish. Functional analyses (canonical pathway and gene set enrichment) indicated extensive effects of IN on PG synthesis pathway, oocyte meiosis, and several other processes consistent with physiological roles of PGs. Transcriptomic data were congruent with PG data; IN-reduced plasma PG F2α concentration, whereas IB and CX did not. Five putative AOPs were developed linking the assumed molecular initiating event of COX inhibition, with PG reduction and the adverse outcome of reproductive failure via reduction of: (1) ovulation, (2) reproductive behaviors mediated by exogenous or endogenous PGs, and (3) oocyte maturation in fish. These pathways were developed using, in part, empirical data from the present study and other publicly available data.
Collapse
Affiliation(s)
| | - Alvine C. Mehinto
- University of Florida, Gainesville, FL, 32611
- Southern California Coastal Water Research Project, Costa Mesa, CA, 92626
| | - Gerald T. Ankley
- U.S. Environmental Protection Agency, National Health and Environmental Effects Research Laboratory, Mid-Continent Ecology Division, Duluth, MN, 55804
| | - Jason P. Berninger
- U.S. Environmental Protection Agency, National Health and Environmental Effects Research Laboratory, Mid-Continent Ecology Division, Duluth, MN, 55804
| | - Timothy W. Collette
- U.S. Environmental Protection Agency, National Exposure Research Laboratory, Ecosystems Research Division, Athens, GA, 30605
| | - John M. Davis
- U.S. Environmental Protection Agency, National Exposure Research Laboratory, Ecosystems Research Division, Athens, GA, 30605
| | | | - Elizabeth J. Durhan
- U.S. Environmental Protection Agency, National Health and Environmental Effects Research Laboratory, Mid-Continent Ecology Division, Duluth, MN, 55804
| | - Evan Eid
- U.S. Environmental Protection Agency, National Health and Environmental Effects Research Laboratory, Mid-Continent Ecology Division, Duluth, MN, 55804
| | - Drew R. Ekman
- U.S. Environmental Protection Agency, National Exposure Research Laboratory, Ecosystems Research Division, Athens, GA, 30605
| | - Kathleen M. Jensen
- U.S. Environmental Protection Agency, National Health and Environmental Effects Research Laboratory, Mid-Continent Ecology Division, Duluth, MN, 55804
| | - Mike D. Kahl
- U.S. Environmental Protection Agency, National Health and Environmental Effects Research Laboratory, Mid-Continent Ecology Division, Duluth, MN, 55804
| | - Carlie A. LaLone
- U.S. Environmental Protection Agency, National Health and Environmental Effects Research Laboratory, Mid-Continent Ecology Division, Duluth, MN, 55804
| | - Quincy Teng
- U.S. Environmental Protection Agency, National Exposure Research Laboratory, Ecosystems Research Division, Athens, GA, 30605
| | - Daniel L. Villeneuve
- U.S. Environmental Protection Agency, National Health and Environmental Effects Research Laboratory, Mid-Continent Ecology Division, Duluth, MN, 55804
| |
Collapse
|
149
|
Li F, Zhang M, Fu G, Ji D. A neural joint model for entity and relation extraction from biomedical text. BMC Bioinformatics 2017; 18:198. [PMID: 28359255 PMCID: PMC5374588 DOI: 10.1186/s12859-017-1609-9] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 03/23/2017] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Extracting biomedical entities and their relations from text has important applications on biomedical research. Previous work primarily utilized feature-based pipeline models to process this task. Many efforts need to be made on feature engineering when feature-based models are employed. Moreover, pipeline models may suffer error propagation and are not able to utilize the interactions between subtasks. Therefore, we propose a neural joint model to extract biomedical entities as well as their relations simultaneously, and it can alleviate the problems above. RESULTS Our model was evaluated on two tasks, i.e., the task of extracting adverse drug events between drug and disease entities, and the task of extracting resident relations between bacteria and location entities. Compared with the state-of-the-art systems in these tasks, our model improved the F1 scores of the first task by 5.1% in entity recognition and 8.0% in relation extraction, and that of the second task by 9.2% in relation extraction. CONCLUSIONS The proposed model achieves competitive performances with less work on feature engineering. We demonstrate that the model based on neural networks is effective for biomedical entity and relation extraction. In addition, parameter sharing is an alternative method for neural models to jointly process this task. Our work can facilitate the research on biomedical text mining.
Collapse
Affiliation(s)
- Fei Li
- School of Computer, Wuhan University, Bayi Road, Wuhan, China
| | - Meishan Zhang
- School of Computer Science and Technology, Heilongjiang University, Xuefu Road, Harbin, China
| | - Guohong Fu
- School of Computer Science and Technology, Heilongjiang University, Xuefu Road, Harbin, China
| | - Donghong Ji
- School of Computer, Wuhan University, Bayi Road, Wuhan, China
| |
Collapse
|
150
|
Ding W, Yang H, Gong S, Shi W, Xiao J, Gu J, Wang Y, He B. Candidate miRNAs and pathogenesis investigation for hepatocellular carcinoma based on bioinformatics analysis. Oncol Lett 2017; 13:3409-3414. [PMID: 28521446 PMCID: PMC5431310 DOI: 10.3892/ol.2017.5913] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 01/26/2017] [Indexed: 12/22/2022] Open
Abstract
The present study aimed to explore the mechanisms behind the development and progression of hepatocellular carcinoma (HCC) and identify information regarding HCC-related microRNAs (miRNAs) or marker genes for the gene therapy of HCC. Gene expression profile of GSE67882, generated from 4 hepatitis B virus infected HCC tissue samples (HCC group) and 8 chronic hepatitis B tissue samples with no fibrosis (control group) were downloaded from the Gene Expression Omnibus database. The differentially expressed miRNAs functional enrichment and pathway analyses of HCC were revealed, followed by transcription factor-miRNA interaction network construction and analyses. A total of 14 upregulated miRNAs and 16 downregulated miRNAs between HCC and control samples were obtained. Differentially expressed miRNAs were mainly involved in biological processes like the regulation of histone H3-K9 methylation, and the KEGG pathways in cancer map05200 demonstrates their involvement in cancer. A total of 3 outstanding regulatory networks of miRNAs: hsa-miR-15a, hsa-miR-125b and hsa-miR-122 were revealed. A total of 11 differentially expressed miRNAs including hsa-miR-146p-5b that regulated the marker genes of HCC were explored. miRNAs such as hsa-miR-15a, hsa-miR-125b, hsa-miR-122 and hsa-miR-146b-5p may be new biomarkers for the gene therapy of HCC. Furthermore, histone H3-K9 methylation and other pathways in cancer observed in the KEGG map05200 may be closely related with the development of HCC.
Collapse
Affiliation(s)
- Wenbin Ding
- Department of Radiology, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Haixia Yang
- Department of Radiology, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Shenchu Gong
- Department of Radiology, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Weixiang Shi
- Department of Radiology, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Jing Xiao
- Department of Epidemiology and Medical Statistics, School of Public Health, Nantong University, Nantong, Jiangsu 226019, P.R. China
| | - Jinhua Gu
- Department of Pathophysiology, Nantong University Medical School, Nantong, Jiangsu 226001, P.R. China
| | - Yilang Wang
- Department of Oncology, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Bosheng He
- Department of Radiology, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| |
Collapse
|