101
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Zou XD, An K, Wu YD, Ye ZQ. PPI network analyses of human WD40 protein family systematically reveal their tendency to assemble complexes and facilitate the complex predictions. BMC SYSTEMS BIOLOGY 2018; 12:41. [PMID: 29745845 PMCID: PMC5998875 DOI: 10.1186/s12918-018-0567-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Background WD40 repeat proteins constitute one of the largest families in eukaryotes, and widely participate in various fundamental cellular processes by interacting with other molecules. Based on individual WD40 proteins, previous work has demonstrated that their structural characteristics should confer great potential of interaction and complex formation, and has speculated that they may serve as hubs in the protein-protein interaction (PPI) network. However, what roles the whole family plays in organizing the PPI network, and whether this information can be utilized in complex prediction remain unclear. To address these issues, quantitative and systematic analyses of WD40 proteins from the perspective of PPI networks are highly required. Results In this work, we built two human PPI networks by using data sets with different confidence levels, and studied the network properties of the whole human WD40 protein family systematically. Our analyses have quantitatively confirmed that the human WD40 protein family, as a whole, tends to be hubs with an odds ratio of about 1.8 or greater, and the network decomposition has revealed that they are prone to enrich near the global center of the whole network with a fold change of two in the median k-values. By integrating expression profiles, we have further shown that WD40 hub proteins are inclined to be intramodular, which is indicative of complex assembling. Based on this information, we have further predicted 1674 potential WD40-associated complexes by choosing a clique-based method, which is more sensitive than others, and an indirect evaluation by co-expression scores has demonstrated its reliability. Conclusions At the systems level but not sporadic examples’ level, this work has provided rich knowledge for better understanding WD40 proteins’ roles in organizing the PPI network. These findings and predicted complexes can offer valuable clues for prioritizing candidates for further studies. Electronic supplementary material The online version of this article (10.1186/s12918-018-0567-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xu-Dong Zou
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, People's Republic of China
| | - Ke An
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, People's Republic of China
| | - Yun-Dong Wu
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, People's Republic of China. .,College of Chemistry, Peking University, Beijing, 100871, People's Republic of China.
| | - Zhi-Qiang Ye
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, People's Republic of China.
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102
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Li C, Liu L, Dinu V. Pathways of topological rank analysis (PoTRA): a novel method to detect pathways involved in hepatocellular carcinoma. PeerJ 2018; 6:e4571. [PMID: 29666752 PMCID: PMC5896492 DOI: 10.7717/peerj.4571] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 03/14/2018] [Indexed: 01/01/2023] Open
Abstract
Complex diseases such as cancer are usually the result of a combination of environmental factors and one or several biological pathways consisting of sets of genes. Each biological pathway exerts its function by delivering signaling through the gene network. Theoretically, a pathway is supposed to have a robust topological structure under normal physiological conditions. However, the pathway's topological structure could be altered under some pathological condition. It is well known that a normal biological network includes a small number of well-connected hub nodes and a large number of nodes that are non-hubs. In addition, it is reported that the loss of connectivity is a common topological trait of cancer networks, which is an assumption of our method. Hence, from normal to cancer, the process of the network losing connectivity might be the process of disrupting the structure of the network, namely, the number of hub genes might be altered in cancer compared to that in normal or the distribution of topological ranks of genes might be altered. Based on this, we propose a new PageRank-based method called Pathways of Topological Rank Analysis (PoTRA) to detect pathways involved in cancer. We use PageRank to measure the relative topological ranks of genes in each biological pathway, then select hub genes for each pathway, and use Fisher's exact test to test if the number of hub genes in each pathway is altered from normal to cancer. Alternatively, if the distribution of topological ranks of gene in a pathway is altered between normal and cancer, this pathway might also be involved in cancer. Hence, we use the Kolmogorov-Smirnov test to detect pathways that have an altered distribution of topological ranks of genes between two phenotypes. We apply PoTRA to study hepatocellular carcinoma (HCC) and several subtypes of HCC. Very interestingly, we discover that all significant pathways in HCC are cancer-associated generally, while several significant pathways in subtypes of HCC are HCC subtype-associated specifically. In conclusion, PoTRA is a new approach to explore and discover pathways involved in cancer. PoTRA can be used as a complement to other existing methods to broaden our understanding of the biological mechanisms behind cancer at the system-level.
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Affiliation(s)
- Chaoxing Li
- School of Life Sciences, Arizona State University, Tempe, AZ, United States of America
| | - Li Liu
- Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ, United States of America
| | - Valentin Dinu
- Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ, United States of America
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103
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Zhang W, Wang SL. An efficient strategy for identifying cancer-related key genes based on graph entropy. Comput Biol Chem 2018; 74:142-148. [PMID: 29609142 DOI: 10.1016/j.compbiolchem.2018.03.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 01/22/2018] [Accepted: 03/20/2018] [Indexed: 02/02/2023]
Abstract
Gene networks are beneficial to identify functional genes that are highly relevant to clinical outcomes. Most of the current methods require information about the interaction of genes or proteins to construct genetic network connection. However, the conclusion of these methods may be bias because of the current incompleteness of human interactome. In this paper, we propose an efficient strategy to use gene expression data and gene mutation data for identifying cancer-related key genes based on graph entropy (iKGGE). Firstly, we construct a gene network using only gene expression data based on the sparse inverse covariance matrix, then, cluster genes use the algorithm of parallel maximal cliques for quickly obtaining a series of subgraphs, and at last, we introduce a novel metric that combine graph entropy and the influence of upstream gene mutations information to measure the impact factors of genes. Testing of the three available cancer datasets shows that our strategy can effectively extract key genes that may play distinct roles in tumorigenesis, and the cancer patient risk groups are well predicted based on key genes.
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Affiliation(s)
- Wei Zhang
- College of Computer Science and Electronics Engineering, Hunan University, Changsha, Hunan, 410082, China.
| | - Shu-Lin Wang
- College of Computer Science and Electronics Engineering, Hunan University, Changsha, Hunan, 410082, China.
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104
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Li S, Musungu B, Lightfoot D, Ji P. The Interactomic Analysis Reveals Pathogenic Protein Networks in Phomopsis longicolla Underlying Seed Decay of Soybean. Front Genet 2018; 9:104. [PMID: 29666630 PMCID: PMC5891612 DOI: 10.3389/fgene.2018.00104] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 03/15/2018] [Indexed: 12/31/2022] Open
Abstract
Phomopsis longicolla T. W. Hobbs (syn. Diaporthe longicolla) is the primary cause of Phomopsis seed decay (PSD) in soybean, Glycine max (L.) Merrill. This disease results in poor seed quality and is one of the most economically important seed diseases in soybean. The objectives of this study were to infer protein-protein interactions (PPI) and to identify conserved global networks and pathogenicity subnetworks in P. longicolla including orthologous pathways for cell signaling and pathogenesis. The interlog method used in the study identified 215,255 unique PPIs among 3,868 proteins. There were 1,414 pathogenicity related genes in P. longicolla identified using the pathogen host interaction (PHI) database. Additionally, 149 plant cell wall degrading enzymes (PCWDE) were detected. The network captured five different classes of carbohydrate degrading enzymes, including the auxiliary activities, carbohydrate esterases, glycoside hydrolases, glycosyl transferases, and carbohydrate binding molecules. From the PPI analysis, novel interacting partners were determined for each of the PCWDE classes. The most predominant class of PCWDE was a group of 60 glycoside hydrolases proteins. The glycoside hydrolase subnetwork was found to be interacting with 1,442 proteins within the network and was among the largest clusters. The orthologous proteins FUS3, HOG, CYP1, SGE1, and the g5566t.1 gene identified in this study could play an important role in pathogenicity. Therefore, the P. longicolla protein interactome (PiPhom) generated in this study can lead to a better understanding of PPIs in soybean pathogens. Furthermore, the PPI may aid in targeting of genes and proteins for further studies of the pathogenicity mechanisms.
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Affiliation(s)
- Shuxian Li
- Crop Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service, Stoneville, MS, United States
| | - Bryan Musungu
- Department of Plant Biology, Southern Illinois University, Carbondale, IL, United States
| | - David Lightfoot
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL, United States
| | - Pingsheng Ji
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
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105
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Collective transcriptomic deregulation of hypertrophic and dilated cardiomyopathy – Importance of fibrotic mechanism in heart failure. Comput Biol Chem 2018; 73:85-94. [DOI: 10.1016/j.compbiolchem.2018.01.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 01/24/2018] [Accepted: 01/25/2018] [Indexed: 12/12/2022]
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106
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Tang Z, Gu J, Sun P, Zhao J, Zhao Y. Identification of functional modules induced by bare-metal stents and paclitaxel-eluting stents in coronary heart disease. Exp Ther Med 2018; 15:3801-3808. [PMID: 29556263 PMCID: PMC5844177 DOI: 10.3892/etm.2018.5879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 01/15/2018] [Indexed: 02/02/2023] Open
Abstract
Bare-metal stents (BMS) and paclitaxel-eluting stent (PES) are frequently used in medicine for the treatment of coronary heart disease, with millions of patients treated worldwide. The protein-protein interactions (PPI) were adopted to construct the networks. The M-module algorithm was used to identify multiple differential modules. Gene Ontology enrichment and pathway enrichment analysis were performed to analyze characteristics of modules. With the PPI and microarray data, two differential co-expressed networks were constructed, module 1 indicating PES and module 2 indicating BMS, with the same genes but different edges. At a module connectivity dynamic score P-value cut-off of <0.05, module 1 was identified with 142 nodes and 460 edges and in the module 2, 73 nodes and 222 edges were identified. Significant biological processes and pathways were found different in the two modules. Through the two differential modules, we revealed the potential molecular changes induced by PES and BMS providing new insights into the underlying mechanisms in human left internal mammary arteries after inserted with a stent.
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Affiliation(s)
- Zhaobin Tang
- Cardiology Second Ward, The First Hospital of Zibo, Zibo, Shandong 255200, P.R. China
| | - Jingjing Gu
- Department of Pharmacy, The Fourth People's Hospital of Zibo, Zibo, Shandong 255200, P.R. China
| | - Ping Sun
- Department of Pharmacy, The Fourth People's Hospital of Zibo, Zibo, Shandong 255200, P.R. China
| | - Jing Zhao
- Medical Record Management Section, The First Hospital of Zibo, Zibo, Shandong 255200, P.R. China
| | - Yonggang Zhao
- Cardiology Second Ward, The First Hospital of Zibo, Zibo, Shandong 255200, P.R. China
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107
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Chen G, Wang Y, Wang L, Xu W. Identifying prognostic biomarkers based on aberrant DNA methylation in kidney renal clear cell carcinoma. Oncotarget 2018; 8:5268-5280. [PMID: 28029655 PMCID: PMC5354907 DOI: 10.18632/oncotarget.14134] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 11/22/2016] [Indexed: 01/09/2023] Open
Abstract
The outcome of kidney renal clear cell carcinoma (KIRC) differs even among individuals with similar clinical characteristics. DNA methylation is regarded as a regulator of gene expression in cancers, which may be a molecular marker of prognosis. In this study, we aimed to mine novel methylation markers of the prognosis of KIRC. We revealed a total of 2793 genes differentially methylated in their promoter regions (DMGs) and 2979 differentially expressed genes (DEGs) in KIRC tissues compared with normal tissues using The Cancer Genome Atlas datasets. Then, we detected 57 and 34 subpathways enriched among the DMGs and DEGs, respectively, using the R package iSubpathwayMiner. We retained 56 subpathways related to both aberrant methylation and expression based on a hypergeometric test for further analysis. An integrated gene regulatory network was constructed using the regulatory relationships between genes in the subpathways. Using the top 15% of the nodes from the network ranked by degree, survival analysis was performed. We validated four DNA methylation signatures (RAC2, PLCB2, VAV1, and PARVG) as being highly correlated with prognosis in KIRC. These findings suggest that DNA methylation might become a prognostic predictor in KIRC and could supplement histological prognostic prediction.
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Affiliation(s)
- Guang Chen
- Department of Urology, The 4th Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - Yihan Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Lu Wang
- Department of Urology, The 4th Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - Wanhai Xu
- Department of Urology, The 4th Affiliated Hospital of Harbin Medical University, Harbin 150001, China
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108
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Jalili M, Gebhardt T, Wolkenhauer O, Salehzadeh-Yazdi A. Unveiling network-based functional features through integration of gene expression into protein networks. Biochim Biophys Acta Mol Basis Dis 2018; 1864:2349-2359. [PMID: 29466699 DOI: 10.1016/j.bbadis.2018.02.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 01/31/2018] [Accepted: 02/13/2018] [Indexed: 02/02/2023]
Abstract
Decoding health and disease phenotypes is one of the fundamental objectives in biomedicine. Whereas high-throughput omics approaches are available, it is evident that any single omics approach might not be adequate to capture the complexity of phenotypes. Therefore, integrated multi-omics approaches have been used to unravel genotype-phenotype relationships such as global regulatory mechanisms and complex metabolic networks in different eukaryotic organisms. Some of the progress and challenges associated with integrated omics studies have been reviewed previously in comprehensive studies. In this work, we highlight and review the progress, challenges and advantages associated with emerging approaches, integrating gene expression and protein-protein interaction networks to unravel network-based functional features. This includes identifying disease related genes, gene prioritization, clustering protein interactions, developing the modules, extract active subnetworks and static protein complexes or dynamic/temporal protein complexes. We also discuss how these approaches contribute to our understanding of the biology of complex traits and diseases. This article is part of a Special Issue entitled: Cardiac adaptations to obesity, diabetes and insulin resistance, edited by Professors Jan F.C. Glatz, Jason R.B. Dyck and Christine Des Rosiers.
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Affiliation(s)
- Mahdi Jalili
- Hematology, Oncology and SCT Research Center, Tehran University of Medical Sciences, Tehran, Iran; Hematologic Malignancies Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Tom Gebhardt
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany
| | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany
| | - Ali Salehzadeh-Yazdi
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany.
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109
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Liu Q, Chen C, Gao A, Tong HH, Xie L. VariFunNet, an integrated multiscale modeling framework to study the effects of rare non-coding variants in Genome-Wide Association Studies: applied to Alzheimer's Disease. PROCEEDINGS. IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE 2017; 2017:2177-2182. [PMID: 29692948 DOI: 10.1109/bibm.2017.8217995] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
It is a grand challenge to reveal the causal effects of DNA variants in complex phenotypes. Although statistical techniques can establish correlations between genotypes and phenotypes in Genome-Wide Association Studies (GWAS), they often fail when the variant is rare. The emerging Network-based Association Studies aim to address this shortcoming in statistical analysis, but are mainly applied to coding variations. Increasing evidences suggest that non-coding variants play critical roles in the etiology of complex diseases. However, few computational tools are available to study the effect of rare non-coding variants on phenotypes. Here we have developed a multiscale modeling variant-to-function-to-network framework VariFunNet to address these challenges. VariFunNet first predict the functional variations of molecular interactions, which result from the non-coding variants. Then we incorporate the genes associated with the functional variation into a tissue-specific gene network, and identify subnetworks that transmit the functional variation to molecular phenotypes. Finally, we quantify the functional implication of the subnetwork, and prioritize the association of the non-coding variants with the phenotype. We have applied VariFunNet to investigating the causal effect of rare non-coding variants on Alzheimer's disease (AD). Among top 21 ranked causal non-coding variants, 16 of them are directly supported by existing evidences. The remaining 5 novel variants dysregulate multiple downstream biological processes, all of which are associated with the pathology of AD. Furthermore, we propose potential new drug targets that may modulate diverse pathways responsible for AD. These findings may shed new light on discovering new biomarkers and therapies for the prevention, diagnosis, and treatment of AD. Our results suggest that multiscale modeling is a potentially powerful approach to studying causal genotype-phenotype associations.
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Affiliation(s)
- Qiao Liu
- Biochemistry, The Graduate Center, The City University of New York, New York, United States
| | - Chen Chen
- School of Computing, Informatics and Decision Systems Engineering, Arizona State University, Tempe, United States
| | - Annie Gao
- Princeton High School, Princeton, United States
| | - Hang Hang Tong
- School of Computing, Informatics and Decision Systems Engineering, Arizona State University, Tempe, United States
| | - Lei Xie
- Department of Computer Science Hunter College, The City University of New York, New York, United States
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110
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Multi-Objective Optimization Algorithm to Discover Condition-Specific Modules in Multiple Networks. Molecules 2017; 22:molecules22122228. [PMID: 29240706 PMCID: PMC6149918 DOI: 10.3390/molecules22122228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/10/2017] [Accepted: 12/11/2017] [Indexed: 02/02/2023] Open
Abstract
The advances in biological technologies make it possible to generate data for multiple conditions simultaneously. Discovering the condition-specific modules in multiple networks has great merit in understanding the underlying molecular mechanisms of cells. The available algorithms transform the multiple networks into a single objective optimization problem, which is criticized for its low accuracy. To address this issue, a multi-objective genetic algorithm for condition-specific modules in multiple networks (MOGA-CSM) is developed to discover the condition-specific modules. By using the artificial networks, we demonstrate that the MOGA-CSM outperforms state-of-the-art methods in terms of accuracy. Furthermore, MOGA-CSM discovers stage-specific modules in breast cancer networks based on The Cancer Genome Atlas (TCGA) data, and these modules serve as biomarkers to predict stages of breast cancer. The proposed model and algorithm provide an effective way to analyze multiple networks.
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111
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Low YS, Daugherty AC, Schroeder EA, Chen W, Seto T, Weber S, Lim M, Hastie T, Mathur M, Desai M, Farrington C, Radin AA, Sirota M, Kenkare P, Thompson CA, Yu PP, Gomez SL, Sledge GW, Kurian AW, Shah NH. Synergistic drug combinations from electronic health records and gene expression. J Am Med Inform Assoc 2017; 24:565-576. [PMID: 27940607 PMCID: PMC6080645 DOI: 10.1093/jamia/ocw161] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Objective Using electronic health records (EHRs) and biomolecular data, we sought to discover drug pairs with synergistic repurposing potential. EHRs provide real-world treatment and outcome patterns, while complementary biomolecular data, including disease-specific gene expression and drug-protein interactions, provide mechanistic understanding. Method We applied Group Lasso INTERaction NETwork (glinternet), an overlap group lasso penalty on a logistic regression model, with pairwise interactions to identify variables and interacting drug pairs associated with reduced 5-year mortality using EHRs of 9945 breast cancer patients. We identified differentially expressed genes from 14 case-control human breast cancer gene expression datasets and integrated them with drug-protein networks. Drugs in the network were scored according to their association with breast cancer individually or in pairs. Lastly, we determined whether synergistic drug pairs found in the EHRs were enriched among synergistic drug pairs from gene-expression data using a method similar to gene set enrichment analysis. Results From EHRs, we discovered 3 drug-class pairs associated with lower mortality: anti-inflammatories and hormone antagonists, anti-inflammatories and lipid modifiers, and lipid modifiers and obstructive airway drugs. The first 2 pairs were also enriched among pairs discovered using gene expression data and are supported by molecular interactions in drug-protein networks and preclinical and epidemiologic evidence. Conclusions This is a proof-of-concept study demonstrating that a combination of complementary data sources, such as EHRs and gene expression, can corroborate discoveries and provide mechanistic insight into drug synergism for repurposing.
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Affiliation(s)
- Yen S Low
- Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA, USA
| | | | | | - William Chen
- Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA, USA
| | - Tina Seto
- Clinical Informatics, Stanford University
| | | | - Michael Lim
- Department of Statistics, Stanford University
| | - Trevor Hastie
- Department of Statistics, Stanford University.,Department of Health Research and Policy, Stanford University
| | - Maya Mathur
- Quantitative Sciences Unit, Stanford University
| | | | | | | | | | - Pragati Kenkare
- Palo Alto Medical Foundation Research Institute, Palo Alto, CA, USA
| | | | - Peter P Yu
- Palo Alto Medical Foundation Research Institute, Palo Alto, CA, USA
| | - Scarlett L Gomez
- Department of Health Research and Policy, Stanford University.,Cancer Prevention Institute of California, Fremont, CA, USA
| | - George W Sledge
- Division of Oncology, Department of Medicine, Stanford University
| | - Allison W Kurian
- Department of Health Research and Policy, Stanford University.,Division of Oncology, Department of Medicine, Stanford University
| | - Nigam H Shah
- Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA, USA
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112
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Kim D, Li R, Lucas A, Verma SS, Dudek SM, Ritchie MD. Using knowledge-driven genomic interactions for multi-omics data analysis: metadimensional models for predicting clinical outcomes in ovarian carcinoma. J Am Med Inform Assoc 2017; 24:577-587. [PMID: 28040685 DOI: 10.1093/jamia/ocw165] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 12/02/2016] [Indexed: 02/07/2023] Open
Abstract
It is common that cancer patients have different molecular signatures even though they have similar clinical features, such as histology, due to the heterogeneity of tumors. To overcome this variability, we previously developed a new approach incorporating prior biological knowledge that identifies knowledge-driven genomic interactions associated with outcomes of interest. However, no systematic approach has been proposed to identify interaction models between pathways based on multi-omics data. Here we have proposed such a novel methodological framework, called metadimensional knowledge-driven genomic interactions (MKGIs). To test the utility of the proposed framework, we applied it to an ovarian cancer dataset including multi-omics profiles from The Cancer Genome Atlas to predict grade, stage, and survival outcome. We found that each knowledge-driven genomic interaction model, based on different genomic datasets, contains different sets of pathway features, which suggests that each genomic data type may contribute to outcomes in ovarian cancer via a different pathway. In addition, MKGI models significantly outperformed the single knowledge-driven genomic interaction model. From the MKGI models, many interactions between pathways associated with outcomes were found, including the mitogen-activated protein kinase (MAPK) signaling pathway and the gonadotropin-releasing hormone (GnRH) signaling pathway, which are known to play important roles in cancer pathogenesis. The beauty of incorporating biological knowledge into the model based on multi-omics data is the ability to improve diagnosis and prognosis and provide better interpretability. Thus, determining variability in molecular signatures based on these interactions between pathways may lead to better diagnostic/treatment strategies for better precision medicine.
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Affiliation(s)
- Dokyoon Kim
- Biomedical and Translational Informatics, Geisinger Health System, Danville, Pennsylvania, USA.,Center for Systems Genomics, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Ruowang Li
- Center for Systems Genomics, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Anastasia Lucas
- Center for Systems Genomics, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Shefali S Verma
- Biomedical and Translational Informatics, Geisinger Health System, Danville, Pennsylvania, USA
| | - Scott M Dudek
- Center for Systems Genomics, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Marylyn D Ritchie
- Biomedical and Translational Informatics, Geisinger Health System, Danville, Pennsylvania, USA.,Center for Systems Genomics, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
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113
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Patkar S, Magen A, Sharan R, Hannenhalli S. A network diffusion approach to inferring sample-specific function reveals functional changes associated with breast cancer. PLoS Comput Biol 2017; 13:e1005793. [PMID: 29190299 PMCID: PMC5708603 DOI: 10.1371/journal.pcbi.1005793] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 09/27/2017] [Indexed: 11/18/2022] Open
Abstract
Guilt-by-association codifies the empirical observation that a gene's function is informed by its neighborhood in a biological network. This would imply that when a gene's network context is altered, for instance in disease condition, so could be the gene's function. Although context-specific changes in biological networks have been explored, the potential changes they may induce on the functional roles of genes are yet to be characterized. Here we analyze, for the first time, the network-induced potential functional changes in breast cancer. Using transcriptomic samples for 1047 breast tumors and 110 healthy breast tissues from TCGA, we derive sample-specific protein interaction networks and assign sample-specific functions to genes via a diffusion strategy. Testing for significant changes in the inferred functions between normal and cancer samples, we find several functions to have significantly gained or lost genes in cancer, not due to differential expression of genes known to perform the function, but rather due to changes in the network topology. Our predicted functional changes are supported by mutational and copy number profiles in breast cancers. Our diffusion-based functional assignment provides a novel characterization of a tumor that is complementary to the standard approach based on functional annotation alone. Importantly, this characterization is effective in predicting patient survival, as well as in predicting several known histopathological subtypes of breast cancer.
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Affiliation(s)
- Sushant Patkar
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
| | - Assaf Magen
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
| | - Roded Sharan
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Sridhar Hannenhalli
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
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114
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Raun N, Mailo J, Spinelli E, He X, McAvena S, Brand L, O'Sullivan J, Andersen J, Richer L, Tang-Wai R, Bolduc FV. Quantitative phenotypic and network analysis of 1q44 microdeletion for microcephaly. Am J Med Genet A 2017; 173:972-977. [PMID: 28328126 DOI: 10.1002/ajmg.a.38139] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Revised: 11/07/2016] [Accepted: 12/05/2016] [Indexed: 11/10/2022]
Abstract
As genome wide techniques become more common, an increasing proportion of patients with intellectual disability (ID) are found to have genetic defects allowing genotype-phenotype correlations. Previously, AKT3 deletion was suggested to be responsible for microcephaly in patients with 1q43-q44 deletion syndrome, but this does not correspond to all cases. We report a case of a de novo 1q44 deletion in an 8-year-old boy with microcephaly in whom AKT3 is not deleted. We used a systematic review of the literature, our patient, and network analysis to gain a better understanding of the genetic basis of microcephaly in 1q deletion patients. Our analysis showed that while AKT3 deletion is associated with more severe (≤3 SD) microcephaly in 1q43-q44 deletion patients, other genes may contribute to microcephaly in AKT3 intact patients with microcephaly and 1q43-44 deletion syndrome. We identified a potential role for HNRNPU, SMYD3, NLRP3, and KIF26B in microcephaly. Overall, our study highlights the need for network analysis and quantitative measures reporting in the phenotypic analysis of a complex genetic syndrome related to copy number variation.
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Affiliation(s)
- Nicholas Raun
- Division of Pediatric Neurology, University of Alberta, Edmonton, Alberta, Canada
| | - Janette Mailo
- Division of Pediatric Neurology, University of Alberta, Edmonton, Alberta, Canada
| | - Egidio Spinelli
- Division of Pediatric Neurology, University of Alberta, Edmonton, Alberta, Canada
| | - Xu He
- Division of Pediatric Neurology, University of Alberta, Edmonton, Alberta, Canada
| | - Sarah McAvena
- Division of Pediatric Neurology, University of Alberta, Edmonton, Alberta, Canada
| | - Logan Brand
- Division of Pediatric Neurology, University of Alberta, Edmonton, Alberta, Canada
| | - Julia O'Sullivan
- Division of Pediatric Neurology, University of Alberta, Edmonton, Alberta, Canada
| | - John Andersen
- Division of Neurodevelopmental and Neuromotor Pediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - Lawrence Richer
- Division of Pediatric Neurology, University of Alberta, Edmonton, Alberta, Canada
| | - Richard Tang-Wai
- Division of Pediatric Neurology, University of Alberta, Edmonton, Alberta, Canada
| | - Francois V Bolduc
- Division of Pediatric Neurology, University of Alberta, Edmonton, Alberta, Canada.,Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Alberta, Canada.,Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
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115
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Alcaraz N, List M, Batra R, Vandin F, Ditzel HJ, Baumbach J. De novo pathway-based biomarker identification. Nucleic Acids Res 2017; 45:e151. [PMID: 28934488 PMCID: PMC5766193 DOI: 10.1093/nar/gkx642] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 07/13/2017] [Indexed: 02/07/2023] Open
Abstract
Gene expression profiles have been extensively discussed as an aid to guide the therapy by predicting disease outcome for the patients suffering from complex diseases, such as cancer. However, prediction models built upon single-gene (SG) features show poor stability and performance on independent datasets. Attempts to mitigate these drawbacks have led to the development of network-based approaches that integrate pathway information to produce meta-gene (MG) features. Also, MG approaches have only dealt with the two-class problem of good versus poor outcome prediction. Stratifying patients based on their molecular subtypes can provide a detailed view of the disease and lead to more personalized therapies. We propose and discuss a novel MG approach based on de novo pathways, which for the first time have been used as features in a multi-class setting to predict cancer subtypes. Comprehensive evaluation in a large cohort of breast cancer samples from The Cancer Genome Atlas (TCGA) revealed that MGs are considerably more stable than SG models, while also providing valuable insight into the cancer hallmarks that drive them. In addition, when tested on an independent benchmark non-TCGA dataset, MG features consistently outperformed SG models. We provide an easy-to-use web service at http://pathclass.compbio.sdu.dk where users can upload their own gene expression datasets from breast cancer studies and obtain the subtype predictions from all the classifiers.
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Affiliation(s)
- Nicolas Alcaraz
- Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark.,Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark.,The Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Markus List
- Computational Biology and Applied Algorithms, Max Planck Institute for Informatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
| | - Richa Batra
- Institute of Computational Biology, Helmholtz Zentrum München, 85764 Munich, Germany.,Department of Dermatology and Allergy, Technical University of Munich, 80802 Munich, Germany
| | - Fabio Vandin
- Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark.,Department of Information and Engineering, University of Padowa, 35122 Padowa, Italy
| | - Henrik J Ditzel
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark.,Department of Oncology, Odense University Hospital, 5000 Odense, Denmark
| | - Jan Baumbach
- Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark.,Computational Systems Biology Group, Max Planck Institute for Informatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
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116
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Computational Resources for Predicting Protein-Protein Interactions. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2017; 110:251-275. [PMID: 29412998 DOI: 10.1016/bs.apcsb.2017.07.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Proteins are the essential building blocks and functional components of a cell. They account for the vital functions of an organism. Proteins interact with each other and form protein interaction networks. These protein interactions play a major role in all the biological processes and pathways. The previous methods of predicting protein interactions were experimental which focused on a small set of proteins or a particular protein. However, these experimental approaches are low-throughput as they are time-consuming and require a significant amount of human effort. This led to the development of computational techniques that uses high-throughput experimental data for analyzing protein-protein interactions. The main purpose of this review is to provide an overview on the computational advancements and tools for the prediction of protein interactions. The major databases for the deposition of these interactions are also described. The advantages, as well as the specific limitations of these tools, are highlighted which will shed light on the computational aspects that can help the biologist and researchers in their research.
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117
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Ma X, Sun P, Qin G. Identifying condition-specific modules by clustering multiple networks. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2017; 15:1636-1648. [PMID: 29028204 DOI: 10.1109/tcbb.2017.2761339] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Condition-specific modules in multiple networks must be determined to reveal the underlying molecular mechanisms of diseases. Current algorithms exhibit limitations such as low accuracy and high sensitivity to the number of networks because these algorithms discover condition-specific modules in multiple networks by separating specificity and modularity of modules. To overcome these limitations, we characterize condition-specific module as a group of genes whose connectivity is strong in the corresponding network and weak in other networks; this strategy can accurately depict the topological structure of condition-specific modules. We then transform the condition-specific module discovery problem into a clustering problem in multiple networks. We develop an efficient heuristic algorithm for the Specific Modules in Multiple Networks (SMMN), which discovers the condition-specific modules by considering multiple networks. By using the artificial networks, we demonstrate that SMMN outperforms state-of-the-art methods. In breast cancer networks, stage-specific modules discovered by SMMN are more discriminative in predicting cancer stages than those obtained by other techniques. In pan-cancer networks, cancer-specific modules are more likely to associate with survival time of patients, which is critical for cancer therapy.
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118
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Optimizing the fragment complementation of APEX2 for detection of specific protein-protein interactions in live cells. Sci Rep 2017; 7:12039. [PMID: 28955036 PMCID: PMC5617831 DOI: 10.1038/s41598-017-12365-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 09/07/2017] [Indexed: 12/23/2022] Open
Abstract
Dynamic protein-protein interactions (PPIs) play crucial roles in cell physiological processes. The protein-fragment complementation (PFC) assay has been developed as a powerful approach for the detection of PPIs, but its potential for identifying protein interacting regions is not optimized. Recently, an ascorbate peroxidase (APEX2)-based proximity-tagging method combined with mass spectrometry was developed to identify potential protein interactions in live cells. In this study, we tested whether APEX2 could be employed for PFC. By screening split APEX2 pairs attached to FK506-binding protein 12 (FKBP) and the FKBP12-rapamycin binding (FRB) domain, which interact with each other only in the presence of rapamycin, we successfully obtained an optimized pair for visualizing the interaction between FRB and FKBP12 with high specificity and sensitivity in live cells. The robustness of this APEX2 pair was confirmed by its application toward detecting the STIM1 and Orial1 homodimers in HEK-293 cells. With a subsequent mass spectrometry analysis, we obtained five different biotinylated sites that were localized to the known interaction region on STIM1 and were only detected when the homodimer formed. These results suggest that our PFC pair of APEX2 provides a potential tool for detecting PPIs and identifying binding regions with high specificity in live cells.
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119
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Tarca AL, Fitzgerald W, Chaemsaithong P, Xu Z, Hassan SS, Grivel J, Gomez‐Lopez N, Panaitescu B, Pacora P, Maymon E, Erez O, Margolis L, Romero R. The cytokine network in women with an asymptomatic short cervix and the risk of preterm delivery. Am J Reprod Immunol 2017; 78:e12686. [PMID: 28585708 PMCID: PMC5575567 DOI: 10.1111/aji.12686] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 03/20/2017] [Indexed: 01/06/2023] Open
Abstract
PROBLEM To characterize the amniotic fluid (AF) inflammatory-related protein (IRP) network in patients with a sonographic short cervix (SCx) and to determine its relation to early preterm delivery (ePTD). METHOD OF STUDY A retrospective cohort study included women with a SCx (≤25 mm; n=223) who had amniocentesis and were classified according to gestational age (GA) at diagnosis and delivery (ePTD <32 weeks of gestation). RESULTS (i) In women with a SCx ≤ 22 1/7 weeks, the concentration of most IRPs increased as the cervix shortened; those with ePTD had a higher rate of increase in MIP-1α, MCP-1, and IL-6 concentrations than those delivering later; and (ii) the concentration of most IRPs and the correlation between several IRP pairs were higher in the ePTD group than for those delivering later. CONCLUSION Women with a SCx at 16-22 1/7 weeks have a unique AF cytokine network that correlates with cervical length at diagnosis and GA at delivery. This network may aid in predicting ePTD.
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Affiliation(s)
- Adi L. Tarca
- Perinatology Research BranchProgram for Perinatal Research and ObstetricsDivision of Intramural ResearchEunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthU.S. Department of Health and Human ServicesBethesdaMD, and Detroit, MIUSA
- Department of Obstetrics and GynecologyWayne State University School of MedicineDetroitMIUSA
| | - Wendy Fitzgerald
- Section on Intercellular InteractionsProgram on Physical BiologyEunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthU.S. Department of Health and Human ServicesBethesdaMDUSA
| | - Piya Chaemsaithong
- Perinatology Research BranchProgram for Perinatal Research and ObstetricsDivision of Intramural ResearchEunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthU.S. Department of Health and Human ServicesBethesdaMD, and Detroit, MIUSA
- Department of Obstetrics and GynecologyWayne State University School of MedicineDetroitMIUSA
| | - Zhonghui Xu
- Perinatology Research BranchProgram for Perinatal Research and ObstetricsDivision of Intramural ResearchEunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthU.S. Department of Health and Human ServicesBethesdaMD, and Detroit, MIUSA
| | - Sonia S. Hassan
- Perinatology Research BranchProgram for Perinatal Research and ObstetricsDivision of Intramural ResearchEunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthU.S. Department of Health and Human ServicesBethesdaMD, and Detroit, MIUSA
- Department of Obstetrics and GynecologyWayne State University School of MedicineDetroitMIUSA
| | - Jean‐Charles Grivel
- Division of Translational MedicineSidra Medical and Research CenterDohaQatar
| | - Nardhy Gomez‐Lopez
- Perinatology Research BranchProgram for Perinatal Research and ObstetricsDivision of Intramural ResearchEunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthU.S. Department of Health and Human ServicesBethesdaMD, and Detroit, MIUSA
- Department of Obstetrics and GynecologyWayne State University School of MedicineDetroitMIUSA
- Department of ImmunologyMicrobiology and BiochemistryWayne State University School of MedicineDetroitMIUSA
| | - Bogdan Panaitescu
- Perinatology Research BranchProgram for Perinatal Research and ObstetricsDivision of Intramural ResearchEunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthU.S. Department of Health and Human ServicesBethesdaMD, and Detroit, MIUSA
- Department of Obstetrics and GynecologyWayne State University School of MedicineDetroitMIUSA
| | - Percy Pacora
- Perinatology Research BranchProgram for Perinatal Research and ObstetricsDivision of Intramural ResearchEunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthU.S. Department of Health and Human ServicesBethesdaMD, and Detroit, MIUSA
- Department of Obstetrics and GynecologyWayne State University School of MedicineDetroitMIUSA
| | - Eli Maymon
- Perinatology Research BranchProgram for Perinatal Research and ObstetricsDivision of Intramural ResearchEunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthU.S. Department of Health and Human ServicesBethesdaMD, and Detroit, MIUSA
- Department of Obstetrics and GynecologyWayne State University School of MedicineDetroitMIUSA
| | - Offer Erez
- Perinatology Research BranchProgram for Perinatal Research and ObstetricsDivision of Intramural ResearchEunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthU.S. Department of Health and Human ServicesBethesdaMD, and Detroit, MIUSA
- Department of Obstetrics and GynecologyWayne State University School of MedicineDetroitMIUSA
| | - Leonid Margolis
- Section on Intercellular InteractionsProgram on Physical BiologyEunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthU.S. Department of Health and Human ServicesBethesdaMDUSA
| | - Roberto Romero
- Perinatology Research BranchProgram for Perinatal Research and ObstetricsDivision of Intramural ResearchEunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthU.S. Department of Health and Human ServicesBethesdaMD, and Detroit, MIUSA
- Department of Obstetrics and GynecologyUniversity of MichiganAnn ArborMIUSA
- Department of Epidemiology and BiostatisticsMichigan State UniversityEast LansingMIUSA
- Center for Molecular Medicine and GeneticsWayne State UniversityDetroitMIUSA
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120
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Safari-Alighiarloo N, Taghizadeh M, Tabatabaei SM, Shahsavari S, Namaki S, Khodakarim S, Rezaei-Tavirani M. Identification of new key genes for type 1 diabetes through construction and analysis of protein-protein interaction networks based on blood and pancreatic islet transcriptomes. J Diabetes 2017; 9:764-777. [PMID: 27625010 DOI: 10.1111/1753-0407.12483] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Revised: 08/17/2016] [Accepted: 09/08/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Type 1 diabetes (T1D) is an autoimmune disease in which pancreatic β-cells are destroyed by infiltrating immune cells. Bilateral cooperation of pancreatic β-cells and immune cells has been proposed in the progression of T1D, but as yet no systems study has investigated this possibility. The aims of the study were to elucidate the underlying molecular mechanisms and identify key genes associated with T1D risk using a network biology approach. METHODS Interactome (protein-protein interaction [PPI]) and transcriptome data were integrated to construct networks of differentially expressed genes in peripheral blood mononuclear cells (PBMCs) and pancreatic β-cells. Centrality, modularity, and clique analyses of networks were used to get more meaningful biological information. RESULTS Analysis of genes expression profiles revealed several cytokines and chemokines in β-cells and their receptors in PBMCs, which is supports the dialogue between these two tissues in terms of PPIs. Functional modules and complexes analysis unraveled most significant biological pathways such as immune response, apoptosis, spliceosome, proteasome, and pathways of protein synthesis in the tissues. Finally, Y-box binding protein 1 (YBX1), SRSF protein kinase 1 (SRPK1), proteasome subunit alpha1/ 3, (PSMA1/3), X-ray repair cross complementing 6 (XRCC6), Cbl proto-oncogene (CBL), SRC proto-oncogene, non-receptor tyrosine kinase (SRC), phosphoinositide-3-kinase regulatory subunit 1 (PIK3R1), phospholipase C gamma 1 (PLCG1), SHC adaptor protein1 (SHC1) and ubiquitin conjugating enzyme E2 N (UBE2N) were identified as key markers that were hub-bottleneck genes involved in functional modules and complexes. CONCLUSIONS This study provide new insights into network biomarkers that may be considered potential therapeutic targets.
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Affiliation(s)
- Nahid Safari-Alighiarloo
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taghizadeh
- Bioinformatics Department, Institute of Biochemistry and Biophysics, Tehran University, Tehran, Iran
| | - Seyyed Mohammad Tabatabaei
- Medical Informatics Department, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soodeh Shahsavari
- Biostatistics Department, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Saeed Namaki
- Department of Immunology, Faculty of Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soheila Khodakarim
- Department of Epidemiology, School of Public Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mostafa Rezaei-Tavirani
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Ressom HW, Di Poto C, Ferrarini A, Nezami Ranjbar MR, Varghese RS, Tadesse MG, Mechref Y. Multi-omic approaches for characterization of hepatocellular carcinoma. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2017; 2016:3437-3440. [PMID: 28269041 DOI: 10.1109/embc.2016.7591467] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Multi-omic approaches offer the opportunity to characterize complex diseases such as cancer at various molecular levels. In this paper, we present transcriptomic, proteomic/glycoproteomic, glycomic, and metabolomic (TPGM) data we acquired by analysis of liver tissues from hepatocellular carcinoma (HCC) cases and patients with liver cirrhosis. We evaluated changes in the levels of transcripts, proteins, glycans, and metabolites between tumor and cirrhotic tissues by statistical methods. We demonstrated the potential of multi-omic approaches and network analysis to investigate the interactions among these biomolecules in the progression of liver cirrhosis to HCC. Also, we showed the significance of multi-omic approaches to identify pathways altered in HCC.
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122
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A Systemic Analysis of Transcriptomic and Epigenomic Data To Reveal Regulation Patterns for Complex Disease. G3-GENES GENOMES GENETICS 2017; 7:2271-2279. [PMID: 28500050 PMCID: PMC5499134 DOI: 10.1534/g3.117.042408] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Integrating diverse genomics data can provide a global view of the complex biological processes related to the human complex diseases. Although substantial efforts have been made to integrate different omics data, there are at least three challenges for multi-omics integration methods: (i) How to simultaneously consider the effects of various genomic factors, since these factors jointly influence the phenotypes; (ii) How to effectively incorporate the information from publicly accessible databases and omics datasets to fully capture the interactions among (epi)genomic factors from diverse omics data; and (iii) Until present, the combination of more than two omics datasets has been poorly explored. Current integration approaches are not sufficient to address all of these challenges together. We proposed a novel integrative analysis framework by incorporating sparse model, multivariate analysis, Gaussian graphical model, and network analysis to address these three challenges simultaneously. Based on this strategy, we performed a systemic analysis for glioblastoma multiforme (GBM) integrating genome-wide gene expression, DNA methylation, and miRNA expression data. We identified three regulatory modules of genomic factors associated with GBM survival time and revealed a global regulatory pattern for GBM by combining the three modules, with respect to the common regulatory factors. Our method can not only identify disease-associated dysregulated genomic factors from different omics, but more importantly, it can incorporate the information from publicly accessible databases and omics datasets to infer a comprehensive interaction map of all these dysregulated genomic factors. Our work represents an innovative approach to enhance our understanding of molecular genomic mechanisms underlying human complex diseases.
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123
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Shotgun and Targeted Plasma Proteomics to Predict Prognosis of Non-Small Cell Lung Cancer. Methods Mol Biol 2017; 1619:385-394. [PMID: 28674898 DOI: 10.1007/978-1-4939-7057-5_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Lung cancer is the leading cause of cancer deaths worldwide. Clinically, the treatment of non-small cell lung cancer (NSCLC) can be improved by the early detection and risk screening among population. To meet this need, here we describe in detail a shotgun following the targeted proteomics workflow that we previously applied for human plasma analysis, which involves (1) the application of extensive peptide-level fractionation coupled with label-free quantitative proteomics for the discovery of plasma biomarker candidates for lung cancer and (2) the usage of the multiple reaction monitoring (MRM) assays for the follow-up validations in the verification phase. The workflow features simplicity, low cost, high transferability, high robustness, and flexibility with specific instrumental settings.
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124
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Spatiotemporal profile of postsynaptic interactomes integrates components of complex brain disorders. Nat Neurosci 2017; 20:1150-1161. [PMID: 28671696 DOI: 10.1038/nn.4594] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 05/17/2017] [Indexed: 12/30/2022]
Abstract
The postsynaptic density (PSD) contains a collection of scaffold proteins used for assembling synaptic signaling complexes. However, it is not known how the core-scaffold machinery associates in protein-interaction networks or how proteins encoded by genes involved in complex brain disorders are distributed through spatiotemporal protein complexes. Here using immunopurification, proteomics and bioinformatics, we isolated 2,876 proteins across 41 in vivo interactomes and determined their protein domain composition, correlation to gene expression levels and developmental integration to the PSD. We defined clusters for enrichment of schizophrenia, autism spectrum disorders, developmental delay and intellectual disability risk factors at embryonic day 14 and adult PSD in mice. Mutations in highly connected nodes alter protein-protein interactions modulating macromolecular complexes enriched in disease risk candidates. These results were integrated into a software platform, Synaptic Protein/Pathways Resource (SyPPRes), enabling the prioritization of disease risk factors and their placement within synaptic protein interaction networks.
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125
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Wilson SJ, Wilkins AD, Lin CH, Lua RC, Lichtarge O. DISCOVERY OF FUNCTIONAL AND DISEASE PATHWAYS BY COMMUNITY DETECTION IN PROTEIN-PROTEIN INTERACTION NETWORKS. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2017; 22:336-347. [PMID: 27896987 DOI: 10.1142/9789813207813_0032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Advances in cellular, molecular, and disease biology depend on the comprehensive characterization of gene interactions and pathways. Traditionally, these pathways are curated manually, limiting their efficient annotation and, potentially, reinforcing field-specific bias. Here, in order to test objective and automated identification of functionally cooperative genes, we compared a novel algorithm with three established methods to search for communities within gene interaction networks. Communities identified by the novel approach and by one of the established method overlapped significantly (q < 0.1) with control pathways. With respect to disease, these communities were biased to genes with pathogenic variants in ClinVar (p ≪ 0.01), and often genes from the same community were co-expressed, including in breast cancers. The interesting subset of novel communities, defined by poor overlap to control pathways also contained co-expressed genes, consistent with a possible functional role. This work shows that community detection based on topological features of networks suggests new, biologically meaningful groupings of genes that, in turn, point to health and disease relevant hypotheses.
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Affiliation(s)
- Stephen J Wilson
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA,
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Huo M, Wang Z, Wu D, Zhang Y, Qiao Y. Using Coexpression Protein Interaction Network Analysis to Identify Mechanisms of Danshensu Affecting Patients with Coronary Heart Disease. Int J Mol Sci 2017. [PMID: 28629174 PMCID: PMC5486119 DOI: 10.3390/ijms18061298] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Salvia miltiorrhiza, known as Danshen, has attracted worldwide interest for its substantial effects on coronary heart disease (CHD). Danshensu (DSS) is one of the main active ingredients of Danshen on CHD. Although it has been proven to have a good clinical effect on CHD, the action mechanisms remain elusive. In the current study, a coexpression network-based approach was used to illustrate the beneficial properties of DSS in the context of CHD. By integrating the gene expression profile data and protein-protein interactions (PPIs) data, two coexpression protein interaction networks (CePIN) in a CHD state (CHD CePIN) and a non-CHD state (non-CHD CePIN) were generated. Then, shared nodes and unique nodes in CHD CePIN were attained by conducting a comparison between CHD CePIN and non-CHD CePIN. By calculating the topological parameters of each shared node and unique node in the networks, and comparing the differentially expressed genes, target proteins involved in disease regulation were attained. Then, Gene Ontology (GO) enrichment was utilized to identify biological processes associated to target proteins. Consequently, it turned out that the treatment of CHD with DSS may be partly attributed to the regulation of immunization and blood circulation. Also, it indicated that sodium/hydrogen exchanger 3 (SLC9A3), Prostaglandin G/H synthase 2 (PTGS2), Oxidized low-density lipoprotein receptor 1 (OLR1), and fibrinogen gamma chain (FGG) may be potential therapeutic targets for CHD. In summary, this study provided a novel coexpression protein interaction network approach to provide an explanation of the mechanisms of DSS on CHD and identify key proteins which maybe the potential therapeutic targets for CHD.
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Affiliation(s)
- Mengqi Huo
- Key Laboratory of Traditional Chinese Medicine Information Engineer of State Administration of Traditional Chinese Medicine; School of Chinese Material Medica, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Zhixin Wang
- Key Laboratory of Traditional Chinese Medicine Information Engineer of State Administration of Traditional Chinese Medicine; School of Chinese Material Medica, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Dongxue Wu
- Key Laboratory of Traditional Chinese Medicine Information Engineer of State Administration of Traditional Chinese Medicine; School of Chinese Material Medica, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Yanling Zhang
- Key Laboratory of Traditional Chinese Medicine Information Engineer of State Administration of Traditional Chinese Medicine; School of Chinese Material Medica, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Yanjiang Qiao
- Key Laboratory of Traditional Chinese Medicine Information Engineer of State Administration of Traditional Chinese Medicine; School of Chinese Material Medica, Beijing University of Chinese Medicine, Beijing 100102, China.
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Drug Target Protein-Protein Interaction Networks: A Systematic Perspective. BIOMED RESEARCH INTERNATIONAL 2017; 2017:1289259. [PMID: 28691014 PMCID: PMC5485489 DOI: 10.1155/2017/1289259] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 03/09/2017] [Accepted: 05/10/2017] [Indexed: 01/17/2023]
Abstract
The identification and validation of drug targets are crucial in biomedical research and many studies have been conducted on analyzing drug target features for getting a better understanding on principles of their mechanisms. But most of them are based on either strong biological hypotheses or the chemical and physical properties of those targets separately. In this paper, we investigated three main ways to understand the functional biomolecules based on the topological features of drug targets. There are no significant differences between targets and common proteins in the protein-protein interactions network, indicating the drug targets are neither hub proteins which are dominant nor the bridge proteins. According to some special topological structures of the drug targets, there are significant differences between known targets and other proteins. Furthermore, the drug targets mainly belong to three typical communities based on their modularity. These topological features are helpful to understand how the drug targets work in the PPI network. Particularly, it is an alternative way to predict potential targets or extract nontargets to test a new drug target efficiently and economically. By this way, a drug target's homologue set containing 102 potential target proteins is predicted in the paper.
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128
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Modeling osteosarcoma progression by measuring the connectivity dynamics using an inference of multiple differential modules algorithm. Mol Med Rep 2017; 16:1047-1054. [PMID: 28586048 PMCID: PMC5562023 DOI: 10.3892/mmr.2017.6703] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 03/08/2017] [Indexed: 02/02/2023] Open
Abstract
Understanding the dynamic changes in connectivity of molecular pathways is important for determining disease prognosis. Thus, the current study used an inference of multiple differential modules (iMDM) algorithm to identify the connectivity changes of sub-network to predict the progression of osteosarcoma (OS) based on the microarray data of OS at four Huvos grades. Initially, multiple differential co-expression networks (M-DCNs) were constructed, and weight values were assigned for each edge, followed by detection of seed genes in M-DCNs according to the topological properties. Using these seed gene as a start, an iMDM algorithm was utilized to identify the multiple candidate modules. The statistical significance was determined to select multiple differential modules (M-DMs) based on the null score distribution of candidate modules generated using randomized networks. Additionally, the significance of Module Connectivity Dynamic Score (MCDS) to quantify the dynamic change of M-DMs connectivity. Further, DAVID was employed for KEGG pathway enrichment analysis of genes in dynamic modules. In addition to the basal condition, four conditions, OS grade 1–4, were also included (M=4). In total, 4 DCNs were constructed, and each of them included 2,138 edges and 272 nodes. A total of 13 genes were identified and termed ‘seed genes’ based on the z-score distribution of 272 nodes in DCNs. Following the module search, module refinement and statistical significance analysis, a total of four 4-DMs (modules 1, 2, 3 and 4) were identified. Only one significant 4-DM (module 3 in the DCNs of grade 1, 2, 3 and 4 OS) with dynamic changes was detected when the MCDS of real 4-DMs were compared to a null distribution of MCDS of random 4-DMs. Notably, the genes of the dynamic module (module 3) were enriched in two significant pathway terms, ubiquitin-mediated proteolysis and ribosome. The seed genes with the highest degrees included protein phosphatase 1 regulatory subunit 12A (PPP1R12A), UTP3, small subunit processome component homolog (UTP3), prostaglandin E synthase 3 (PTGES3). Thus, pathway functions (ubiquitin-mediated proteolysis and ribosome) and several seed genes (PPP1R12A, UTP3, and PTGES3) in the dynamic module 3 may be associated with the progression of OS and may serve as potential therapeutic targets in OS.
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129
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Santiago JA, Bottero V, Potashkin JA. Dissecting the Molecular Mechanisms of Neurodegenerative Diseases through Network Biology. Front Aging Neurosci 2017; 9:166. [PMID: 28611656 PMCID: PMC5446999 DOI: 10.3389/fnagi.2017.00166] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 05/12/2017] [Indexed: 12/27/2022] Open
Abstract
Neurodegenerative diseases are rarely caused by a mutation in a single gene but rather influenced by a combination of genetic, epigenetic and environmental factors. Emerging high-throughput technologies such as RNA sequencing have been instrumental in deciphering the molecular landscape of neurodegenerative diseases, however, the interpretation of such large amounts of data remains a challenge. Network biology has become a powerful platform to integrate multiple omics data to comprehensively explore the molecular networks in the context of health and disease. In this review article, we highlight recent advances in network biology approaches with an emphasis in brain-networks that have provided insights into the molecular mechanisms leading to the most prevalent neurodegenerative diseases including Alzheimer’s (AD), Parkinson’s (PD) and Huntington’s diseases (HD). We discuss how integrative approaches using multi-omics data from different tissues have been valuable for identifying biomarkers and therapeutic targets. In addition, we discuss the challenges the field of network medicine faces toward the translation of network-based findings into clinically actionable tools for personalized medicine applications.
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Affiliation(s)
- Jose A Santiago
- Department of Cellular and Molecular Pharmacology, The Chicago Medical School, Rosalind Franklin University of Medicine and ScienceNorth Chicago, IL, United States
| | - Virginie Bottero
- Department of Cellular and Molecular Pharmacology, The Chicago Medical School, Rosalind Franklin University of Medicine and ScienceNorth Chicago, IL, United States
| | - Judith A Potashkin
- Department of Cellular and Molecular Pharmacology, The Chicago Medical School, Rosalind Franklin University of Medicine and ScienceNorth Chicago, IL, United States
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130
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Zhou J, Chen C, Li HF, Hu YJ, Xie HL. Revealing radiotherapy- and chemoradiation-induced pathway dynamics in glioblastoma by analyzing multiple differential networks. Mol Med Rep 2017; 16:696-702. [PMID: 28560382 PMCID: PMC5482131 DOI: 10.3892/mmr.2017.6641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 03/02/2017] [Indexed: 02/02/2023] Open
Abstract
The progression of glioblastoma (GBM) is driven by dynamic alterations in the activity and connectivity of gene pathways. Revealing these dynamic events is necessary in order to understand the pathological mechanisms of, and develop effective treatments for, GBM. The present study aimed to investigate dynamic alterations in pathway activity and connectivity across radiotherapy and chemoradiation conditions in GBM, and to give system-level insights into molecular mechanisms for GBM therapy. A total of two differential co-expression networks (DCNs) were constructed using Pearson correlation coefficient analysis and one sided t-tests, based on gene expression profiles and protein-protein interaction networks, one for each condition. Subsequently, shared differential modules across DCNs were detected via significance analysis for candidate modules, which were obtained according to seed selection, module search by seed expansion and refinement of searched modules. As condition-specific differential modules mediate differential biological processes, the module connectivity dynamic score (MCDS) was implemented to explore dynamic alterations among them. Based on DCNs with 287 nodes and 1,052 edges, a total of 28 seed genes and seven candidate modules were identified. Following significance analysis, five shared differential modules were identified in total. Dynamic alterations among these differential modules were identified using the MCDS, and one module with significant dynamic alterations was identified, termed the dynamic module. The present study revealed the dynamic alterations of shared differential modules, identified one dynamic module between the radiotherapy and chemoradiation conditions, and demonstrated that pathway dynamics may applied to the study of the pathogenesis and therapy of GBM.
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Affiliation(s)
- Jia Zhou
- Department of Geratology, Hangzhou Hospital of Traditional Chinese Medicine, Hangzhou, Zhejiang 310007, P.R. China
| | - Chao Chen
- Department of Radiotherapy, Zhejiang Provincial Hospital of Traditional Chinese Medicine, Hangzhou, Zhejiang 310006, P.R. China
| | - Hua-Feng Li
- Department of Radiotherapy, Zhejiang Provincial Hospital of Traditional Chinese Medicine, Hangzhou, Zhejiang 310006, P.R. China
| | - Yu-Jie Hu
- Department of Radiotherapy, Zhejiang Provincial Hospital of Traditional Chinese Medicine, Hangzhou, Zhejiang 310006, P.R. China
| | - Hong-Ling Xie
- Department of Radiotherapy, Zhejiang Provincial Hospital of Traditional Chinese Medicine, Hangzhou, Zhejiang 310006, P.R. China
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131
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Belling K, Russo F, Jensen AB, Dalgaard MD, Westergaard D, Rajpert-De Meyts E, Skakkebæk NE, Juul A, Brunak S. Klinefelter syndrome comorbidities linked to increased X chromosome gene dosage and altered protein interactome activity. Hum Mol Genet 2017; 26:1219-1229. [PMID: 28369266 PMCID: PMC5390676 DOI: 10.1093/hmg/ddx014] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 12/21/2016] [Indexed: 01/10/2023] Open
Abstract
Klinefelter syndrome (KS) (47,XXY) is the most common male sex chromosome aneuploidy. Diagnosis and clinical supervision remain a challenge due to varying phenotypic presentation and insufficient characterization of the syndrome. Here we combine health data-driven epidemiology and molecular level systems biology to improve the understanding of KS and the molecular interplay influencing its comorbidities. In total, 78 overrepresented KS comorbidities were identified using in- and out-patient registry data from the entire Danish population covering 6.8 million individuals. The comorbidities extracted included both clinically well-known (e.g. infertility and osteoporosis) and still less established KS comorbidities (e.g. pituitary gland hypofunction and dental caries). Several systems biology approaches were applied to identify key molecular players underlying KS comorbidities: Identification of co-expressed modules as well as central hubs and gene dosage perturbed protein complexes in a KS comorbidity network build from known disease proteins and their protein–protein interactions. The systems biology approaches together pointed to novel aspects of KS disease phenotypes including perturbed Jak-STAT pathway, dysregulated genes important for disturbed immune system (IL4), energy balance (POMC and LEP) and erythropoietin signalling in KS. We present an extended epidemiological study that links KS comorbidities to the molecular level and identify potential causal players in the disease biology underlying the identified comorbidities.
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Affiliation(s)
- Kirstine Belling
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Francesco Russo
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders B Jensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marlene D Dalgaard
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - David Westergaard
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ewa Rajpert-De Meyts
- Department of Growth and Reproduction, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.,International Research and Research Training Centre in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Niels E Skakkebæk
- Department of Growth and Reproduction, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.,International Research and Research Training Centre in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Anders Juul
- Department of Growth and Reproduction, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.,International Research and Research Training Centre in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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132
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Pedersen HK, Gudmundsdottir V, Brunak S. Pancreatic Islet Protein Complexes and Their Dysregulation in Type 2 Diabetes. Front Genet 2017; 8:43. [PMID: 28473845 PMCID: PMC5397424 DOI: 10.3389/fgene.2017.00043] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/27/2017] [Indexed: 12/18/2022] Open
Abstract
Type 2 diabetes (T2D) is a complex disease that involves multiple genes. Numerous risk loci have already been associated with T2D, although many susceptibility genes remain to be identified given heritability estimates. Systems biology approaches hold potential for discovering novel T2D genes by considering their biological context, such as tissue-specific protein interaction partners. Pancreatic islets are a key T2D tissue and many of the known genetic risk variants lead to impaired islet function, hence a better understanding of the islet-specific dysregulation in the disease-state is essential to unveil the full potential of person-specific profiles. Here we identify 3,692 overlapping pancreatic islet protein complexes (containing 10,805 genes) by integrating islet gene and protein expression data with protein interactions. We found 24 of these complexes to be significantly enriched for genes associated with diabetic phenotypes through heterogeneous evidence sources, including genetic variation, methylation, and gene expression in islets. The analysis specifically revealed ten T2D candidate genes with probable roles in islets (ANPEP, HADH, FAM105A, PDLIM4, PDLIM5, MAP2K4, PPP2R5E, SNX13, GNAS, and FRS2), of which the last six are novel in the context of T2D and the data that went into the analysis. Fifteen of the twenty-four complexes were further enriched for combined genetic associations with glycemic traits, exemplifying how perturbation of protein complexes by multiple small effects can give rise to diabetic phenotypes. The complex nature of T2D ultimately prompts an understanding of the individual patients at the network biology level. We present the foundation for such work by exposing a subset of the global interactome that is dysregulated in T2D and consequently provides a good starting point when evaluating an individual's alterations at the genome, transcriptome, or proteome level in relation to T2D in clinical settings.
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Affiliation(s)
- Helle Krogh Pedersen
- Department of Bio and Health Informatics, Technical University of DenmarkKgs Lyngby, Denmark
| | - Valborg Gudmundsdottir
- Department of Bio and Health Informatics, Technical University of DenmarkKgs Lyngby, Denmark
| | - Søren Brunak
- Department of Bio and Health Informatics, Technical University of DenmarkKgs Lyngby, Denmark
- Disease Systems Biology, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of CopenhagenCopenhagen, Denmark
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133
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Will T, Helms V. Rewiring of the inferred protein interactome during blood development studied with the tool PPICompare. BMC SYSTEMS BIOLOGY 2017; 11:44. [PMID: 28376810 PMCID: PMC5379774 DOI: 10.1186/s12918-017-0400-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 01/26/2017] [Indexed: 12/24/2022]
Abstract
BACKGROUND Differential analysis of cellular conditions is a key approach towards understanding the consequences and driving causes behind biological processes such as developmental transitions or diseases. The progress of whole-genome expression profiling enabled to conveniently capture the state of a cell's transcriptome and to detect the characteristic features that distinguish cells in specific conditions. In contrast, mapping the physical protein interactome for many samples is experimentally infeasible at the moment. For the understanding of the whole system, however, it is equally important how the interactions of proteins are rewired between cellular states. To overcome this deficiency, we recently showed how condition-specific protein interaction networks that even consider alternative splicing can be inferred from transcript expression data. Here, we present the differential network analysis tool PPICompare that was specifically designed for isoform-sensitive protein interaction networks. RESULTS Besides detecting significant rewiring events between the interactomes of grouped samples, PPICompare infers which alterations to the transcriptome caused each rewiring event and what is the minimal set of alterations necessary to explain all between-group changes. When applied to the development of blood cells, we verified that a reasonable amount of rewiring events were reported by the tool and found that differential gene expression was the major determinant of cellular adjustments to the interactome. Alternative splicing events were consistently necessary in each developmental step to explain all significant alterations and were especially important for rewiring in the context of transcriptional control. CONCLUSIONS Applying PPICompare enabled us to investigate the dynamics of the human protein interactome during developmental transitions. A platform-independent implementation of the tool PPICompare is available at https://sourceforge.net/projects/ppicompare/ .
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Affiliation(s)
- Thorsten Will
- Center for Bioinformatics, Saarland University, Campus E2.1, Saarbrücken, 66123 Germany
- Graduate School of Computer Science, Saarland University, Campus E1.3, Saarbrücken, 66123 Germany
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, Campus E2.1, Saarbrücken, 66123 Germany
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134
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Jana T, Ghosh A, Das Mandal S, Banerjee R, Saha S. PPIMpred: a web server for high-throughput screening of small molecules targeting protein-protein interaction. ROYAL SOCIETY OPEN SCIENCE 2017; 4:160501. [PMID: 28484602 PMCID: PMC5414239 DOI: 10.1098/rsos.160501] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 03/20/2017] [Indexed: 05/31/2023]
Abstract
PPIMpred is a web server that allows high-throughput screening of small molecules for targeting specific protein-protein interactions, namely Mdm2/P53, Bcl2/Bak and c-Myc/Max. Three different kernels of support vector machine (SVM), namely, linear, polynomial and radial basis function (RBF), and two other machine learning techniques including Naive Bayes and Random Forest were used to train the models. A fivefold cross-validation technique was used to measure the performance of these classifiers. The RBF kernel of SVM outperformed and/or was comparable with all other methods with accuracy values of 83%, 79% and 90% for Mdm2/P53, Bcl2/Bak and c-Myc/Max, respectively. About 80% of the predicted SVM scores of training/testing datasets from Mdm2/P53 and Bcl2/Bak have significant IC50 values and docking scores. The proposed models achieved an accuracy of 66-90% with blind sets. The three mentioned (Mdm2/P53, Bcl2/Bak and c-Myc/Max) proposed models were screened in a large dataset of 265 242 small chemicals from National Cancer Institute open database. To further realize the robustness of this approach, hits with high and random SVM scores were used for molecular docking in AutoDock Vina wherein the molecules with high and random predicted SVM scores yielded moderately significant docking scores (p-values < 0.1). In addition to the above-mentioned classification scheme, this web server also allows users to get the structural and chemical similarities with known chemical modulators or drug-like molecules based on Tanimoto coefficient similarity search algorithm. PPIMpred is freely available at http://bicresources.jcbose.ac.in/ssaha4/PPIMpred/.
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Affiliation(s)
- Tanmoy Jana
- Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Road, Scheme-VII (M), Kolkata, West Bengal, India
| | - Abhirupa Ghosh
- Department of Bioinformatics, Bose Institute, P 1/12, C.I.T. Road, Scheme-VII (M), Kolkata, West Bengal, India
| | - Sukhen Das Mandal
- Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Road, Scheme-VII (M), Kolkata, West Bengal, India
| | - Raja Banerjee
- Department of Bioinformatics, Bose Institute, P 1/12, C.I.T. Road, Scheme-VII (M), Kolkata, West Bengal, India
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, West Bengal, India
| | - Sudipto Saha
- Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Road, Scheme-VII (M), Kolkata, West Bengal, India
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135
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Integrating personalized gene expression profiles into predictive disease-associated gene pools. NPJ Syst Biol Appl 2017. [PMID: 28649437 PMCID: PMC5445628 DOI: 10.1038/s41540-017-0009-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Gene expression data are routinely used to identify genes that on average exhibit different expression levels between a case and a control group. Yet, very few of such differentially expressed genes are detectably perturbed in individual patients. Here, we develop a framework to construct personalized perturbation profiles for individual subjects, identifying the set of genes that are significantly perturbed in each individual. This allows us to characterize the heterogeneity of the molecular manifestations of complex diseases by quantifying the expression-level similarities and differences among patients with the same phenotype. We show that despite the high heterogeneity of the individual perturbation profiles, patients with asthma, Parkinson and Huntington's disease share a broadpool of sporadically disease-associated genes, and that individuals with statistically significant overlap with this pool have a 80-100% chance of being diagnosed with the disease. The developed framework opens up the possibility to apply gene expression data in the context of precision medicine, with important implications for biomarker identification, drug development, diagnosis and treatment.
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136
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Zheng H, Wang C, Wang H. Analysis of Organization of the Interactome Using Dominating Sets: A Case Study on Cell Cycle Interaction Networks. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2017; 14:282-289. [PMID: 28368806 DOI: 10.1109/tcbb.2015.2459712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In this study, a minimum dominating set based approach was developed and implemented as a Cytoscape plugin to identify critical and redundant proteins in a protein interaction network. We focused on the investigation of the properties associated with critical proteins in the context of the analysis of interaction networks specific to cell cycle in both yeast and human. A total of 132 yeast genes and 129 human proteins have been identified as critical nodes while 950 in yeast and 980 in human have been categorized as redundant nodes. A clear distinction between critical and redundant proteins was observed when examining their topological parameters including betweenness centrality, suggesting a central role of critical proteins in the control of a network. The significant differences in terms of gene coexpression and functional similarity were observed between the two sets of proteins in yeast. Critical proteins were found to be enriched with essential genes in both networks and have a more deleterious effect on the network integrity than their redundant counterparts. Furthermore, we obtained statistically significant enrichments of proteins that govern human diseases including cancer-related and virus-targeted genes in the corresponding set of critical proteins.
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137
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Chiu YC, Wang LJ, Lu TP, Hsiao TH, Chuang EY, Chen Y. Differential correlation analysis of glioblastoma reveals immune ceRNA interactions predictive of patient survival. BMC Bioinformatics 2017; 18:132. [PMID: 28241741 PMCID: PMC5330036 DOI: 10.1186/s12859-017-1557-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 02/21/2017] [Indexed: 12/21/2022] Open
Abstract
Background Recent studies illuminated a novel role of microRNA (miRNA) in the competing endogenous RNA (ceRNA) interaction: two genes (ceRNAs) can achieve coexpression by competing for a pool of common targeting miRNAs. Individual biological investigations implied ceRNA interaction performs crucial oncogenic/tumor suppressive functions in glioblastoma multiforme (GBM). Yet, a systematic analysis has not been conducted to explore the functional landscape and prognostic significance of ceRNA interaction. Results Incorporating the knowledge that ceRNA interaction is highly condition-specific and modulated by the expressional abundance of miRNAs, we devised a ceRNA inference by differential correlation analysis to identify the miRNA-modulated ceRNA pairs. Analyzing sample-paired miRNA and gene expression profiles of GBM, our data showed that this alternative layer of gene interaction is essential in global information flow. Functional annotation analysis revealed its involvement in activated processes in brain, such as synaptic transmission, as well as critical tumor-associated functions. Notably, a systematic survival analysis suggested the strength of ceRNA-ceRNA interactions, rather than expressional abundance of individual ceRNAs, among three immune response genes (CCL22, IL2RB, and IRF4) is predictive of patient survival. The prognostic value was validated in two independent cohorts. Conclusions This work addresses the lack of a comprehensive exploration into the functional and prognostic relevance of ceRNA interaction in GBM. The proposed efficient and reliable method revealed its significance in GBM-related functions and prognosis. The highlighted roles of ceRNA interaction provide a basis for further biological and clinical investigations. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1557-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yu-Chiao Chiu
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.,Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, No. 1, Section 4, Roosevelt Rd., Taipei, 10617, Taiwan.,Department of Medical Research, Taichung Veterans General Hospital, No. 1650, Section 4, Taiwan Blvd., Xitun District, Taichung City, 40705, Taiwan
| | - Li-Ju Wang
- Department of Medical Research, Taichung Veterans General Hospital, No. 1650, Section 4, Taiwan Blvd., Xitun District, Taichung City, 40705, Taiwan
| | - Tzu-Pin Lu
- Department of Public Health, National Taiwan University, Taipei, 10055, Taiwan
| | - Tzu-Hung Hsiao
- Department of Medical Research, Taichung Veterans General Hospital, No. 1650, Section 4, Taiwan Blvd., Xitun District, Taichung City, 40705, Taiwan.
| | - Eric Y Chuang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, No. 1, Section 4, Roosevelt Rd., Taipei, 10617, Taiwan. .,Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taipei, 10055, Taiwan.
| | - Yidong Chen
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA. .,Department of Epidemiology and Biostatistics, University of Texas Health Science Center at San Antonio, 8403 Floyd Curl Dr., San Antonio, TX, 78229, USA.
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138
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Kirk IK, Weinhold N, Belling K, Skakkebæk NE, Jensen TS, Leffers H, Juul A, Brunak S. Chromosome-wise Protein Interaction Patterns and Their Impact on Functional Implications of Large-Scale Genomic Aberrations. Cell Syst 2017; 4:357-364.e3. [PMID: 28215527 DOI: 10.1016/j.cels.2017.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Revised: 10/23/2016] [Accepted: 01/05/2017] [Indexed: 10/20/2022]
Abstract
Gene copy-number changes influence phenotypes through gene-dosage alteration and subsequent changes of protein complex stoichiometry. Human trisomies where gene copy numbers are increased uniformly over entire chromosomes provide generic cases for studying these relationships. In most trisomies, gene and protein level alterations have fatal consequences. We used genome-wide protein-protein interaction data to identify chromosome-specific patterns of protein interactions. We found that some chromosomes encode proteins that interact infrequently with each other, chromosome 21 in particular. We combined the protein interaction data with transcriptome data from human brain tissue to investigate how this pattern of global interactions may affect cellular function. We identified highly connected proteins that also had coordinated gene expression. These proteins were associated with important neurological functions affecting the characteristic phenotypes for Down syndrome and have previously been validated in mouse knockout experiments. Our approach is general and applicable to other gene-dosage changes, such as arm-level amplifications in cancer.
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Affiliation(s)
- Isa Kristina Kirk
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark; Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Nils Weinhold
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark; Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kirstine Belling
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark; Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Niels Erik Skakkebæk
- Department of Growth and Reproduction, Rigshospitalet and University of Copenhagen, 2100 Copenhagen, Denmark
| | - Thomas Skøt Jensen
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Henrik Leffers
- Department of Growth and Reproduction, Rigshospitalet and University of Copenhagen, 2100 Copenhagen, Denmark
| | - Anders Juul
- Department of Growth and Reproduction, Rigshospitalet and University of Copenhagen, 2100 Copenhagen, Denmark
| | - Søren Brunak
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark; Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
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139
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Screening for Novel Small-Molecule Inhibitors Targeting the Assembly of Influenza Virus Polymerase Complex by a Bimolecular Luminescence Complementation-Based Reporter System. J Virol 2017; 91:JVI.02282-16. [PMID: 28031371 DOI: 10.1128/jvi.02282-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 11/30/2016] [Indexed: 11/20/2022] Open
Abstract
Influenza virus RNA-dependent RNA polymerase consists of three viral protein subunits: PA, PB1, and PB2. Protein-protein interactions (PPIs) of these subunits play pivotal roles in assembling the functional polymerase complex, which is essential for the replication and transcription of influenza virus RNA. Here we developed a highly specific and robust bimolecular luminescence complementation (BiLC) reporter system to facilitate the investigation of influenza virus polymerase complex formation. Furthermore, by combining computational modeling and the BiLC reporter assay, we identified several novel small-molecule compounds that selectively inhibited PB1-PB2 interaction. Function of one such lead compound was confirmed by its activity in suppressing influenza virus replication. In addition, our studies also revealed that PA plays a critical role in enhancing interactions between PB1 and PB2, which could be important in targeting sites for anti-influenza intervention. Collectively, these findings not only aid the development of novel inhibitors targeting the formation of influenza virus polymerase complex but also present a new tool to investigate the exquisite mechanism of PPIs. IMPORTANCE Formation of the functional influenza virus polymerase involves complex protein-protein interactions (PPIs) of PA, PB1, and PB2 subunits. In this work, we developed a novel BiLC assay system which is sensitive and specific to quantify both strong and weak PPIs between influenza virus polymerase subunits. More importantly, by combining in silico modeling and our BiLC assay, we identified a small molecule that can suppress influenza virus replication by disrupting the polymerase assembly. Thus, we developed an innovative method to investigate PPIs of multisubunit complexes effectively and to identify new molecules inhibiting influenza virus polymerase assembly.
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140
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Lee H, Shin M. Mining pathway associations for disease-related pathway activity analysis based on gene expression and methylation data. BioData Min 2017; 10:3. [PMID: 28168005 PMCID: PMC5286825 DOI: 10.1186/s13040-017-0127-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 01/26/2017] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The problem of discovering genetic markers as disease signatures is of great significance for the successful diagnosis, treatment, and prognosis of complex diseases. Even if many earlier studies worked on identifying disease markers from a variety of biological resources, they mostly focused on the markers of genes or gene-sets (i.e., pathways). However, these markers may not be enough to explain biological interactions between genetic variables that are related to diseases. Thus, in this study, our aim is to investigate distinctive associations among active pathways (i.e., pathway-sets) shown each in case and control samples which can be observed from gene expression and/or methylation data. RESULTS The pathway-sets are obtained by identifying a set of associated pathways that are often active together over a significant number of class samples. For this purpose, gene expression or methylation profiles are first analyzed to identify significant (active) pathways via gene-set enrichment analysis. Then, regarding these active pathways, an association rule mining approach is applied to examine interesting pathway-sets in each class of samples (case or control). By doing so, the sets of associated pathways often working together in activity profiles are finally chosen as our distinctive signature of each class. The identified pathway-sets are aggregated into a pathway activity network (PAN), which facilitates the visualization of differential pathway associations between case and control samples. From our experiments with two publicly available datasets, we could find interesting PAN structures as the distinctive signatures of breast cancer and uterine leiomyoma cancer, respectively. CONCLUSIONS Our pathway-set markers were shown to be superior or very comparable to other genetic markers (such as genes or gene-sets) in disease classification. Furthermore, the PAN structure, which can be constructed from the identified markers of pathway-sets, could provide deeper insights into distinctive associations between pathway activities in case and control samples.
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Affiliation(s)
- Hyeonjeong Lee
- Bio-Intelligence & Data Mining Laboratory, Graduate School of Electronics Engineering, Kyungpook National University, 80, Daehak-ro, Buk-gu, Daegu, 41566 Republic of Korea
| | - Miyoung Shin
- School of Electronics Engineering, Kyungpook National University, 80, Daehak-ro, Buk-gu, Daegu, 41566 Republic of Korea
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141
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Huang DW, Yu ZG. Dynamic-Sensitive centrality of nodes in temporal networks. Sci Rep 2017; 7:41454. [PMID: 28150735 PMCID: PMC5288707 DOI: 10.1038/srep41454] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 12/20/2016] [Indexed: 11/28/2022] Open
Abstract
Locating influential nodes in temporal networks has attracted a lot of attention as data driven and diverse applications. Classic works either looked at analysing static networks or placed too much emphasis on the topological information but rarely highlighted the dynamics. In this paper, we take account the network dynamics and extend the concept of Dynamic-Sensitive centrality to temporal network. According to the empirical results on three real-world temporal networks and a theoretical temporal network for susceptible-infected-recovered (SIR) models, the temporal Dynamic-Sensitive centrality (TDC) is more accurate than both static versions and temporal versions of degree, closeness and betweenness centrality. As an application, we also use TDC to analyse the impact of time-order on spreading dynamics, we find that both topological structure and dynamics contribute the impact on the spreading influence of nodes, and the impact of time-order on spreading influence will be stronger when spreading rate b deviated from the epidemic threshold bc, especially for the temporal scale-free networks.
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Affiliation(s)
- Da-Wen Huang
- Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education and Hunan Key Laboratory for Computation and Simulation in Science and Engineering, Xiangtan University, Xiangtan, Hunan 411105, China
| | - Zu-Guo Yu
- Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education and Hunan Key Laboratory for Computation and Simulation in Science and Engineering, Xiangtan University, Xiangtan, Hunan 411105, China
- School of Mathematical Sciences, Queensland University of Technology, GPO Box 2434, Brisbane, Q4001, Australia
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142
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Gladilin E. Graph-theoretical model of global human interactome reveals enhanced long-range communicability in cancer networks. PLoS One 2017; 12:e0170953. [PMID: 28141819 PMCID: PMC5283687 DOI: 10.1371/journal.pone.0170953] [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] [Received: 02/24/2016] [Accepted: 01/13/2017] [Indexed: 12/22/2022] Open
Abstract
Malignant transformation is known to involve substantial rearrangement of the molecular genetic landscape of the cell. A common approach to analysis of these alterations is a reductionist one and consists of finding a compact set of differentially expressed genes or associated signaling pathways. However, due to intrinsic tumor heterogeneity and tissue specificity, biomarkers defined by a small number of genes/pathways exhibit substantial variability. As an alternative to compact differential signatures, global features of genetic cell machinery are conceivable. Global network descriptors suggested in previous works are, however, known to potentially be biased by overrepresentation of interactions between frequently studied genes-proteins. Here, we construct a cellular network of 74538 directional and differential gene expression weighted protein-protein and gene regulatory interactions, and perform graph-theoretical analysis of global human interactome using a novel, degree-independent feature—the normalized total communicability (NTC). We apply this framework to assess differences in total information flow between different cancer (BRCA/COAD/GBM) and non-cancer interactomes. Our experimental results reveal that different cancer interactomes are characterized by significant enhancement of long-range NTC, which arises from circulation of information flow within robustly organized gene subnetworks. Although enhancement of NTC emerges in different cancer types from different genomic profiles, we identified a subset of 90 common genes that are related to elevated NTC in all studied tumors. Our ontological analysis shows that these genes are associated with enhanced cell division, DNA replication, stress response, and other cellular functions and processes typically upregulated in cancer. We conclude that enhancement of long-range NTC manifested in the correlated activity of genes whose tight coordination is required for survival and proliferation of all tumor cells, and, thus, can be seen as a graph-theoretical equivalent to some hallmarks of cancer. The computational framework for differential network analysis presented herein is of potential interest for a wide range of network perturbation problems given by single or multiple gene-protein activation-inhibition.
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Affiliation(s)
- Evgeny Gladilin
- Division of Theoretical Bioinformatics, German Cancer Research Center, Berliner Str. 41, 69120 Heidelberg, Germany
- BioQuant and IPMB, University Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
- * E-mail:
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143
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Ma X, Liu Z, Zhang Z, Huang X, Tang W. Multiple network algorithm for epigenetic modules via the integration of genome-wide DNA methylation and gene expression data. BMC Bioinformatics 2017; 18:72. [PMID: 28137264 PMCID: PMC5282853 DOI: 10.1186/s12859-017-1490-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Accepted: 01/20/2017] [Indexed: 02/05/2023] Open
Abstract
Background With the increase in the amount of DNA methylation and gene expression data, the epigenetic mechanisms of cancers can be extensively investigate. Available methods integrate the DNA methylation and gene expression data into a network by specifying the anti-correlation between them. However, the correlation between methylation and expression is usually unknown and difficult to determine. Results To address this issue, we present a novel multiple network framework for epigenetic modules, namely, Epigenetic Module based on Differential Networks (EMDN) algorithm, by simultaneously analyzing DNA methylation and gene expression data. The EMDN algorithm prevents the specification of the correlation between methylation and expression. The accuracy of EMDN algorithm is more efficient than that of modern approaches. On the basis of The Cancer Genome Atlas (TCGA) breast cancer data, we observe that the EMDN algorithm can recognize positively and negatively correlated modules and these modules are significantly more enriched in the known pathways than those obtained by other algorithms. These modules can serve as bio-markers to predict breast cancer subtypes by using methylation profiles, where positively and negatively correlated modules are of equal importance in the classification of cancer subtypes. Epigenetic modules also estimate the survival time of patients, and this factor is critical for cancer therapy. Conclusions The proposed model and algorithm provide an effective method for the integrative analysis of DNA methylation and gene expression. The algorithm is freely available as an R-package at https://github.com/william0701/EMDN. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1490-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaoke Ma
- School of Computer Science and Technology, Xidian University, No.2 South TaiBai Road, Xi'an, People's Republic of China.,Xidian-Ningbo Information Technology Institute, Xidian University, No. 777 Zhongguanxi Road, Ningbo, People's Republic of China
| | - Zaiyi Liu
- Department of Radiology, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Zhongshan Road, Guangzhou, People's Republic of China
| | - Zhongyuan Zhang
- School of Statistics and Mathematics, Central University of Finance and Economics, 39 South College Road, Haidian District, Beijing, People's Republic of China
| | - Xiaotai Huang
- School of Computer Science and Technology, Xidian University, No.2 South TaiBai Road, Xi'an, People's Republic of China
| | - Wanxin Tang
- Department of Nephrology, West China Hospital, Sichuan University, Wuhou District, Chengdu, People's Republic of China.
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144
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Gough A, Stern AM, Maier J, Lezon T, Shun TY, Chennubhotla C, Schurdak ME, Haney SA, Taylor DL. Biologically Relevant Heterogeneity: Metrics and Practical Insights. SLAS DISCOVERY 2017; 22:213-237. [PMID: 28231035 DOI: 10.1177/2472555216682725] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Heterogeneity is a fundamental property of biological systems at all scales that must be addressed in a wide range of biomedical applications, including basic biomedical research, drug discovery, diagnostics, and the implementation of precision medicine. There are a number of published approaches to characterizing heterogeneity in cells in vitro and in tissue sections. However, there are no generally accepted approaches for the detection and quantitation of heterogeneity that can be applied in a relatively high-throughput workflow. This review and perspective emphasizes the experimental methods that capture multiplexed cell-level data, as well as the need for standard metrics of the spatial, temporal, and population components of heterogeneity. A recommendation is made for the adoption of a set of three heterogeneity indices that can be implemented in any high-throughput workflow to optimize the decision-making process. In addition, a pairwise mutual information method is suggested as an approach to characterizing the spatial features of heterogeneity, especially in tissue-based imaging. Furthermore, metrics for temporal heterogeneity are in the early stages of development. Example studies indicate that the analysis of functional phenotypic heterogeneity can be exploited to guide decisions in the interpretation of biomedical experiments, drug discovery, diagnostics, and the design of optimal therapeutic strategies for individual patients.
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Affiliation(s)
- Albert Gough
- 1 Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.,2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
| | - Andrew M Stern
- 1 Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.,2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
| | - John Maier
- 3 Department of Family Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Timothy Lezon
- 1 Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.,2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
| | - Tong-Ying Shun
- 2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
| | - Chakra Chennubhotla
- 1 Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.,2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
| | - Mark E Schurdak
- 1 Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.,2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA.,4 University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Steven A Haney
- 5 Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, USA
| | - D Lansing Taylor
- 1 Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.,2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA.,4 University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
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145
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Dynamic versus static biomarkers in cancer immune checkpoint blockade: unravelling complexity. Nat Rev Drug Discov 2017; 16:264-272. [PMID: 28057932 DOI: 10.1038/nrd.2016.233] [Citation(s) in RCA: 155] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Recently, there has been a coordinated effort from academic institutions and the pharmaceutical industry to identify biomarkers that can predict responses to immune checkpoint blockade in cancer. Several biomarkers have been identified; however, none has reliably predicted response in a sufficiently rigorous manner for routine use. Here, we argue that the therapeutic response to immune checkpoint blockade is a critical state transition of a complex system. Such systems are highly sensitive to initial conditions, and critical transitions are notoriously difficult to predict far in advance. Nevertheless, warning signals can be detected closer to the tipping point. Advances in mathematics and network biology are starting to make it possible to identify such warning signals. We propose that these dynamic biomarkers could prove to be useful in distinguishing responding from non-responding patients, as well as facilitate the identification of new therapeutic targets for combination therapy.
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146
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Wang Y, Huang T, Xie L, Liu L. Integrative analysis of methylation and transcriptional profiles to predict aging and construct aging specific cross-tissue networks. BMC SYSTEMS BIOLOGY 2016; 10:132. [PMID: 28155676 PMCID: PMC5260078 DOI: 10.1186/s12918-016-0354-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND Aging is a complex process relating multi-scale omics data. Finding key age markers in normal tissues could help to provide reliable aging predictions in human. However, predicting age based on multi-omics data with both accuracy and informative biological function has not been performed systematically, thus relative cross-tissue analysis has not been investigated entirely, either. RESULTS Here we have developed an improved prediction pipeline, the Integrating and Stepwise Age-Prediction (ISAP) method, to regress age and find key aging markers effectively. Furthermore, we have performed a serious of network analyses, such as the PPI network, cross-tissue networks and pathway interaction networks. CONCLUSION Our results find important coordinated aging patterns between different tissues. Both co-profiling and cross-pathway analyses identify more thorough functions of aging, and could help to find aging markers, pathways and relative aging disease researches.
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Affiliation(s)
- Yin Wang
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Tao Huang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, People's Republic of China
| | - Lu Xie
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, 201203, China
| | - Lei Liu
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, 201203, China.
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147
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Rodrigo G, Daròs JA, Elena SF. Virus-host interactome: Putting the accent on how it changes. J Proteomics 2016; 156:1-4. [PMID: 28007618 DOI: 10.1016/j.jprot.2016.12.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/26/2016] [Accepted: 12/16/2016] [Indexed: 12/27/2022]
Abstract
Viral infections are extremely complex processes that could only be well understood by precisely characterizing the interaction networks between the virus and the host components. In recent years, much effort has gone in this direction with the aim of unveiling the molecular basis of viral pathology. These networks are mostly formed by viral and host proteins, and are expected to be dynamic both with time and space (i.e., with the progression of infection, as well as with the virus and host genotypes; what we call plastodynamic). This largely overlooked spatio-temporal evolution urgently calls for a change both in the conceptual paradigms and experimental techniques used so far to characterize virus-host interactions. More generally, molecular plasticity and temporal dynamics are unavoidable components of the mechanisms that underlie any complex disease; components whose understanding will eventually enhance our ability to modulate those networks with the aim of improving disease treatments.
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Affiliation(s)
- Guillermo Rodrigo
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas - Universidad Politécnica de Valencia, 46022, Valencia, Spain; Instituto de Biología Integrativa y de Sistemas, Consejo Superior de Investigaciones Científicas - Universitat de València, 46980 Paterna, Spain.
| | - José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas - Universidad Politécnica de Valencia, 46022, Valencia, Spain.
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas - Universidad Politécnica de Valencia, 46022, Valencia, Spain; Instituto de Biología Integrativa y de Sistemas, Consejo Superior de Investigaciones Científicas - Universitat de València, 46980 Paterna, Spain; Santa Fe Institute, Santa Fe, NM 87501, USA.
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148
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Jinawath N, Bunbanjerdsuk S, Chayanupatkul M, Ngamphaiboon N, Asavapanumas N, Svasti J, Charoensawan V. Bridging the gap between clinicians and systems biologists: from network biology to translational biomedical research. J Transl Med 2016; 14:324. [PMID: 27876057 PMCID: PMC5120462 DOI: 10.1186/s12967-016-1078-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 11/08/2016] [Indexed: 01/22/2023] Open
Abstract
With the wealth of data accumulated from completely sequenced genomes and other high-throughput experiments, global studies of biological systems, by simultaneously investigating multiple biological entities (e.g. genes, transcripts, proteins), has become a routine. Network representation is frequently used to capture the presence of these molecules as well as their relationship. Network biology has been widely used in molecular biology and genetics, where several network properties have been shown to be functionally important. Here, we discuss how such methodology can be useful to translational biomedical research, where scientists traditionally focus on one or a small set of genes, diseases, and drug candidates at any one time. We first give an overview of network representation frequently used in biology: what nodes and edges represent, and review its application in preclinical research to date. Using cancer as an example, we review how network biology can facilitate system-wide approaches to identify targeted small molecule inhibitors. These types of inhibitors have the potential to be more specific, resulting in high efficacy treatments with less side effects, compared to the conventional treatments such as chemotherapy. Global analysis may provide better insight into the overall picture of human diseases, as well as identify previously overlooked problems, leading to rapid advances in medicine. From the clinicians’ point of view, it is necessary to bridge the gap between theoretical network biology and practical biomedical research, in order to improve the diagnosis, prevention, and treatment of the world’s major diseases.
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Affiliation(s)
- Natini Jinawath
- Integrative Computational BioScience (ICBS) Center, Mahidol University, Nakhon Pathom, Thailand.,Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Sacarin Bunbanjerdsuk
- Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Maneerat Chayanupatkul
- Department of Physiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Division of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Nuttapong Ngamphaiboon
- Medical Oncology Unit, Department of Medicine Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Nithi Asavapanumas
- Department of Physiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Jisnuson Svasti
- Integrative Computational BioScience (ICBS) Center, Mahidol University, Nakhon Pathom, Thailand.,Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand.,Laboratory of Biochemistry, Chulabhorn Research Institute, Bangkok, Thailand
| | - Varodom Charoensawan
- Integrative Computational BioScience (ICBS) Center, Mahidol University, Nakhon Pathom, Thailand. .,Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand. .,Systems Biology of Diseases Research Unit, Faculty of Science, Mahidol University, Bangkok, Thailand.
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149
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Ma X, Tang W, Wang P, Guo X, Gao L. Extracting Stage-Specific and Dynamic Modules Through Analyzing Multiple Networks Associated with Cancer Progression. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2016; 15:647-658. [PMID: 27845671 DOI: 10.1109/tcbb.2016.2625791] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Determining the dynamics of pathways associated with cancer progression is critical for understanding the etiology of diseases. Advances in biological technology have facilitated the simultaneous genomic profiling of multiple patients at different clinical stages, thus generating the dynamic genomic data for cancers. Such data provide enable investigation of the dynamics of related pathways. However, methods for integrative analysis of dynamic genomic data are inadequate. In this study, we develop a novel nonnegative matrix factorization algorithm for dynamic modules ( NMF-DM), which simultaneously analyzes multiple networks for the identification of stage-specific and dynamic modules. NMF-DM applies the temporal smoothness framework by balancing the networks at the current stage and the previous stage. Experimental results indicate that the NMF-DM algorithm is more accurate than the state-of-the-art methods in artificial dynamic networks. In breast cancer networks, NMF-DM reveals the dynamic modules that are important for cancer stage transitions. Furthermore, the stage-specific and dynamic modules have distinct topological and biochemical properties. Finally, we demonstrate that the stage-specific modules significantly improve the accuracy of cancer stage prediction. The proposed algorithm provides an effective way to explore the time-dependent cancer genomic data.
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150
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Yang MQ, Elnitski L. A Systems Biology Comparison of Ovarian Cancers Implicates Putative Somatic Driver Mutations through Protein-Protein Interaction Models. PLoS One 2016; 11:e0163353. [PMID: 27788148 PMCID: PMC5082879 DOI: 10.1371/journal.pone.0163353] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 09/07/2016] [Indexed: 12/14/2022] Open
Abstract
Ovarian carcinomas can be aggressive with a high mortality rate (e.g., high-grade serous ovarian carcinomas, or HGSOCs), or indolent with much better long-term outcomes (e.g., low-malignant-potential, or LMP, serous ovarian carcinomas). By comparing LMP and HGSOC tumors, we can gain insight into the mechanisms underlying malignant progression in ovarian cancer. However, previous studies of the two subtypes have been focused on gene expression analysis. Here, we applied a systems biology approach, integrating gene expression profiles derived from two independent data sets containing both LMP and HGSOC tumors with protein-protein interaction data. Genes and related networks implicated by both data sets involved both known and novel disease mechanisms and highlighted the different roles of BRCA1 and CREBBP in the two tumor types. In addition, the incorporation of somatic mutation data revealed that amplification of PAK4 is associated with poor survival in patients with HGSOC. Thus, perturbations in protein interaction networks demonstrate differential trafficking of network information between malignant and benign ovarian cancers. The novel network-based molecular signatures identified here may be used to identify new targets for intervention and to improve the treatment of invasive ovarian cancer as well as early diagnosis.
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Affiliation(s)
- Mary Qu Yang
- MidSouth Bioinformatics Center and Joint Bioinformatics Ph.D. Program, University of Arkansas at Little Rock and University of Arkansas for Medical Sciences, 2801 S. University Avenue, Little Rock, Arkansas, 72204, United States of America
- * E-mail: (MQY); (LE)
| | - Laura Elnitski
- National Human Genome Research Institute, National Institutes of Health, Rockville, MD, 20852, United States of America
- * E-mail: (MQY); (LE)
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