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Huang KC, Yang KC, Lin H, Tsao TTH, Lee SA. Transcriptome alterations of mitochondrial and coagulation function in schizophrenia by cortical sequencing analysis. BMC Genomics 2014; 15 Suppl 9:S6. [PMID: 25522158 PMCID: PMC4290619 DOI: 10.1186/1471-2164-15-s9-s6] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Background Transcriptome sequencing of brain samples provides detailed enrichment analysis of differential expression and genetic interactions for evaluation of mitochondrial and coagulation function of schizophrenia. It is implicated that schizophrenia genetic and protein interactions may give rise to biological dysfunction of energy metabolism and hemostasis. These findings may explain the biological mechanisms responsible for negative and withdraw symptoms of schizophrenia and antipsychotic-induced venous thromboembolism. We conducted a comparison of schizophrenic candidate genes from literature reviews and constructed the schizophrenia-mediator network (SCZMN) which consists of schizophrenic candidate genes and associated mediator genes by applying differential expression analysis to BA22 RNA-Seq brain data. The network was searched against pathway databases such as PID, Reactome, HumanCyc, and Cell-Map. The candidate complexes were identified by MCL clustering using CORUM for potential pathogenesis of schizophrenia. Results Published BA22 RNA-Seq brain data of 9 schizophrenic patients and 9 controls samples were analyzed. The differentially expressed genes in the BA22 brain samples of schizophrenia are proposed as schizophrenia candidate marker genes (SCZCGs). The genetic interactions between mitochondrial genes and many under-expressed SCZCGs indicate the genetic predisposition of mitochondria dysfunction in schizophrenia. The biological functions of SCZCGs, as listed in the Pathway Interaction Database (PID), indicate that these genes have roles in DNA binding transcription factor, signal and cancer-related pathways, coagulation and cell cycle regulation and differentiation pathways. In the query-query protein-protein interaction (QQPPI) network of SCZCGs, TP53, PRKACA, STAT3 and SP1 were identified as the central "hub" genes. Mitochondrial function was modulated by dopamine inhibition of respiratory complex I activity. The genetic interaction between mitochondria function and schizophrenia may be revealed by DRD2 linked to NDUFS7 through protein-protein interactions of FLNA and ARRB2. The biological mechanism of signaling pathway of coagulation cascade was illustrated by the PPI network of the SCZCGs and the coagulation-associated genes. The relationship between antipsychotic target genes (DRD2/3 and HTR2A) and coagulation factor genes (F3, F7 and F10) appeared to cascade the following hemostatic process implicating the bottleneck of coagulation genetic network by the bridging of actin-binding protein (FLNA). Conclusions It is implicated that the energy metabolism and hemostatic process have important roles in the pathogenesis for schizophrenia. The cross-talk of genetic interaction by these co-expressed genes and reached candidate genes may address the key network in disease pathology. The accuracy of candidate genes evaluated from different quantification tools could be improved by crosstalk analysis of overlapping genes in genetic networks.
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102
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Sahu A, Kumar S, Sreenivasamurthy SK, Selvan LDN, Madugundu AK, Yelamanchi SD, Puttamallesh VN, Dey G, Anil AK, Srinivasan A, Mukherjee KK, Gowda H, Satishchandra P, Mahadevan A, Pandey A, Prasad TSK, Shankar SK. Host response profile of human brain proteome in toxoplasma encephalitis co-infected with HIV. Clin Proteomics 2014; 11:39. [PMID: 25404878 PMCID: PMC4232683 DOI: 10.1186/1559-0275-11-39] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 09/02/2014] [Indexed: 01/27/2023] Open
Abstract
Background Toxoplasma encephalitis is caused by the opportunistic protozoan parasite Toxoplasma gondii. Primary infection with T. gondii in immunocompetent individuals remains largely asymptomatic. In contrast, in immunocompromised individuals, reactivation of the parasite results in severe complications and mortality. Molecular changes at the protein level in the host central nervous system and proteins associated with pathogenesis of toxoplasma encephalitis are largely unexplored. We used a global quantitative proteomic strategy to identify differentially regulated proteins and affected molecular networks in the human host during T. gondii infection with HIV co-infection. Results We identified 3,496 proteins out of which 607 proteins were differentially expressed (≥1.5-fold) when frontal lobe of the brain from patients diagnosed with toxoplasma encephalitis was compared to control brain tissues. We validated differential expression of 3 proteins through immunohistochemistry, which was confirmed to be consistent with mass spectrometry analysis. Pathway analysis of differentially expressed proteins indicated deregulation of several pathways involved in antigen processing, immune response, neuronal growth, neurotransmitter transport and energy metabolism. Conclusions Global quantitative proteomic approach adopted in this study generated a comparative proteome profile of brain tissues from toxoplasma encephalitis patients co-infected with HIV. Differentially expressed proteins include previously reported and several new proteins in the context of T. gondii and HIV infection, which can be further investigated. Molecular pathways identified to be associated with the disease should enhance our understanding of pathogenesis in toxoplasma encephalitis. Electronic supplementary material The online version of this article (doi:10.1186/1559-0275-11-39) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Apeksha Sahu
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066 India ; Bioinformatics Centre, School of Life Sciences, Pondicherry University, Puducherry, 605014 India
| | - Satwant Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066 India
| | - Sreelakshmi K Sreenivasamurthy
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066 India ; Manipal University, Madhav Nagar, Manipal, 576104 India
| | - Lakshmi Dhevi N Selvan
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066 India ; Amrita School of Biotechnology, Amrita University, Kollam, 690525 India
| | - Anil K Madugundu
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066 India ; Bioinformatics Centre, School of Life Sciences, Pondicherry University, Puducherry, 605014 India
| | - Soujanya D Yelamanchi
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066 India ; School of Biotechnology, KIIT University, Bhubaneswar, 751024 India
| | | | - Gourav Dey
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066 India ; Manipal University, Madhav Nagar, Manipal, 576104 India
| | | | - Anand Srinivasan
- Department of Pharmacology, Postgraduate Institute of Medical Education & Research, Chandigarh, 160012 India
| | - Kanchan K Mukherjee
- Department of Neurosurgery, Postgraduate Institute of Medical Education & Research, Chandigarh, 160012 India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066 India
| | | | - Anita Mahadevan
- Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bangalore, 560029 India ; Human Brain Tissue Repository, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, Bangalore, 560029 India
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA ; Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 1205 USA ; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA ; The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Thottethodi Subrahmanya Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066 India ; Bioinformatics Centre, School of Life Sciences, Pondicherry University, Puducherry, 605014 India ; Manipal University, Madhav Nagar, Manipal, 576104 India ; Amrita School of Biotechnology, Amrita University, Kollam, 690525 India ; NIMHANS-IOB Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, Bangalore, 560029 India
| | - Susarla Krishna Shankar
- Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bangalore, 560029 India ; Human Brain Tissue Repository, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, Bangalore, 560029 India
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Zhang Q, Yang B, Chen X, Xu J, Mei C, Mao Z. Renal Gene Expression Database (RGED): a relational database of gene expression profiles in kidney disease. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2014; 2014:bau092. [PMID: 25252782 PMCID: PMC4173636 DOI: 10.1093/database/bau092] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
UNLABELLED We present a bioinformatics database named Renal Gene Expression Database (RGED), which contains comprehensive gene expression data sets from renal disease research. The web-based interface of RGED allows users to query the gene expression profiles in various kidney-related samples, including renal cell lines, human kidney tissues and murine model kidneys. Researchers can explore certain gene profiles, the relationships between genes of interests and identify biomarkers or even drug targets in kidney diseases. The aim of this work is to provide a user-friendly utility for the renal disease research community to query expression profiles of genes of their own interest without the requirement of advanced computational skills. AVAILABILITY AND IMPLEMENTATION Website is implemented in PHP, R, MySQL and Nginx and freely available from http://rged.wall-eva.net. DATABASE URL http://rged.wall-eva.net.
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Affiliation(s)
- Qingzhou Zhang
- Kidney Institute of CPLA, Division of Nephrology, Changzheng Hospital, Second Military Medical University, 415 Fengyang Road, Shanghai 200003, China
| | - Bo Yang
- Kidney Institute of CPLA, Division of Nephrology, Changzheng Hospital, Second Military Medical University, 415 Fengyang Road, Shanghai 200003, China
| | - Xujiao Chen
- Kidney Institute of CPLA, Division of Nephrology, Changzheng Hospital, Second Military Medical University, 415 Fengyang Road, Shanghai 200003, China
| | - Jing Xu
- Kidney Institute of CPLA, Division of Nephrology, Changzheng Hospital, Second Military Medical University, 415 Fengyang Road, Shanghai 200003, China
| | - Changlin Mei
- Kidney Institute of CPLA, Division of Nephrology, Changzheng Hospital, Second Military Medical University, 415 Fengyang Road, Shanghai 200003, China
| | - Zhiguo Mao
- Kidney Institute of CPLA, Division of Nephrology, Changzheng Hospital, Second Military Medical University, 415 Fengyang Road, Shanghai 200003, China
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Integration strategy is a key step in network-based analysis and dramatically affects network topological properties and inferring outcomes. BIOMED RESEARCH INTERNATIONAL 2014; 2014:296349. [PMID: 25243127 PMCID: PMC4163410 DOI: 10.1155/2014/296349] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 07/14/2014] [Accepted: 07/17/2014] [Indexed: 01/17/2023]
Abstract
An increasing number of experiments have been designed to detect intracellular and intercellular molecular interactions. Based on these molecular interactions (especially protein interactions), molecular networks have been built for using in several typical applications, such as the discovery of new disease genes and the identification of drug targets and molecular complexes. Because the data are incomplete and a considerable number of false-positive interactions exist, protein interactions from different sources are commonly integrated in network analyses to build a stable molecular network. Although various types of integration strategies are being applied in current studies, the topological properties of the networks from these different integration strategies, especially typical applications based on these network integration strategies, have not been rigorously evaluated. In this paper, systematic analyses were performed to evaluate 11 frequently used methods using two types of integration strategies: empirical and machine learning methods. The topological properties of the networks of these different integration strategies were found to significantly differ. Moreover, these networks were found to dramatically affect the outcomes of typical applications, such as disease gene predictions, drug target detections, and molecular complex identifications. The analysis presented in this paper could provide an important basis for future network-based biological researches.
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105
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Su G, Morris JH, Demchak B, Bader GD. Biological network exploration with Cytoscape 3. ACTA ACUST UNITED AC 2014; 47:8.13.1-24. [PMID: 25199793 DOI: 10.1002/0471250953.bi0813s47] [Citation(s) in RCA: 619] [Impact Index Per Article: 61.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Cytoscape is one of the most popular open-source software tools for the visual exploration of biomedical networks composed of protein, gene, and other types of interactions. It offers researchers a versatile and interactive visualization interface for exploring complex biological interconnections supported by diverse annotation and experimental data, thereby facilitating research tasks such as predicting gene function and constructing pathways. Cytoscape provides core functionality to load, visualize, search, filter, and save networks, and hundreds of Apps extend this functionality to address specific research needs. The latest generation of Cytoscape (version 3.0 and later) has substantial improvements in function, user interface, and performance relative to previous versions. This protocol aims to jump-start new users with specific protocols for basic Cytoscape functions, such as installing Cytoscape and Cytoscape Apps, loading data, visualizing and navigating the networks, visualizing network associated data (attributes), and identifying clusters. It also highlights new features that benefit experienced users.
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Affiliation(s)
- Gang Su
- Molecular Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, Michigan
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Li X, Battle A, Karczewski K, Zappala Z, Knowles D, Smith K, Kukurba K, Wu E, Simon N, Montgomery S. Transcriptome sequencing of a large human family identifies the impact of rare noncoding variants. Am J Hum Genet 2014; 95:245-56. [PMID: 25192044 PMCID: PMC4157143 DOI: 10.1016/j.ajhg.2014.08.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 08/12/2014] [Indexed: 12/26/2022] Open
Abstract
Recent and rapid human population growth has led to an excess of rare genetic variants that are expected to contribute to an individual's genetic burden of disease risk. To date, much of the focus has been on rare protein-coding variants, for which potential impact can be estimated from the genetic code, but determining the impact of rare noncoding variants has been more challenging. To improve our understanding of such variants, we combined high-quality genome sequencing and RNA sequencing data from a 17-individual, three-generation family to contrast expression quantitative trait loci (eQTLs) and splicing quantitative trait loci (sQTLs) within this family to eQTLs and sQTLs within a population sample. Using this design, we found that eQTLs and sQTLs with large effects in the family were enriched with rare regulatory and splicing variants (minor allele frequency < 0.01). They were also more likely to influence essential genes and genes involved in complex disease. In addition, we tested the capacity of diverse noncoding annotation to predict the impact of rare noncoding variants. We found that distance to the transcription start site, evolutionary constraint, and epigenetic annotation were considerably more informative for predicting the impact of rare variants than for predicting the impact of common variants. These results highlight that rare noncoding variants are important contributors to individual gene-expression profiles and further demonstrate a significant capability for genomic annotation to predict the impact of rare noncoding variants.
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107
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Zhang Y, Tao C, Jiang G, Nair AA, Su J, Chute CG, Liu H. Network-based analysis reveals distinct association patterns in a semantic MEDLINE-based drug-disease-gene network. J Biomed Semantics 2014; 5:33. [PMID: 25170419 PMCID: PMC4137727 DOI: 10.1186/2041-1480-5-33] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Accepted: 07/02/2014] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND A huge amount of associations among different biological entities (e.g., disease, drug, and gene) are scattered in millions of biomedical articles. Systematic analysis of such heterogeneous data can infer novel associations among different biological entities in the context of personalized medicine and translational research. Recently, network-based computational approaches have gained popularity in investigating such heterogeneous data, proposing novel therapeutic targets and deciphering disease mechanisms. However, little effort has been devoted to investigating associations among drugs, diseases, and genes in an integrative manner. RESULTS We propose a novel network-based computational framework to identify statistically over-expressed subnetwork patterns, called network motifs, in an integrated disease-drug-gene network extracted from Semantic MEDLINE. The framework consists of two steps. The first step is to construct an association network by extracting pair-wise associations between diseases, drugs and genes in Semantic MEDLINE using a domain pattern driven strategy. A Resource Description Framework (RDF)-linked data approach is used to re-organize the data to increase the flexibility of data integration, the interoperability within domain ontologies, and the efficiency of data storage. Unique associations among drugs, diseases, and genes are extracted for downstream network-based analysis. The second step is to apply a network-based approach to mine the local network structure of this heterogeneous network. Significant network motifs are then identified as the backbone of the network. A simplified network based on those significant motifs is then constructed to facilitate discovery. We implemented our computational framework and identified five network motifs, each of which corresponds to specific biological meanings. Three case studies demonstrate that novel associations are derived from the network topology analysis of reconstructed networks of significant network motifs, further validated by expert knowledge and functional enrichment analyses. CONCLUSIONS We have developed a novel network-based computational approach to investigate the heterogeneous drug-gene-disease network extracted from Semantic MEDLINE. We demonstrate the power of this approach by prioritizing candidate disease genes, inferring potential disease relationships, and proposing novel drug targets, within the context of the entire knowledge. The results indicate that such approach will facilitate the formulization of novel research hypotheses, which is critical for translational medicine research and personalized medicine.
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Affiliation(s)
- Yuji Zhang
- Division of Biostatistics and Bioinformatics, University of Maryland Greenebaum Cancer Center and Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Cui Tao
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Guoqian Jiang
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Asha A Nair
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Jian Su
- Radiology Informatics Laboratory, Department of Radiology, Mayo Clinic, Rochester, MN, USA
| | - Christopher G Chute
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Hongfang Liu
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
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108
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Ding YD, Chang JW, Guo J, Chen D, Li S, Xu Q, Deng XX, Cheng YJ, Chen LL. Prediction and functional analysis of the sweet orange protein-protein interaction network. BMC PLANT BIOLOGY 2014; 14:213. [PMID: 25091279 PMCID: PMC4236729 DOI: 10.1186/s12870-014-0213-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 07/24/2014] [Indexed: 05/04/2023]
Abstract
BACKGROUND Sweet orange (Citrus sinensis) is one of the most important fruits world-wide. Because it is a woody plant with a long growth cycle, genetic studies of sweet orange are lagging behind those of other species. RESULTS In this analysis, we employed ortholog identification and domain combination methods to predict the protein-protein interaction (PPI) network for sweet orange. The K-nearest neighbors (KNN) classification method was used to verify and filter the network. The final predicted PPI network, CitrusNet, contained 8,195 proteins with 124,491 interactions. The quality of CitrusNet was evaluated using gene ontology (GO) and Mapman annotations, which confirmed the reliability of the network. In addition, we calculated the expression difference of interacting genes (EDI) in CitrusNet using RNA-seq data from four sweet orange tissues, and also analyzed the EDI distribution and variation in different sub-networks. CONCLUSIONS Gene expression in CitrusNet has significant modular features. Target of rapamycin (TOR) protein served as the central node of the hormone-signaling sub-network. All evidence supported the idea that TOR can integrate various hormone signals and affect plant growth. CitrusNet provides valuable resources for the study of biological functions in sweet orange.
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Affiliation(s)
- Yu-Duan Ding
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People’s Republic of China
| | - Ji-Wei Chang
- Agricultural Bioinformatics Key laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, People’s Republic of China
| | - Jing Guo
- Agricultural Bioinformatics Key laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, People’s Republic of China
| | - DiJun Chen
- Agricultural Bioinformatics Key laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, People’s Republic of China
| | - Sen Li
- Agricultural Bioinformatics Key laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, People’s Republic of China
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People’s Republic of China
| | - Xiu-Xin Deng
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People’s Republic of China
| | - Yun-Jiang Cheng
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People’s Republic of China
| | - Ling-Ling Chen
- Agricultural Bioinformatics Key laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, People’s Republic of China
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109
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J. D'Souza RC, Knittle AM, Nagaraj N, van Dinther M, Choudhary C, ten Dijke P, Mann M, Sharma K. Time-resolved dissection of early phosphoproteome and ensuing proteome changes in response to TGF-. Sci Signal 2014; 7:rs5. [DOI: 10.1126/scisignal.2004856] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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110
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Murthy KR, Goel R, Subbannayya Y, Jacob HK, Murthy PR, Manda SS, Patil AH, Sharma R, Sahasrabuddhe NA, Parashar A, Nair BG, Krishna V, Prasad TK, Gowda H, Pandey A. Proteomic analysis of human vitreous humor. Clin Proteomics 2014; 11:29. [PMID: 25097467 PMCID: PMC4106660 DOI: 10.1186/1559-0275-11-29] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 05/16/2014] [Indexed: 12/11/2022] Open
Abstract
Background The vitreous humor is a transparent, gelatinous mass whose main constituent is water. It plays an important role in providing metabolic nutrient requirements of the lens, coordinating eye growth and providing support to the retina. It is in close proximity to the retina and reflects many of the changes occurring in this tissue. The biochemical changes occurring in the vitreous could provide a better understanding about the pathophysiological processes that occur in vitreoretinopathy. In this study, we investigated the proteome of normal human vitreous humor using high resolution Fourier transform mass spectrometry. Results The vitreous humor was subjected to multiple fractionation techniques followed by LC-MS/MS analysis. We identified 1,205 proteins, 682 of which have not been described previously in the vitreous humor. Most proteins were localized to the extracellular space (24%), cytoplasm (20%) or plasma membrane (14%). Classification based on molecular function showed that 27% had catalytic activity, 10% structural activity, 10% binding activity, 4% cell and 4% transporter activity. Categorization for biological processes showed 28% participate in metabolism, 20% in cell communication and 13% in cell growth. The data have been deposited to the ProteomeXchange with identifier PXD000957. Conclusion This large catalog of vitreous proteins should facilitate biomedical research into pathological conditions of the eye including diabetic retinopathy, retinal detachment and cataract.
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Affiliation(s)
- Krishna R Murthy
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India.,Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, Kerala 690 525, India.,Vittala International Institute Of Ophthalmology, Bangalore, Karnataka 560085, India
| | - Renu Goel
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India.,Department of Biotechnology, Kuvempu University, Shankaraghatta, Karnataka 577 451, India
| | - Yashwanth Subbannayya
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - Harrys Kc Jacob
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - Praveen R Murthy
- Vittala International Institute Of Ophthalmology, Bangalore, Karnataka 560085, India
| | - Srikanth Srinivas Manda
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India.,Centre of Excellence in Bioinformatics, Bioinformatics Centre, School of Life Sciences, Pondicherry University, Puducherry 605 014, India
| | - Arun H Patil
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - Rakesh Sharma
- Department of Neurochemistry, National Institute of Mental Health and Neuro Sciences, Bangalore 560 006, India
| | | | | | - Bipin G Nair
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, Kerala 690 525, India
| | | | - Ts Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India.,Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, Kerala 690 525, India.,Centre of Excellence in Bioinformatics, Bioinformatics Centre, School of Life Sciences, Pondicherry University, Puducherry 605 014, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - Akhilesh Pandey
- Department of Biological Chemistry, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore 21205 MD, USA.,Department of Oncology and Pathology, Johns Hopkins University School of Medicine, Baltimore 21205 MD, USA
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Andreani J, Guerois R. Evolution of protein interactions: From interactomes to interfaces. Arch Biochem Biophys 2014; 554:65-75. [DOI: 10.1016/j.abb.2014.05.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 04/28/2014] [Accepted: 05/12/2014] [Indexed: 12/16/2022]
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112
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Chen YA, Eschrich SA. Computational methods and opportunities for phosphorylation network medicine. Transl Cancer Res 2014; 3:266-278. [PMID: 25530950 PMCID: PMC4271781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Protein phosphorylation, one of the most ubiquitous post-translational modifications (PTM) of proteins, is known to play an essential role in cell signaling and regulation. With the increasing understanding of the complexity and redundancy of cell signaling, there is a growing recognition that targeting the entire network or system could be a necessary and advantageous strategy for treating cancer. Protein kinases, the proteins that add a phosphate group to the substrate proteins during phosphorylation events, have become one of the largest groups of 'druggable' targets in cancer therapeutics in recent years. Kinase inhibitors are being regularly used in clinics for cancer treatment. This therapeutic paradigm shift in cancer research is partly due to the generation and availability of high-dimensional proteomics data. Generation of this data, in turn, is enabled by increased use of mass-spectrometry (MS)-based or other high-throughput proteomics platforms as well as companion public databases and computational tools. This review briefly summarizes the current state and progress on phosphoproteomics identification, quantification, and platform related characteristics. We review existing database resources, computational tools, methods for phosphorylation network inference, and ultimately demonstrate the connection to therapeutics. Finally, many research opportunities exist for bioinformaticians or biostatisticians based on developments and limitations of the current and emerging technologies.
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Affiliation(s)
- Yian Ann Chen
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, 12902 Magnolia Drive Tampa, FL 33612, USA
| | - Steven A Eschrich
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, 12902 Magnolia Drive Tampa, FL 33612, USA
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A crosslinker based on a tethered electrophile for mapping kinase-substrate networks. ACTA ACUST UNITED AC 2014; 21:585-90. [PMID: 24746561 DOI: 10.1016/j.chembiol.2014.02.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 02/21/2014] [Accepted: 02/25/2014] [Indexed: 12/23/2022]
Abstract
Despite the continuing progress made toward mapping kinase signaling networks, there are still many phosphorylation events for which the responsible kinase has not yet been identified. We are interested in addressing this problem through forming covalent crosslinks between a peptide substrate and the corresponding phosphorylating kinase. Previously we reported a dialdehyde-based kinase-binding probe capable of such a reaction with a peptide containing a cysteine substituted for the phosphorylatable ser/thr/tyr residue. Here, we examine the yield of a previously reported dialdehyde-based probe and report that the dialdehyde-based probes possess a significant limitation in terms of crosslinked kinase-substrate product yield. To address this limitation, we developed a crosslinking scheme based on a kinase activity-based probe, and this crosslinker provides an increase in efficiency and substrate specificity, including in the context of cell lysate.
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Bonacci T, Audebert S, Camoin L, Baudelet E, Bidaut G, Garcia M, Witzel II, Perkins ND, Borg JP, Iovanna JL, Soubeyran P. Identification of new mechanisms of cellular response to chemotherapy by tracking changes in post-translational modifications by ubiquitin and ubiquitin-like proteins. J Proteome Res 2014; 13:2478-94. [PMID: 24654937 DOI: 10.1021/pr401258d] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a very aggressive malignancy characterized by an excessive resistance to all known anticancer therapies, a still largely elusive phenomenon. To identify original mechanisms, we have explored the role of post-translational modifications (PTMs) mediated by members of the ubiquitin family. Although alterations of these pathways have been reported in different cancers, no methodical search for these kinds of anomalies has been performed so far. Therefore, we studied the ubiquitin-, Nedd8-, and SUMO1-specific proteomes of a pancreatic cancer cell line (MiaPaCa-2) and identified changes induced by gemcitabine, the standard PDAC's chemotherapeutic drug. These PTMs profiles contained both known major substrates of all three modifiers as well as original ones. Gemcitabine treatment altered the PTM profile of proteins involved in various biological functions, some known cancer associated genes, many potentially cancer-associated genes, and several cancer-signaling networks, including canonical and noncanonical WNT and PI3K/Akt/MTOR pathways. Some of these altered PTMs formed groups of functionally and physically associated proteins. Importantly, we could validate the gemcitabine-induced PTMs variations of relevant candidates and we could demonstrate the biological significance of such altered PTMs by studying in detail the sumoylation of SNIP1, one of these new targets.
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Affiliation(s)
- Thomas Bonacci
- CRCM, INSERM U1068; Institut Paoli-Calmettes; Aix-Marseille Université, UM105; CNRS, UMR7258, 163 Av de Luminy, F-13009 Marseille, France
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115
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Sobolev BN, Veselovsky AV, Poroikov VV. Prediction of protein post-translational modifications: main trends and methods. RUSSIAN CHEMICAL REVIEWS 2014. [DOI: 10.1070/rc2014v083n02abeh004377] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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116
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Li S, Zhang B. Traditional Chinese medicine network pharmacology: theory, methodology and application. Chin J Nat Med 2014; 11:110-20. [PMID: 23787177 DOI: 10.1016/s1875-5364(13)60037-0] [Citation(s) in RCA: 567] [Impact Index Per Article: 56.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Indexed: 02/06/2023]
Abstract
Traditional Chinese medicine (TCM) has a long history of viewing an individual or patient as a system with different statuses, and has accumulated numerous herbal formulae. The holistic philosophy of TCM shares much with the key ideas of emerging network pharmacology and network biology, and meets the requirements of overcoming complex diseases, such as cancer, in a systematic manner. To discover TCM from a systems perspective and at the molecular level, a novel TCM network pharmacology approach was established by updating the research paradigm from the current "one target, one drug" mode to a new "network target, multi-components" mode. Subsequently, a set of TCM network pharmacology methods were created to prioritize disease-associated genes, to predict the target profiles and pharmacological actions of herbal compounds, to reveal drug-gene-disease co-module associations, to screen synergistic multi-compounds from herbal formulae in a high-throughput manner, and to interpret the combinatorial rules and network regulation effects of herbal formulae. The effectiveness of the network-based methods was demonstrated for the discovery of bioactive compounds and for the elucidation of the mechanisms of action of herbal formulae, such as Qing-Luo-Yin and the Liu-Wei-Di-Huang pill. The studies suggest that the TCM network pharmacology approach provides a new research paradigm for translating TCM from an experience-based medicine to an evidence-based medicine system, which will accelerate TCM drug discovery, and also improve current drug discovery strategies.
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Affiliation(s)
- Shao Li
- Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China.
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117
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Tovar-Mendez A, Miernyk JA, Hoyos E, Randall DD. A functional genomic analysis of Arabidopsis thaliana PP2C clade D. PROTOPLASMA 2014; 251:265-271. [PMID: 23832523 DOI: 10.1007/s00709-013-0526-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 06/24/2013] [Indexed: 06/02/2023]
Abstract
In the reference dicot plant Arabidopsis thaliana, the PP2C family of P-protein phosphatases includes the products of 80 genes that have been separated into ten multi-protein clades plus six singletons. Clade D includes the products of nine genes distributed among three chromosomes (APD1, At3g12620; APD2, At3g17090; APD3, At3g51370; APD4, At3g55050; APD5, At4g33920; APD6, At4g38520; APD7, At5g02760; APD8, At5g06750; and APD9, At5g66080). As part of a functional genomics analysis of protein phosphorylation, we retrieved expression data from public databases and determined the subcellular protein localization of the members of clade D. While the nine proteins have been grouped together based upon primary sequence alignments, we observed no obvious common patterns in expression or localization. We found chimera with the GFP associated with the nucleus, plasma membrane, the endomembrane system, and mitochondria in transgenic plants.
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118
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Yao Q, Ge H, Wu S, Zhang N, Chen W, Xu C, Gao J, Thelen JJ, Xu D. P³DB 3.0: From plant phosphorylation sites to protein networks. Nucleic Acids Res 2013; 42:D1206-13. [PMID: 24243849 PMCID: PMC3965113 DOI: 10.1093/nar/gkt1135] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
In the past few years, the Plant Protein Phosphorylation Database (P3DB, http://p3db.org) has become one of the most significant in vivo data resources for studying plant phosphoproteomics. We have substantially updated P3DB with respect to format, new datasets and analytic tools. In the P3DB 3.0, there are altogether 47 923 phosphosites in 16 477 phosphoproteins curated across nine plant organisms from 32 studies, which have met our multiple quality standards for acquisition of in vivo phosphorylation site data. Centralized by these phosphorylation data, multiple related data and annotations are provided, including protein–protein interaction (PPI), gene ontology, protein tertiary structures, orthologous sequences, kinase/phosphatase classification and Kinase Client Assay (KiC Assay) data—all of which provides context for the phosphorylation event. In addition, P3DB 3.0 incorporates multiple network viewers for the above features, such as PPI network, kinase-substrate network, phosphatase-substrate network, and domain co-occurrence network to help study phosphorylation from a systems point of view. Furthermore, the new P3DB reflects a community-based design through which users can share datasets and automate data depository processes for publication purposes. Each of these new features supports the goal of making P3DB a comprehensive, systematic and interactive platform for phosphoproteomics research.
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Affiliation(s)
- Qiuming Yao
- Department of Computer Science, University of Missouri, Columbia, MO 65211, USA, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA, School of Communication and Information Engineering, Shanghai University, Shanghai 200444, People's Republic of China, Department of Biology, Brandeis University, MA 02453, USA, Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA and Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
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119
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Huang KC, Yang KC, Lin H, Tsao Tsun-Hui T, Lee WK, Lee SA, Kao CY. Analysis of schizophrenia and hepatocellular carcinoma genetic network with corresponding modularity and pathways: novel insights to the immune system. BMC Genomics 2013; 14 Suppl 5:S10. [PMID: 24564241 PMCID: PMC3852078 DOI: 10.1186/1471-2164-14-s5-s10] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Background Schizophrenic patients show lower incidences of cancer, implicating schizophrenia may be a protective factor against cancer. To study the genetic correlation between the two diseases, a specific PPI network was constructed with candidate genes of both schizophrenia and hepatocellular carcinoma. The network, designated schizophrenia-hepatocellular carcinoma network (SHCN), was analysed and cliques were identified as potential functional modules or complexes. The findings were compared with information from pathway databases such as KEGG, Reactome, PID and ConsensusPathDB. Results The functions of mediator genes from SHCN show immune system and cell cycle regulation have important roles in the eitology mechanism of schizophrenia. For example, the over-expressing schizophrenia candidate genes, SIRPB1, SYK and LCK, are responsible for signal transduction in cytokine production; immune responses involving IL-2 and TREM-1/DAP12 pathways are relevant for the etiology mechanism of schizophrenia. Novel treatments were proposed by searching the target genes of FDA approved drugs with genes in potential protein complexes and pathways. It was found that Vitamin A, retinoid acid and a few other immune response agents modulated by RARA and LCK genes may be potential treatments for both schizophrenia and hepatocellular carcinoma. Conclusions This is the first study showing specific mediator genes in the SHCN which may suppress tumors. We also show that the schizophrenic protein interactions and modulation with cancer implicates the importance of immune system for etiology of schizophrenia.
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120
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Battle A, Mostafavi S, Zhu X, Potash JB, Weissman MM, McCormick C, Haudenschild CD, Beckman KB, Shi J, Mei R, Urban AE, Montgomery SB, Levinson DF, Koller D. Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals. Genome Res 2013. [PMID: 24092820 DOI: 10.1101/gr.155192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Understanding the consequences of regulatory variation in the human genome remains a major challenge, with important implications for understanding gene regulation and interpreting the many disease-risk variants that fall outside of protein-coding regions. Here, we provide a direct window into the regulatory consequences of genetic variation by sequencing RNA from 922 genotyped individuals. We present a comprehensive description of the distribution of regulatory variation--by the specific expression phenotypes altered, the properties of affected genes, and the genomic characteristics of regulatory variants. We detect variants influencing expression of over ten thousand genes, and through the enhanced resolution offered by RNA-sequencing, for the first time we identify thousands of variants associated with specific phenotypes including splicing and allelic expression. Evaluating the effects of both long-range intra-chromosomal and trans (cross-chromosomal) regulation, we observe modularity in the regulatory network, with three-dimensional chromosomal configuration playing a particular role in regulatory modules within each chromosome. We also observe a significant depletion of regulatory variants affecting central and critical genes, along with a trend of reduced effect sizes as variant frequency increases, providing evidence that purifying selection and buffering have limited the deleterious impact of regulatory variation on the cell. Further, generalizing beyond observed variants, we have analyzed the genomic properties of variants associated with expression and splicing and developed a Bayesian model to predict regulatory consequences of genetic variants, applicable to the interpretation of individual genomes and disease studies. Together, these results represent a critical step toward characterizing the complete landscape of human regulatory variation.
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Affiliation(s)
- Alexis Battle
- Department of Computer Science, Stanford University, Stanford, California 94305, USA
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121
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Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals. Genome Res 2013; 24:14-24. [PMID: 24092820 PMCID: PMC3875855 DOI: 10.1101/gr.155192.113] [Citation(s) in RCA: 381] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Understanding the consequences of regulatory variation in the human genome remains a major challenge, with important implications for understanding gene regulation and interpreting the many disease-risk variants that fall outside of protein-coding regions. Here, we provide a direct window into the regulatory consequences of genetic variation by sequencing RNA from 922 genotyped individuals. We present a comprehensive description of the distribution of regulatory variation—by the specific expression phenotypes altered, the properties of affected genes, and the genomic characteristics of regulatory variants. We detect variants influencing expression of over ten thousand genes, and through the enhanced resolution offered by RNA-sequencing, for the first time we identify thousands of variants associated with specific phenotypes including splicing and allelic expression. Evaluating the effects of both long-range intra-chromosomal and trans (cross-chromosomal) regulation, we observe modularity in the regulatory network, with three-dimensional chromosomal configuration playing a particular role in regulatory modules within each chromosome. We also observe a significant depletion of regulatory variants affecting central and critical genes, along with a trend of reduced effect sizes as variant frequency increases, providing evidence that purifying selection and buffering have limited the deleterious impact of regulatory variation on the cell. Further, generalizing beyond observed variants, we have analyzed the genomic properties of variants associated with expression and splicing and developed a Bayesian model to predict regulatory consequences of genetic variants, applicable to the interpretation of individual genomes and disease studies. Together, these results represent a critical step toward characterizing the complete landscape of human regulatory variation.
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122
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Goel R, Murthy KR, Srikanth SM, Pinto SM, Bhattacharjee M, Kelkar DS, Madugundu AK, Dey G, Mohan SS, Krishna V, Prasad TK, Chakravarti S, Harsha HC, Pandey A. Characterizing the normal proteome of human ciliary body. Clin Proteomics 2013; 10:9. [PMID: 23914977 PMCID: PMC3750387 DOI: 10.1186/1559-0275-10-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 07/16/2013] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The ciliary body is the circumferential muscular tissue located just behind the iris in the anterior chamber of the eye. It plays a pivotal role in the production of aqueous humor, maintenance of the lens zonules and accommodation by changing the shape of the crystalline lens. The ciliary body is the major target of drugs against glaucoma as its inhibition leads to a drop in intraocular pressure. A molecular study of the ciliary body could provide a better understanding about the pathophysiological processes that occur in glaucoma. Thus far, no large-scale proteomic investigation has been reported for the human ciliary body. RESULTS In this study, we have carried out an in-depth LC-MS/MS-based proteomic analysis of normal human ciliary body and have identified 2,815 proteins. We identified a number of proteins that were previously not described in the ciliary body including importin 5 (IPO5), atlastin-2 (ATL2), B-cell receptor associated protein 29 (BCAP29), basigin (BSG), calpain-1 (CAPN1), copine 6 (CPNE6), fibulin 1 (FBLN1) and galectin 1 (LGALS1). We compared the plasma proteome with the ciliary body proteome and found that the large majority of proteins in the ciliary body were also detectable in the plasma while 896 proteins were unique to the ciliary body. We also classified proteins using pathway enrichment analysis and found most of proteins associated with ubiquitin pathway, EIF2 signaling, glycolysis and gluconeogenesis. CONCLUSIONS More than 95% of the identified proteins have not been previously described in the ciliary body proteome. This is the largest catalogue of proteins reported thus far in the ciliary body that should provide new insights into our understanding of the factors involved in maintaining the secretion of aqueous humor. The identification of these proteins will aid in understanding various eye diseases of the anterior segment such as glaucoma and presbyopia.
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Affiliation(s)
- Renu Goel
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India.,Department of Biotechnology, Kuvempu University, Shankaraghatta, Shimoga 577 451, Karnataka, India
| | - Krishna R Murthy
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India.,Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690 525, Kerala, India.,Vittala International Institute Of Ophthalmology, Bangalore 560 085, Karnataka, India
| | - Srinivas M Srikanth
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India.,Centre of Excellence in Bioinformatics, Bioinformatics Centre, School of Life Sciences, Pondicherry University, Puducherry 605 014, India
| | - Sneha M Pinto
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India.,Manipal University, Madhav Nagar, Manipal 576104, Karnataka, India
| | - Mitali Bhattacharjee
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India.,Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690 525, Kerala, India
| | - Dhanashree S Kelkar
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India.,Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690 525, Kerala, India
| | - Anil K Madugundu
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - Gourav Dey
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - Sujatha S Mohan
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India.,Department of Biotechnology, Kuvempu University, Shankaraghatta, Shimoga 577 451, Karnataka, India.,Research Unit for Immunoinformatics, RIKEN Research Center for Allergy and Immunology, RIKEN Yokohama Institute, Kanagawa 230 0045, Japan
| | - Venkatarangaiah Krishna
- Department of Biotechnology, Kuvempu University, Shankaraghatta, Shimoga 577 451, Karnataka, India
| | - Ts Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India.,Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690 525, Kerala, India.,Manipal University, Madhav Nagar, Manipal 576104, Karnataka, India
| | - Shukti Chakravarti
- Johns Hopkins University School of Medicine, Baltimore 21205, MD, USA.,Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Department of Ophthalmology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - H C Harsha
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - Akhilesh Pandey
- Johns Hopkins University School of Medicine, Baltimore 21205, MD, USA.,McKusick-Nathans Institute of Genetic Medicine, Departments of Biological Chemistry, Oncology and Pathology, Johns Hopkins University School of Medicine, Baltimore 21205, MD, USA
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123
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Stress response and adaptation: A new molecular toolkit for the 21st century. Comp Biochem Physiol A Mol Integr Physiol 2013; 165:417-28. [DOI: 10.1016/j.cbpa.2013.01.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 01/15/2013] [Accepted: 01/17/2013] [Indexed: 12/18/2022]
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124
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Kortenhorst MSQ, Wissing MD, Rodríguez R, Kachhap SK, Jans JJM, Van der Groep P, Verheul HMW, Gupta A, Aiyetan PO, van der Wall E, Carducci MA, Van Diest PJ, Marchionni L. Analysis of the genomic response of human prostate cancer cells to histone deacetylase inhibitors. Epigenetics 2013; 8:907-20. [PMID: 23880963 DOI: 10.4161/epi.25574] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Histone deacetylases (HDACs) have emerged as important targets for cancer treatment. HDAC-inhibitors (HDACis) are well tolerated in patients and have been approved for the treatment of patients with cutaneous T-cell lymphoma (CTCL). To improve the clinical benefit of HDACis in solid tumors, combination strategies with HDACis could be employed. In this study, we applied Analysis of Functional Annotation (AFA) to provide a comprehensive list of genes and pathways affected upon HDACi-treatment in prostate cancer cells. This approach provides an unbiased and objective approach to high throughput data mining. By performing AFA on gene expression data from prostate cancer cell lines DU-145 (an HDACi-sensitive cell line) and PC3 (a relatively HDACi-resistant cell line) treated with HDACis valproic acid or vorinostat, we identified biological processes that are affected by HDACis and are therefore potential treatment targets for combination therapy. Our analysis revealed that HDAC-inhibition resulted among others in upregulation of major histocompatibility complex (MHC) genes and deregulation of the mitotic spindle checkpoint by downregulation of genes involved in mitosis. These findings were confirmed by AFA on publicly available data sets from HDACi-treated prostate cancer cells. In total, we analyzed 375 microarrays with HDACi treated and non-treated (control) prostate cancer cells. All results from this extensive analysis are provided as an online research source (available at the journal's website and at http://luigimarchionni.org/HDACIs.html). By publishing this data, we aim to enhance our understanding of the cellular changes after HDAC-inhibition, and to identify novel potential combination strategies with HDACis for the treatment of prostate cancer patients.
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Affiliation(s)
- Madeleine S Q Kortenhorst
- Department of Gynecology; Catharina Hospital Eindhoven; Eindhoven, The Netherlands; Prostate Cancer Program; Sidney Kimmel Comprehensive Cancer Center; Johns Hopkins University School of Medicine; Baltimore, MD USA; These authors contributed equally to this work
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125
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Dey G, Radhakrishnan A, Syed N, Thomas JK, Nadig A, Srikumar K, Mathur PP, Pandey A, Lin SK, Raju R, Prasad TSK. Signaling network of Oncostatin M pathway. J Cell Commun Signal 2013; 7:103-8. [PMID: 23255051 PMCID: PMC3660694 DOI: 10.1007/s12079-012-0186-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 12/03/2012] [Indexed: 12/23/2022] Open
Affiliation(s)
- Gourav Dey
- />Institute of Bioinformatics, International Tech Park, Whitefield, Bangalore, 560 066 India
| | - Aneesha Radhakrishnan
- />Institute of Bioinformatics, International Tech Park, Whitefield, Bangalore, 560 066 India
- />Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, 605 014 India
| | - Nazia Syed
- />Institute of Bioinformatics, International Tech Park, Whitefield, Bangalore, 560 066 India
- />Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, 605 014 India
| | - Joji Kurian Thomas
- />Institute of Bioinformatics, International Tech Park, Whitefield, Bangalore, 560 066 India
- />School of Biotechnology, Amrita Vishwa Vidhyapeetam, Kollam, 690 525 India
| | - Arpitha Nadig
- />Department of Bioinformatics, Kuvempu University, Karnataka Shankaraghatta, 577 451 India
| | - Kotteazeth Srikumar
- />Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, 605 014 India
| | - Premendu Prakash Mathur
- />Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, 605 014 India
- />KIIT University, Bhubaneswar, 751 024 India
| | - Akhilesh Pandey
- />McKusick-Nathans Institute of Genetic Medicine and Departments of Biological Chemistry, Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Sze-Kwan Lin
- />School of Dentistry, College of Medicine, National Taiwan University, 1 Chang-Te Street, Taipei, 10016 Taiwan
| | - Rajesh Raju
- />Institute of Bioinformatics, International Tech Park, Whitefield, Bangalore, 560 066 India
| | - T. S. Keshava Prasad
- />Institute of Bioinformatics, International Tech Park, Whitefield, Bangalore, 560 066 India
- />School of Biotechnology, Amrita Vishwa Vidhyapeetam, Kollam, 690 525 India
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126
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Csermely P, Korcsmáros T, Kiss HJM, London G, Nussinov R. Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. Pharmacol Ther 2013; 138:333-408. [PMID: 23384594 PMCID: PMC3647006 DOI: 10.1016/j.pharmthera.2013.01.016] [Citation(s) in RCA: 512] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 01/22/2013] [Indexed: 02/02/2023]
Abstract
Despite considerable progress in genome- and proteome-based high-throughput screening methods and in rational drug design, the increase in approved drugs in the past decade did not match the increase of drug development costs. Network description and analysis not only give a systems-level understanding of drug action and disease complexity, but can also help to improve the efficiency of drug design. We give a comprehensive assessment of the analytical tools of network topology and dynamics. The state-of-the-art use of chemical similarity, protein structure, protein-protein interaction, signaling, genetic interaction and metabolic networks in the discovery of drug targets is summarized. We propose that network targeting follows two basic strategies. The "central hit strategy" selectively targets central nodes/edges of the flexible networks of infectious agents or cancer cells to kill them. The "network influence strategy" works against other diseases, where an efficient reconfiguration of rigid networks needs to be achieved by targeting the neighbors of central nodes/edges. It is shown how network techniques can help in the identification of single-target, edgetic, multi-target and allo-network drug target candidates. We review the recent boom in network methods helping hit identification, lead selection optimizing drug efficacy, as well as minimizing side-effects and drug toxicity. Successful network-based drug development strategies are shown through the examples of infections, cancer, metabolic diseases, neurodegenerative diseases and aging. Summarizing >1200 references we suggest an optimized protocol of network-aided drug development, and provide a list of systems-level hallmarks of drug quality. Finally, we highlight network-related drug development trends helping to achieve these hallmarks by a cohesive, global approach.
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Affiliation(s)
- Peter Csermely
- Department of Medical Chemistry, Semmelweis University, P.O. Box 260, H-1444 Budapest 8, Hungary.
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127
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Iacucci E, Tranchevent LC, Popovic D, Pavlopoulos GA, De Moor B, Schneider R, Moreau Y. ReLiance: a machine learning and literature-based prioritization of receptor--ligand pairings. ACTA ACUST UNITED AC 2013; 28:i569-i574. [PMID: 22962483 PMCID: PMC3436818 DOI: 10.1093/bioinformatics/bts391] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Motivation: The prediction of receptor—ligand pairings is an important area of research as intercellular communications are mediated by the successful interaction of these key proteins. As the exhaustive assaying of receptor—ligand pairs is impractical, a computational approach to predict pairings is necessary. We propose a workflow to carry out this interaction prediction task, using a text mining approach in conjunction with a state of the art prediction method, as well as a widely accessible and comprehensive dataset. Among several modern classifiers, random forests have been found to be the best at this prediction task. The training of this classifier was carried out using an experimentally validated dataset of Database of Ligand-Receptor Partners (DLRP) receptor—ligand pairs. New examples, co-cited with the training receptors and ligands, are then classified using the trained classifier. After applying our method, we find that we are able to successfully predict receptor—ligand pairs within the GPCR family with a balanced accuracy of 0.96. Upon further inspection, we find several supported interactions that were not present in the Database of Interacting Proteins (DIPdatabase). We have measured the balanced accuracy of our method resulting in high quality predictions stored in the available database ReLiance. Availability:http://homes.esat.kuleuven.be/~bioiuser/ReLianceDB/index.php Contact:yves.moreau@esat.kuleuven.be; ernesto.iacucci@gmail.com Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ernesto Iacucci
- IBBT Future Health Department/ESAT-SCD, KU Leuven, Kasteelpark Arenberg 10, 3001, Heverlee-Leuven, Belgium.
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Sandhya VK, Raju R, Verma R, Advani J, Sharma R, Radhakrishnan A, Nanjappa V, Narayana J, Somani BL, Mukherjee KK, Pandey A, Christopher R, Prasad TSK. A network map of BDNF/TRKB and BDNF/p75NTR signaling system. J Cell Commun Signal 2013; 7:301-7. [PMID: 23606317 DOI: 10.1007/s12079-013-0200-z] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 04/09/2013] [Indexed: 01/15/2023] Open
Affiliation(s)
- Varot K Sandhya
- Institute of Bioinformatics, International Tech Park, Whitefield, Bangalore, 560066, India,
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de Matos P, Cham JA, Cao H, Alcántara R, Rowland F, Lopez R, Steinbeck C. The Enzyme Portal: a case study in applying user-centred design methods in bioinformatics. BMC Bioinformatics 2013; 14:103. [PMID: 23514033 PMCID: PMC3623738 DOI: 10.1186/1471-2105-14-103] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Accepted: 02/08/2013] [Indexed: 11/29/2022] Open
Abstract
User-centred design (UCD) is a type of user interface design in which the needs and desires of users are taken into account at each stage of the design process for a service or product; often for software applications and websites. Its goal is to facilitate the design of software that is both useful and easy to use. To achieve this, you must characterise users' requirements, design suitable interactions to meet their needs, and test your designs using prototypes and real life scenarios.For bioinformatics, there is little practical information available regarding how to carry out UCD in practice. To address this we describe a complete, multi-stage UCD process used for creating a new bioinformatics resource for integrating enzyme information, called the Enzyme Portal (http://www.ebi.ac.uk/enzymeportal). This freely-available service mines and displays data about proteins with enzymatic activity from public repositories via a single search, and includes biochemical reactions, biological pathways, small molecule chemistry, disease information, 3D protein structures and relevant scientific literature.We employed several UCD techniques, including: persona development, interviews, 'canvas sort' card sorting, user workflows, usability testing and others. Our hope is that this case study will motivate the reader to apply similar UCD approaches to their own software design for bioinformatics. Indeed, we found the benefits included more effective decision-making for design ideas and technologies; enhanced team-working and communication; cost effectiveness; and ultimately a service that more closely meets the needs of our target audience.
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Affiliation(s)
- Paula de Matos
- EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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130
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Subbannayya T, Balakrishnan L, Sudarshan G, Advani J, Kumar S, Mahmood R, Nair B, Sirdeshmukh R, Mukherjee KK, Umathe SN, Raju R, Prasad TSK. An integrated map of corticotropin-releasing hormone signaling pathway. J Cell Commun Signal 2013; 7:295-300. [PMID: 23504413 DOI: 10.1007/s12079-013-0197-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 03/01/2013] [Indexed: 01/17/2023] Open
Affiliation(s)
- Tejaswini Subbannayya
- Institute of Bioinformatics, International Technology Park, Whitefield, Bangalore, 560 066, India,
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131
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Functional site plasticity in domain superfamilies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:874-89. [PMID: 23499848 PMCID: PMC3787744 DOI: 10.1016/j.bbapap.2013.02.042] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 02/20/2013] [Accepted: 02/28/2013] [Indexed: 11/21/2022]
Abstract
We present, to our knowledge, the first quantitative analysis of functional site diversity in homologous domain superfamilies. Different types of functional sites are considered separately. Our results show that most diverse superfamilies are very plastic in terms of the spatial location of their functional sites. This is especially true for protein–protein interfaces. In contrast, we confirm that catalytic sites typically occupy only a very small number of topological locations. Small-ligand binding sites are more diverse than expected, although in a more limited manner than protein–protein interfaces. In spite of the observed diversity, our results also confirm the previously reported preferential location of functional sites. We identify a subset of homologous domain superfamilies where diversity is particularly extreme, and discuss possible reasons for such plasticity, i.e. structural diversity. Our results do not contradict previous reports of preferential co-location of sites among homologues, but rather point at the importance of not ignoring other sites, especially in large and diverse superfamilies. Data on sites exploited by different relatives, within each well annotated domain superfamily, has been made accessible from the CATH website in order to highlight versatile superfamilies or superfamilies with highly preferential sites. This information is valuable for system biology and knowledge of any constraints on protein interactions could help in understanding the dynamic control of networks in which these proteins participate. The novelty of our work lies in the comprehensive nature of the analysis – we have used a significantly larger dataset than previous studies – and the fact that in many superfamilies we show that different parts of the domain surface are exploited by different relatives for ligand/protein interactions, particularly in superfamilies which are diverse in sequence and structure, an observation not previously reported on such a large scale. This article is part of a Special Issue entitled: The emerging dynamic view of proteins: Protein plasticity in allostery, evolution and self-assembly. Most diverse domain superfamilies have very diverse functional site locations. Catalytic sites are found in a small, restricted number of topological positions. Location of small-ligand binding sites is more diverse than expected. Protein–protein interfaces display the most flexibility in functional site locations.
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132
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Vandermarliere E, Martens L. Protein structure as a means to triage proposed PTM sites. Proteomics 2013; 13:1028-35. [PMID: 23172737 DOI: 10.1002/pmic.201200232] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 08/13/2012] [Accepted: 09/05/2012] [Indexed: 11/07/2022]
Abstract
PTMs such as phosphorylation are often important actors in protein regulation and recognition. These functions require both visibility and accessibility to other proteins; that the modification is located at the surface of the protein. Currently, many repositories provide information on PTMs but structural information is often lacking. This study, which focuses on phosphorylation sites available in UniProtKB/Swiss-Prot, illustrates that most phosphorylation sites are indeed found at the surface of the protein, but that some sites are found buried in the core of the protein. Several of these identified buried phosphorylation sites can easily become accessible upon small conformational changes while others would require the whole protein to unfold and are hence most unlikely modification sites. Subsequent analysis of phosphorylation sites available in PRIDE demonstrates that taking the structure of the protein into account would be a good guide in the identification of the actual phosphorylated positions in phophoproteomics experiments. This analysis illustrates that care must be taken when simply accepting the position of a PTM without first analyzing its position within the protein structure if the latter is available.
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Affiliation(s)
- Elien Vandermarliere
- Department of Medical Protein Research, VIB, Ghent, Belgium; Department of Biochemistry, Ghent University, Ghent, Belgium
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133
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Singh H, Farouk M, Bose BB, Singh P. Novel genes underlying beta cell survival in metabolic stress. Bioinformation 2013; 9:37-41. [PMID: 23390342 PMCID: PMC3563414 DOI: 10.6026/97320630009037] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Accepted: 12/26/2012] [Indexed: 02/07/2023] Open
Abstract
Relative insulin deficiency, in response to increased metabolic demand (obesity, genetic insulin resistance, pregnancy and aging) lead to Type2 diabetes. Susceptibility of the type 2 diabetes has a genetic basis, as a subset of people with risk factors (obesity, Insulin Resistance, pregnancy), develop Type2 Diabetes. We aimed to identify 'cluster' of overexpressed genes, underlying increased beta cell survival in diabetes resistant C57BL/6J ob/ob mice (compared to diabetes susceptible BTBR ob/ob mice). We used 'consensus' overexpression status to identify 'cluster' of 11 genes consisting of Aldh18a1, Rfc4, Dynlt3, Prom1, H13, Psen1, Ssr4, Dad1, Anpep, Fam111a and Plk1. Information (biological processes, molecular functions, cellular components, protein-protein interactions/associations, gene deletion/knockout/inhibition studies) of all the genes in 'cluster' were collected by text mining using different literature search tools, gene information databases and protein-protein interaction databases. Beta cell specific function of these genes were also inferred using meta analysis tool of Beta Cell Biology Consortium, by studying the expression pattern of these genes in microarray studies related to beta-cell stimulation/injury, pancreas development and growth and cell differentiation. In the 'clusters', 6 genes (Dad1, Psen1, Ssr4, Rfc4, H13, Plk1) have a role in cell survival. Only Psen1 was previously identified to have role in successful beta cell compensation. We advocate these genes to be potentially involved in successful beta cell compensation and prevent T2D in humans, by conferring protection against diabetogenic insults.
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Affiliation(s)
- Himadri Singh
- Sevayan Medical and Research Centre, Dr BG Bose Lane, Munger, 811201, India
| | - Mohammed Farouk
- Institute of Liver Disease and Transplantation, Global Hospitals, Chennai, India
| | - Barish Baran Bose
- Sevayan Medical and Research Centre, Dr BG Bose Lane, Munger, 811201, India
| | - Prabhakar Singh
- Sevayan Medical and Research Centre, Dr BG Bose Lane, Munger, 811201, India
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134
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Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, von Mering C, Jensen LJ. STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res 2013; 41:D808-15. [PMID: 23203871 PMCID: PMC3531103 DOI: 10.1093/nar/gks1094] [Citation(s) in RCA: 3246] [Impact Index Per Article: 295.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2012] [Revised: 10/15/2012] [Accepted: 10/18/2012] [Indexed: 12/12/2022] Open
Abstract
Complete knowledge of all direct and indirect interactions between proteins in a given cell would represent an important milestone towards a comprehensive description of cellular mechanisms and functions. Although this goal is still elusive, considerable progress has been made-particularly for certain model organisms and functional systems. Currently, protein interactions and associations are annotated at various levels of detail in online resources, ranging from raw data repositories to highly formalized pathway databases. For many applications, a global view of all the available interaction data is desirable, including lower-quality data and/or computational predictions. The STRING database (http://string-db.org/) aims to provide such a global perspective for as many organisms as feasible. Known and predicted associations are scored and integrated, resulting in comprehensive protein networks covering >1100 organisms. Here, we describe the update to version 9.1 of STRING, introducing several improvements: (i) we extend the automated mining of scientific texts for interaction information, to now also include full-text articles; (ii) we entirely re-designed the algorithm for transferring interactions from one model organism to the other; and (iii) we provide users with statistical information on any functional enrichment observed in their networks.
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Affiliation(s)
- Andrea Franceschini
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Switzerland, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark, Biotechnology Center, Technical University Dresden, Germany, Department of Computer Science, University of Milan, Italy, European Molecular Biology Laboratory, Heidelberg and Max-Delbrück-Centre for Molecular Medicine, Berlin, Germany
| | - Damian Szklarczyk
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Switzerland, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark, Biotechnology Center, Technical University Dresden, Germany, Department of Computer Science, University of Milan, Italy, European Molecular Biology Laboratory, Heidelberg and Max-Delbrück-Centre for Molecular Medicine, Berlin, Germany
| | - Sune Frankild
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Switzerland, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark, Biotechnology Center, Technical University Dresden, Germany, Department of Computer Science, University of Milan, Italy, European Molecular Biology Laboratory, Heidelberg and Max-Delbrück-Centre for Molecular Medicine, Berlin, Germany
| | - Michael Kuhn
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Switzerland, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark, Biotechnology Center, Technical University Dresden, Germany, Department of Computer Science, University of Milan, Italy, European Molecular Biology Laboratory, Heidelberg and Max-Delbrück-Centre for Molecular Medicine, Berlin, Germany
| | - Milan Simonovic
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Switzerland, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark, Biotechnology Center, Technical University Dresden, Germany, Department of Computer Science, University of Milan, Italy, European Molecular Biology Laboratory, Heidelberg and Max-Delbrück-Centre for Molecular Medicine, Berlin, Germany
| | - Alexander Roth
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Switzerland, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark, Biotechnology Center, Technical University Dresden, Germany, Department of Computer Science, University of Milan, Italy, European Molecular Biology Laboratory, Heidelberg and Max-Delbrück-Centre for Molecular Medicine, Berlin, Germany
| | - Jianyi Lin
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Switzerland, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark, Biotechnology Center, Technical University Dresden, Germany, Department of Computer Science, University of Milan, Italy, European Molecular Biology Laboratory, Heidelberg and Max-Delbrück-Centre for Molecular Medicine, Berlin, Germany
| | - Pablo Minguez
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Switzerland, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark, Biotechnology Center, Technical University Dresden, Germany, Department of Computer Science, University of Milan, Italy, European Molecular Biology Laboratory, Heidelberg and Max-Delbrück-Centre for Molecular Medicine, Berlin, Germany
| | - Peer Bork
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Switzerland, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark, Biotechnology Center, Technical University Dresden, Germany, Department of Computer Science, University of Milan, Italy, European Molecular Biology Laboratory, Heidelberg and Max-Delbrück-Centre for Molecular Medicine, Berlin, Germany
| | - Christian von Mering
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Switzerland, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark, Biotechnology Center, Technical University Dresden, Germany, Department of Computer Science, University of Milan, Italy, European Molecular Biology Laboratory, Heidelberg and Max-Delbrück-Centre for Molecular Medicine, Berlin, Germany
| | - Lars J. Jensen
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Switzerland, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark, Biotechnology Center, Technical University Dresden, Germany, Department of Computer Science, University of Milan, Italy, European Molecular Biology Laboratory, Heidelberg and Max-Delbrück-Centre for Molecular Medicine, Berlin, Germany
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135
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De Arras L, Seng A, Lackford B, Keikhaee MR, Bowerman B, Freedman JH, Schwartz DA, Alper S. An evolutionarily conserved innate immunity protein interaction network. J Biol Chem 2012; 288:1967-78. [PMID: 23209288 DOI: 10.1074/jbc.m112.407205] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The innate immune response plays a critical role in fighting infection; however, innate immunity also can affect the pathogenesis of a variety of diseases, including sepsis, asthma, cancer, and atherosclerosis. To identify novel regulators of innate immunity, we performed comparative genomics RNA interference screens in the nematode Caenorhabditis elegans and mouse macrophages. These screens have uncovered many candidate regulators of the response to lipopolysaccharide (LPS), several of which interact physically in multiple species to form an innate immunity protein interaction network. This protein interaction network contains several proteins in the canonical LPS-responsive TLR4 pathway as well as many novel interacting proteins. Using RNAi and overexpression studies, we show that almost every gene in this network can modulate the innate immune response in mouse cell lines. We validate the importance of this network in innate immunity regulation in vivo using available mutants in C. elegans and mice.
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Affiliation(s)
- Lesly De Arras
- Integrated Department of Immunology, National Jewish Health and University of Colorado, Denver, Colorado 80206, USA
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136
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Knepper MA. Systems biology in physiology: the vasopressin signaling network in kidney. Am J Physiol Cell Physiol 2012; 303:C1115-24. [PMID: 22932685 DOI: 10.1152/ajpcell.00270.2012] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Over the past 80 years, physiological research has moved progressively in a reductionist direction, providing mechanistic information on a smaller and smaller scale. This trend has culminated in the present focus on "molecular physiology," which deals with the function of single molecules responsible for cellular function. There is a need to assemble the information from the molecular level into models that explain physiological function at cellular, tissue, organ, and whole organism levels. Such integration is the major focus of an approach called "systems biology." The genome sequencing projects provide a basis for a new kind of systems biology called "data-rich" systems biology that is based on large-scale data acquisition methods including protein mass spectrometry, DNA microarrays, and deep sequencing of nucleic acids. These techniques allow investigators to measure thousands of variables simultaneously in response to an external stimulus. My laboratory is applying such an approach to the question: "How does the peptide hormone vasopressin regulate water permeability in the renal collecting duct?" We are using protein mass spectrometry to identify and quantify the phosphoproteome of collecting duct cells. The response to vasopressin, presented in the form of a network model, includes a general downregulation of proline-directed kinases (MAP kinases and cyclin-dependent kinases) and upregulation of basophilic kinases (ACG kinases and calmodulin-dependent kinases). Further progress depends on characterization and localization of candidate protein kinases in these families. The ultimate goal is to use multivariate statistical techniques and differential equations to obtain predictive models describing vasopressin signaling in the renal collecting duct.
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Affiliation(s)
- Mark A Knepper
- National Institutes of Health, 10 Center Dr., Bldg. 10, Rm. 6N260, Bethesda, MD 20892-1603,USA.
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137
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Creamer MS, Stites EC, Aziz M, Cahill JA, Tan CW, Berens ME, Han H, Bussey KJ, Von Hoff DD, Hlavacek WS, Posner RG. Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling. BMC SYSTEMS BIOLOGY 2012; 6:107. [PMID: 22913808 PMCID: PMC3485121 DOI: 10.1186/1752-0509-6-107] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Accepted: 08/02/2012] [Indexed: 12/21/2022]
Abstract
BACKGROUND Mathematical/computational models are needed to understand cell signaling networks, which are complex. Signaling proteins contain multiple functional components and multiple sites of post-translational modification. The multiplicity of components and sites of modification ensures that interactions among signaling proteins have the potential to generate myriad protein complexes and post-translational modification states. As a result, the number of chemical species that can be populated in a cell signaling network, and hence the number of equations in an ordinary differential equation model required to capture the dynamics of these species, is prohibitively large. To overcome this problem, the rule-based modeling approach has been developed for representing interactions within signaling networks efficiently and compactly through coarse-graining of the chemical kinetics of molecular interactions. RESULTS Here, we provide a demonstration that the rule-based modeling approach can be used to specify and simulate a large model for ERBB receptor signaling that accounts for site-specific details of protein-protein interactions. The model is considered large because it corresponds to a reaction network containing more reactions than can be practically enumerated. The model encompasses activation of ERK and Akt, and it can be simulated using a network-free simulator, such as NFsim, to generate time courses of phosphorylation for 55 individual serine, threonine, and tyrosine residues. The model is annotated and visualized in the form of an extended contact map. CONCLUSIONS With the development of software that implements novel computational methods for calculating the dynamics of large-scale rule-based representations of cellular signaling networks, it is now possible to build and analyze models that include a significant fraction of the protein interactions that comprise a signaling network, with incorporation of the site-specific details of the interactions. Modeling at this level of detail is important for understanding cellular signaling.
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Affiliation(s)
- Matthew S Creamer
- Clinical Translational Research Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
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138
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Prabakaran S, Lippens G, Steen H, Gunawardena J. Post-translational modification: nature's escape from genetic imprisonment and the basis for dynamic information encoding. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2012; 4:565-83. [PMID: 22899623 DOI: 10.1002/wsbm.1185] [Citation(s) in RCA: 223] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
We discuss protein post-translational modification (PTM) from an information processing perspective. PTM at multiple sites on a protein creates a combinatorial explosion in the number of potential 'mod-forms', or global patterns of modification. Distinct mod-forms can elicit distinct downstream responses, so that the overall response depends partly on the effectiveness of a particular mod-form to elicit a response and partly on the stoichiometry of that mod-form in the molecular population. We introduce the 'mod-form distribution'-the relative stoichiometries of each mod-form-as the most informative measure of a protein's state. Distinct mod-form distributions may summarize information about distinct cellular and physiological conditions and allow downstream processes to interpret this information accordingly. Such information 'encoding' by PTMs may facilitate evolution by weakening the need to directly link upstream conditions to downstream responses. Mod-form distributions provide a quantitative framework in which to interpret ideas of 'PTM codes' that are emerging in several areas of biology, as we show by reviewing examples of ion channels, GPCRs, microtubules, and transcriptional co-regulators. We focus particularly on examples other than the well-known 'histone code', to emphasize the pervasive use of information encoding in molecular biology. Finally, we touch briefly on new methods for measuring mod-form distributions.
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139
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Reimand J, Hui S, Jain S, Law B, Bader GD. Domain-mediated protein interaction prediction: From genome to network. FEBS Lett 2012; 586:2751-63. [PMID: 22561014 DOI: 10.1016/j.febslet.2012.04.027] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2012] [Accepted: 04/17/2012] [Indexed: 11/19/2022]
Abstract
Protein-protein interactions (PPIs), involved in many biological processes such as cellular signaling, are ultimately encoded in the genome. Solving the problem of predicting protein interactions from the genome sequence will lead to increased understanding of complex networks, evolution and human disease. We can learn the relationship between genomes and networks by focusing on an easily approachable subset of high-resolution protein interactions that are mediated by peptide recognition modules (PRMs) such as PDZ, WW and SH3 domains. This review focuses on computational prediction and analysis of PRM-mediated networks and discusses sequence- and structure-based interaction predictors, techniques and datasets for identifying physiologically relevant PPIs, and interpreting high-resolution interaction networks in the context of evolution and human disease.
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Affiliation(s)
- Jüri Reimand
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario, Canada.
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140
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Zizak M, Chen T, Bartonicek D, Sarker R, Zachos NC, Cha B, Kovbasnjuk O, Korac J, Mohan S, Cole R, Chen Y, Tse CM, Donowitz M. Calmodulin kinase II constitutively binds, phosphorylates, and inhibits brush border Na+/H+ exchanger 3 (NHE3) by a NHERF2 protein-dependent process. J Biol Chem 2012; 287:13442-56. [PMID: 22371496 DOI: 10.1074/jbc.m111.307256] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The epithelial brush border (BB) Na(+)/H(+) exchanger 3 (NHE3) accounts for most renal and intestinal Na(+) absorption. Ca(2+)/calmodulin-dependent protein kinase II (CaMKII) inhibits NHE3 activity under basal conditions in intact intestine, acting in the BB, but the mechanism is unclear. We now demonstrate that in both PS120 fibroblasts and polarized Caco-2BBe cells expressing NHE3, CaMKII inhibits basal NHE3 activity, because the CaMKII-specific inhibitors KN-93 and KN-62 stimulate NHE3 activity. This inhibition requires NHERF2. CaMKIIγ associates with NHE3 between aa 586 and 605 in the NHE3 C terminus in a Ca(2+)-dependent manner, with less association when Ca(2+) is increased. CaMKII inhibits NHE3 by an effect on its turnover number, not changing surface expression. Back phosphorylation demonstrated that NHE3 is phosphorylated by CaMKII under basal conditions. This overall phosphorylation of NHE3 is not affected by the presence of NHERF2. Amino acids downstream of NHE3 aa 690 are required for CaMKII to inhibit basal NHE3 activity, and mutations of the three putative CaMKII phosphorylation sites downstream of aa 690 each prevented KN-93 stimulation of NHE3 activity. These studies demonstrate that CaMKIIγ is a novel NHE3-binding protein, and this association is reduced by elevated Ca(2+). CaMKII inhibits basal NHE3 activity associated with phosphorylation of NHE3 by effects requiring aa downstream of NHE3 aa 690 and of the CaMKII-binding site on NHE3. CaMKII binding to and phosphorylation of the NHE3 C terminus are parts of the physiologic regulation of NHE3 that occurs in fibroblasts as well as in the BB of an intestinal Na(+)-absorptive cell.
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Affiliation(s)
- Mirza Zizak
- Division of Gastroenterology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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