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Investigation of Anti-Liver Cancer Activity of the Herbal Drug FDY003 Using Network Pharmacology. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:5765233. [PMID: 36118098 PMCID: PMC9481369 DOI: 10.1155/2022/5765233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 08/10/2022] [Indexed: 11/18/2022]
Abstract
Globally, liver cancer (LC) is the sixth-most frequently occurring and the second-most fatal malignancy, responsible for 0.83 million deaths annually. Although the application of herbal drugs in cancer therapies has increased, their anti-LC activity and relevant mechanisms have not been fully studied from a systems perspective. To address these issues, we conducted a system-perspective network pharmacological investigation into the activity and mechanisms underlying the action of the herbal drug. FDY003 reduced the viability of human LC treatment. FDY003 reduced the viability of human LC cells and elevated their chemosensitivity. There were a total of 16 potential bioactive chemical components in FDY003 and they had 91 corresponding targets responsible for the pathological processes in LC. These FDY003 targets were functionally involved in regulating the survival, proliferation, apoptosis, and cell cycle of LC cells. Additionally, we found that FDY003 may target key signaling cascades connected to diverse LC pathological mechanisms, namely, PI3K-Akt, focal adhesion, IL-17, FoxO, MAPK, and TNF pathways. Overall, this study contributed to integrative mechanistic insights into the anti-LC potential of FDY003.
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In silico Methods for Identification of Potential Therapeutic Targets. Interdiscip Sci 2022; 14:285-310. [PMID: 34826045 PMCID: PMC8616973 DOI: 10.1007/s12539-021-00491-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 10/19/2021] [Accepted: 11/01/2021] [Indexed: 11/01/2022]
Abstract
AbstractAt the initial stage of drug discovery, identifying novel targets with maximal efficacy and minimal side effects can improve the success rate and portfolio value of drug discovery projects while simultaneously reducing cycle time and cost. However, harnessing the full potential of big data to narrow the range of plausible targets through existing computational methods remains a key issue in this field. This paper reviews two categories of in silico methods—comparative genomics and network-based methods—for finding potential therapeutic targets among cellular functions based on understanding their related biological processes. In addition to describing the principles, databases, software, and applications, we discuss some recent studies and prospects of the methods. While comparative genomics is mostly applied to infectious diseases, network-based methods can be applied to infectious and non-infectious diseases. Nonetheless, the methods often complement each other in their advantages and disadvantages. The information reported here guides toward improving the application of big data-driven computational methods for therapeutic target discovery.
Graphical abstract
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3
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Li M, Lu Z, Wu Y, Li Y. BACPI: a bi-directional attention neural network for compound-protein interaction and binding affinity prediction. Bioinformatics 2022; 38:1995-2002. [PMID: 35043942 DOI: 10.1093/bioinformatics/btac035] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/06/2021] [Accepted: 01/14/2022] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION The identification of compound-protein interactions (CPIs) is an essential step in the process of drug discovery. The experimental determination of CPIs is known for a large amount of funds and time it consumes. Computational model has therefore become a promising and efficient alternative for predicting novel interactions between compounds and proteins on a large scale. Most supervised machine learning prediction models are approached as a binary classification problem, which aim to predict whether there is an interaction between the compound and the protein or not. However, CPI is not a simple binary on-off relationship, but a continuous value reflects how tightly the compound binds to a particular target protein, also called binding affinity. RESULTS In this study, we propose an end-to-end neural network model, called BACPI, to predict CPI and binding affinity. We employ graph attention network and convolutional neural network (CNN) to learn the representations of compounds and proteins and develop a bi-directional attention neural network model to integrate the representations. To evaluate the performance of BACPI, we use three CPI datasets and four binding affinity datasets in our experiments. The results show that, when predicting CPIs, BACPI significantly outperforms other available machine learning methods on both balanced and unbalanced datasets. This suggests that the end-to-end neural network model that predicts CPIs directly from low-level representations is more robust than traditional machine learning-based methods. And when predicting binding affinities, BACPI achieves higher performance on large datasets compared to other state-of-the-art deep learning methods. This comparison result suggests that the proposed method with bi-directional attention neural network can capture the important regions of compounds and proteins for binding affinity prediction. AVAILABILITY AND IMPLEMENTATION Data and source codes are available at https://github.com/CSUBioGroup/BACPI.
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Affiliation(s)
- Min Li
- School of Computer Science and Engineering, Central South University, Changsha, Hunan, 410083, China
| | - Zhangli Lu
- School of Computer Science and Engineering, Central South University, Changsha, Hunan, 410083, China
| | - Yifan Wu
- School of Computer Science and Engineering, Central South University, Changsha, Hunan, 410083, China
| | - YaoHang Li
- Department of Computer Science, Old Dominion University, Norfolk, VA, USA
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4
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Pan Y, Lei X, Zhang Y. Association predictions of genomics, proteinomics, transcriptomics, microbiome, metabolomics, pathomics, radiomics, drug, symptoms, environment factor, and disease networks: A comprehensive approach. Med Res Rev 2021; 42:441-461. [PMID: 34346083 DOI: 10.1002/med.21847] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 05/22/2021] [Accepted: 07/07/2021] [Indexed: 12/12/2022]
Abstract
Currently, the research of multi-omics, such as genomics, proteinomics, transcriptomics, microbiome, metabolomics, pathomics, and radiomics, are hot spots. The relationship between multi-omics data, drugs, and diseases has received extensive attention from researchers. At the same time, multi-omics can effectively predict the diagnosis, prognosis, and treatment of diseases. In essence, these research entities, such as genes, RNAs, proteins, microbes, metabolites, pathways as well as pathological and medical imaging data, can all be represented by the network at different levels. And some computer and biology scholars have tried to use computational methods to explore the potential relationships between biological entities. We summary a comprehensive research strategy, that is to build a multi-omics heterogeneous network, covering multimodal data, and use the current popular computational methods to make predictions. In this study, we first introduce the calculation method of the similarity of biological entities at the data level, second discuss multimodal data fusion and methods of feature extraction. Finally, the challenges and opportunities at this stage are summarized. Some scholars have used such a framework to calculate and predict. We also summarize them and discuss the challenges. We hope that our review could help scholars who are interested in the field of bioinformatics, biomedical image, and computer research.
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Affiliation(s)
- Yi Pan
- Faculty of Computer Science and Control Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xiujuan Lei
- School of Computer Science, Shaanxi Normal University, Xi'an, China
| | - Yuchen Zhang
- School of Computer Science, Shaanxi Normal University, Xi'an, China
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5
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Zhou M, Zheng C, Xu R. Combining phenome-driven drug-target interaction prediction with patients' electronic health records-based clinical corroboration toward drug discovery. Bioinformatics 2021; 36:i436-i444. [PMID: 32657406 PMCID: PMC7355254 DOI: 10.1093/bioinformatics/btaa451] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Motivation Predicting drug–target interactions (DTIs) using human phenotypic data have the potential in eliminating the translational gap between animal experiments and clinical outcomes in humans. One challenge in human phenome-driven DTI predictions is integrating and modeling diverse drug and disease phenotypic relationships. Leveraging large amounts of clinical observed phenotypes of drugs and diseases and electronic health records (EHRs) of 72 million patients, we developed a novel integrated computational drug discovery approach by seamlessly combining DTI prediction and clinical corroboration. Results We developed a network-based DTI prediction system (TargetPredict) by modeling 855 904 phenotypic and genetic relationships among 1430 drugs, 4251 side effects, 1059 diseases and 17 860 genes. We systematically evaluated TargetPredict in de novo cross-validation and compared it to a state-of-the-art phenome-driven DTI prediction approach. We applied TargetPredict in identifying novel repositioned candidate drugs for Alzheimer’s disease (AD), a disease affecting over 5.8 million people in the United States. We evaluated the clinical efficiency of top repositioned drug candidates using EHRs of over 72 million patients. The area under the receiver operating characteristic (ROC) curve was 0.97 in the de novo cross-validation when evaluated using 910 drugs. TargetPredict outperformed a state-of-the-art phenome-driven DTI prediction system as measured by precision–recall curves [measured by average precision (MAP): 0.28 versus 0.23, P-value < 0.0001]. The EHR-based case–control studies identified that the prescriptions top-ranked repositioned drugs are significantly associated with lower odds of AD diagnosis. For example, we showed that the prescription of liraglutide, a type 2 diabetes drug, is significantly associated with decreased risk of AD diagnosis [adjusted odds ratios (AORs): 0.76; 95% confidence intervals (CI) (0.70, 0.82), P-value < 0.0001]. In summary, our integrated approach that seamlessly combines computational DTI prediction and large-scale patients’ EHRs-based clinical corroboration has high potential in rapidly identifying novel drug targets and drug candidates for complex diseases. Availability and implementation nlp.case.edu/public/data/TargetPredict.
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Affiliation(s)
- Mengshi Zhou
- Center for Artificial Intelligence in Drug Discovery, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.,Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Chunlei Zheng
- Center for Artificial Intelligence in Drug Discovery, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Rong Xu
- Center for Artificial Intelligence in Drug Discovery, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
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6
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Wang KX, Gao Y, Gong WX, Ye XF, Fan LY, Wang C, Gao XF, Gao L, Du GH, Qin XM, Lu AP, Guan DG. A Novel Strategy for Decoding and Validating the Combination Principles of Huanglian Jiedu Decoction From Multi-Scale Perspective. Front Pharmacol 2020; 11:567088. [PMID: 33424585 PMCID: PMC7789881 DOI: 10.3389/fphar.2020.567088] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 11/12/2020] [Indexed: 12/12/2022] Open
Abstract
Traditional Chinese medicine (TCM) formulas treat complex diseases through combined botanical drugs which follow specific compatibility rules to reduce toxicity and increase efficiency. "Jun, Chen, Zuo and Shi" is one of most used compatibility rules in the combination of botanical drugs. However, due to the deficiency of traditional research methods, the quantified theoretical basis of herbal compatibility including principles of "Jun, Chen, Zuo and Shi" are still unclear. Network pharmacology is a new strategy based on system biology and multi-disciplines, which can systematically and comprehensively observe the intervention of drugs on disease networks, and is especially suitable for the research of TCM in the treatment of complex diseases. In this study, we systematically decoded the "Jun, Chen, Zuo and Shi" rules of Huanglian Jiedu Decoction (HJD) in the treatment of diseases for the first time. This interpretation method considered three levels of data. The data in the first level mainly depicts the characteristics of each component in single botanical drug of HJD, include the physical and chemical properties of component, ADME properties and functional enrichment analysis of component targets. The second level data is the characterization of component-target-protein (C-T-P) network in the whole protein-protein interaction (PPI) network, mainly include the characterization of degree and key communities in C-T-P network. The third level data is the characterization of intervention propagation properties of HJD in the treatment of different complex diseases, mainly include target coverage of pathogenic genes and propagation coefficient of intervention effect between target proteins and pathogenic genes. Finally, our method was validated by metabolic data, which could be used to detect the components absorbed into blood. This research shows the scientific basis of "Jun-Chen-Zuo-Shi" from a multi-dimensional perspective, and provides a good methodological reference for the subsequent interpretation of key components and speculation mechanism of the formula.
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Affiliation(s)
- Ke-Xin Wang
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, China.,Institute of Integrated Bioinformedicine and Translational Science, Hong Kong Baptist University, Hong Kong, China
| | - Yao Gao
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, China.,Institute of Integrated Bioinformedicine and Translational Science, Hong Kong Baptist University, Hong Kong, China
| | - Wen-Xia Gong
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, China
| | - Xiao-Feng Ye
- Institute of Integrated Bioinformedicine and Translational Science, Hong Kong Baptist University, Hong Kong, China
| | - Liu-Yi Fan
- Department of Orthopaedics and Traumatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Chun Wang
- Institute of Basic Theory for Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xue-Fei Gao
- Department of Physiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Li Gao
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, China
| | - Guan-Hua Du
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, China.,Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xue-Mei Qin
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, China
| | - Ai-Ping Lu
- Institute of Integrated Bioinformedicine and Translational Science, Hong Kong Baptist University, Hong Kong, China
| | - Dao-Gang Guan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Guangdong Key Laboratory of Biochip Technology, Southern Medical University, Guangzhou, China
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7
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Zhou M, Chen Y, Xu R. A Drug-Side Effect Context-Sensitive Network approach for drug target prediction. Bioinformatics 2020; 35:2100-2107. [PMID: 30428013 DOI: 10.1093/bioinformatics/bty906] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 10/05/2018] [Accepted: 11/13/2018] [Indexed: 01/21/2023] Open
Abstract
SUMMARY Computational drug target prediction has become an important process in drug discovery. Network-based approaches are commonly used in computational drug-target interaction (DTI) prediction. Existing network-based approaches are limited in capturing the contextual information on how diseases, drugs and genes are connected. Here, we proposed a context-sensitive network (CSN) model for DTI prediction by modeling contextual drug phenotypic relationships. We constructed a Drug-Side Effect Context-Sensitive Network (DSE-CSN) of 139 760 drug-side effect pairs, representing 1480 drugs and 5868 side effects. We also built a protein-protein interaction network (PPIN) of 15 267 gene nodes and 178 972 weighted edges. A heterogeneous network was built by connecting the DSE-CSN and the PPIN through 3684 known DTIs. For each drug on the DSE-CSN, its genetic targets were predicted and prioritized using a network-based ranking algorithm. Our approach was evaluated in both de novo and leave-one-out cross-validation analysis using known DTIs as the gold standard. We compared our DSE-CSN-based model to the traditional similarity-based network (SBN)-based prediction model. The results suggested that the DSE-CSN-based model was able to rank known DTIs highly. In a de novo cross-validation, the area under the receiver operating characteristic (ROC) curve was 0.95. In a leave-one-out cross-validation, the average rank was top 3.2% for known DTIs. When it was compared to the SBN-based model using the Precision-Recall curve, our CSN-based model achieved a higher mean average precision (MAP) (0.23 versus 0.19, P-value<1e-4) in a de novo cross-validation analysis. We further improved the CSN-based DTI prediction by differentially weighting the drug-side effect pairs on the network and showed a significant improvement of the MAP (0.29 versus 0.23, P-value<1e-4). We also showed that the CSN-based model consistently achieved better performances than the traditional SBN-based model across different drug classes. Moreover, we demonstrated that our novel DTI predictions can be supported by published literature. In summary, the CSN-based model, by modeling the context-specific inter-relationships among drugs and side effects, has a high potential in drug target prediction. AVAILABILITY AND IMPLEMENTATION nlp/case/edu/public/data/DSE/CSN_DTI.
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Affiliation(s)
| | - Yang Chen
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Rong Xu
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
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8
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Liu J, Lian X, Liu F, Yan X, Cheng C, Cheng L, Sun X, Shi Z. Identification of Novel Key Targets and Candidate Drugs in Oral Squamous Cell Carcinoma. Curr Bioinform 2020. [DOI: 10.2174/1574893614666191127101836] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Background:
Oral Squamous Cell Carcinoma (OSCC) is the most common malignant
epithelial neoplasm. It is located within the top 10 ranking incidence of cancers with a poor
prognosis and low survival rates. New breakthroughs of therapeutic strategies are therefore needed
to improve the survival rate of OSCC harboring patients.
Objective:
Since targeted therapy is considered as the most promising therapeutic strategies in
cancer, it is of great significance to identify novel targets and drugs for the treatment of OSCC.
Methods:
A series of bioinformatics approaches were launched to identify the hub proteins and
their potential agents. Microarray analysis and several online functional activity network analysis
were firstly utilized to recognize drug targets in OSCC. Subsequently, molecular docking was used
to screen their potential drugs from the specs chemistry database. At the same time, the assessment
of ligand-based virtual screening model was also evaluated.
Results:
In this study, two microarray data (GSE31056, GSE23558) were firstly selected and
analyzed to get consensus candidate genes including 681 candidate genes. Additionally, we
selected 33 candidate genes based on whether they belong to the kinases and transcription factors
and further clustered candidate hub targets based on functions and signaling pathways with
significant enrichment analysis by using DAVID and STRING online databases. Then, core PPI
network was then identified and we manually selected GRB2 and IGF1 as the key drug targets
according to the network analysis and previous references. Lastly, virtual screening was performed
to identify potential small molecules which could target these two targets, and such small
molecules can serve as the promising candidate agents for future drug development.
Conclusion:
In summary, our study might provide novel insights for understanding of the
underlying molecular events of OSCC, and our discovered candidate targets and candidate agents
could be used as the promising therapeutic strategies for the treatment of OSCC.
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Affiliation(s)
- Juan Liu
- School of Medicine & Sichuan Industrial Institute of Antibiotics & Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu 610015, China
| | - Xinjie Lian
- School of Medicine & Sichuan Industrial Institute of Antibiotics & Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu 610015, China
| | - Feng Liu
- School of Medicine & Sichuan Industrial Institute of Antibiotics & Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu 610015, China
| | - Xueling Yan
- School of Medicine & Sichuan Industrial Institute of Antibiotics & Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu 610015, China
| | - Chunyan Cheng
- School of Medicine & Sichuan Industrial Institute of Antibiotics & Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu 610015, China
| | - Lijia Cheng
- School of Medicine & Sichuan Industrial Institute of Antibiotics & Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu 610015, China
| | - Xiaolin Sun
- Department of Radiotherapy, the Central Hospital of Xuzhou, Xuzhou 221000, China
| | - Zheng Shi
- School of Medicine & Sichuan Industrial Institute of Antibiotics & Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu 610015, China
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9
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Sanchez R, Mackenzie SA. Integrative Network Analysis of Differentially Methylated and Expressed Genes for Biomarker Identification in Leukemia. Sci Rep 2020; 10:2123. [PMID: 32034170 PMCID: PMC7005804 DOI: 10.1038/s41598-020-58123-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 01/07/2020] [Indexed: 02/01/2023] Open
Abstract
Genome-wide DNA methylation and gene expression are commonly altered in pediatric acute lymphoblastic leukemia (PALL). Integrated network analysis of cytosine methylation and expression datasets has the potential to provide deeper insights into the complex disease states and their causes than individual disconnected analyses. With the purpose of identifying reliable cancer-associated methylation signal in gene regions from leukemia patients, we present an integrative network analysis of differentially methylated (DMGs) and differentially expressed genes (DEGs). The application of a novel signal detection-machine learning approach to methylation analysis of whole genome bisulfite sequencing (WGBS) data permitted a high level of methylation signal resolution in cancer-associated genes and pathways. This integrative network analysis approach revealed that gene expression and methylation consistently targeted the same gene pathways relevant to cancer: Pathways in cancer, Ras signaling pathway, PI3K-Akt signaling pathway, and Rap1 signaling pathway, among others. Detected gene hubs and hub sub-networks were integrated by signature loci associated with cancer that include, for example, NOTCH1, RAC1, PIK3CD, BCL2, and EGFR. Statistical analysis disclosed a stochastic deterministic relationship between methylation and gene expression within the set of genes simultaneously identified as DEGs and DMGs, where larger values of gene expression changes were probabilistically associated with larger values of methylation changes. Concordance analysis of the overlap between enriched pathways in DEG and DMG datasets revealed statistically significant agreement between gene expression and methylation changes. These results support the potential identification of reliable and stable methylation biomarkers at genes for cancer diagnosis and prognosis.
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Affiliation(s)
- Robersy Sanchez
- Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA.
| | - Sally A Mackenzie
- Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA. .,Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA.
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10
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Rigoglio NN, Rabelo ACS, Borghesi J, de Sá Schiavo Matias G, Fratini P, Prazeres PHDM, Pimentel CMMM, Birbrair A, Miglino MA. The Tumor Microenvironment: Focus on Extracellular Matrix. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1245:1-38. [PMID: 32266651 DOI: 10.1007/978-3-030-40146-7_1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The extracellular matrix (ECM) regulates the development and maintains tissue homeostasis. The ECM is composed of a complex network of molecules presenting distinct biochemical properties to regulate cell growth, survival, motility, and differentiation. Among their components, proteoglycans (PGs) are considered one of the main components of ECM. Its composition, biomechanics, and anisotropy are exquisitely tuned to reflect the physiological state of the tissue. The loss of ECM's homeostasis is seen as one of the hallmarks of cancer and, typically, defines transitional events in tumor progression and metastasis. In this chapter, we discuss the types of proteoglycans and their roles in cancer. It has been observed that the amount of some ECM components is increased, while others are decreased, depending on the type of tumor. However, both conditions corroborate with tumor progression and malignancy. Therefore, ECM components have an increasingly important role in carcinogenesis and this leads us to believe that their understanding may be a key in the discovery of new anti-tumor therapies. In this book, the main ECM components will be discussed in more detail in each chapter.
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Affiliation(s)
- Nathia Nathaly Rigoglio
- Department of Surgery, School of Veterinary Medicine and Animal Science, University of Sao Paulo, Sao Paulo, Brazil
| | - Ana Carolina Silveira Rabelo
- Department of Surgery, School of Veterinary Medicine and Animal Science, University of Sao Paulo, Sao Paulo, Brazil
| | - Jessica Borghesi
- Department of Surgery, School of Veterinary Medicine and Animal Science, University of Sao Paulo, Sao Paulo, Brazil
| | - Gustavo de Sá Schiavo Matias
- Department of Surgery, School of Veterinary Medicine and Animal Science, University of Sao Paulo, Sao Paulo, Brazil
| | - Paula Fratini
- Department of Surgery, School of Veterinary Medicine and Animal Science, University of Sao Paulo, Sao Paulo, Brazil
| | | | | | - Alexander Birbrair
- Department of Radiology, Columbia University Medical Center, New York, NY, USA
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Maria Angelica Miglino
- Department of Surgery, School of Veterinary Medicine and Animal Science, University of Sao Paulo, Sao Paulo, Brazil.
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11
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Kønig SM, Rissler V, Terkelsen T, Lambrughi M, Papaleo E. Alterations of the interactome of Bcl-2 proteins in breast cancer at the transcriptional, mutational and structural level. PLoS Comput Biol 2019; 15:e1007485. [PMID: 31825969 PMCID: PMC6927658 DOI: 10.1371/journal.pcbi.1007485] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 12/23/2019] [Accepted: 10/12/2019] [Indexed: 12/11/2022] Open
Abstract
Apoptosis is an essential defensive mechanism against tumorigenesis. Proteins of the B-cell lymphoma-2 (Bcl-2) family regulate programmed cell death by the mitochondrial apoptosis pathway. In response to intracellular stress, the apoptotic balance is governed by interactions of three distinct subgroups of proteins; the activator/sensitizer BH3 (Bcl-2 homology 3)-only proteins, the pro-survival, and the pro-apoptotic executioner proteins. Changes in expression levels, stability, and functional impairment of pro-survival proteins can lead to an imbalance in tissue homeostasis. Their overexpression or hyperactivation can result in oncogenic effects. Pro-survival Bcl-2 family members carry out their function by binding the BH3 short linear motif of pro-apoptotic proteins in a modular way, creating a complex network of protein-protein interactions. Their dysfunction enables cancer cells to evade cell death. The critical role of Bcl-2 proteins in homeostasis and tumorigenesis, coupled with mounting insight in their structural properties, make them therapeutic targets of interest. A better understanding of gene expression, mutational profile, and molecular mechanisms of pro-survival Bcl-2 proteins in different cancer types, could help to clarify their role in cancer development and may guide advancement in drug discovery. Here, we shed light on the pro-survival Bcl-2 proteins in breast cancer using different bioinformatic approaches, linking -omics with structural data. We analyzed the changes in the expression of the Bcl-2 proteins and their BH3-containing interactors in breast cancer samples. We then studied, at the structural level, a selection of interactions, accounting for effects induced by mutations found in the breast cancer samples. We find two complexes between the up-regulated Bcl2A1 and two down-regulated BH3-only candidates (i.e., Hrk and Nr4a1) as targets associated with reduced apoptosis in breast cancer samples for future experimental validation. Furthermore, we predict L99R, M75R as damaging mutations altering protein stability, and Y120C as a possible allosteric mutation from an exposed surface to the BH3-binding site.
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Affiliation(s)
- Simon Mathis Kønig
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Vendela Rissler
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Thilde Terkelsen
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Matteo Lambrughi
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
- Translational Disease Systems Biology, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research University of Copenhagen, Copenhagen, Denmark
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12
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Li Q, Yang Z, Zhao Z, Luo L, Li Z, Wang L, Zhang Y, Lin H, Wang J, Zhang Y. HMNPPID-human malignant neoplasm protein-protein interaction database. Hum Genomics 2019; 13:44. [PMID: 31639057 PMCID: PMC6805303 DOI: 10.1186/s40246-019-0223-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Protein-protein interaction (PPI) information extraction from biomedical literature helps unveil the molecular mechanisms of biological processes. Especially, the PPIs associated with human malignant neoplasms can unveil the biology behind these neoplasms. However, such PPI database is not currently available. RESULTS In this work, a database of protein-protein interactions associated with 171 kinds of human malignant neoplasms named HMNPPID is constructed. In addition, a visualization program, named VisualPPI, is provided to facilitate the analysis of the PPI network for a specific neoplasm. CONCLUSIONS HMNPPID can hopefully become an important resource for the research on PPIs of human malignant neoplasms since it provides readily available data for healthcare professionals. Thus, they do not need to dig into a large amount of biomedical literatures any more, which may accelerate the researches on the PPIs of malignant neoplasms.
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Affiliation(s)
- Qingqing Li
- College of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Zhihao Yang
- College of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China.
| | - Zhehuan Zhao
- College of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Ling Luo
- College of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Zhiheng Li
- College of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Lei Wang
- Beijing Institute of Health Administration and Medical Information, Beijing, 100850, China.
| | - Yin Zhang
- Beijing Institute of Health Administration and Medical Information, Beijing, 100850, China
| | - Hongfei Lin
- College of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Jian Wang
- College of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Yijia Zhang
- College of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
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Haider S, Ponnusamy K, Singh RKB, Chakraborti A, Bamezai RNK. Hamiltonian energy as an efficient approach to identify the significant key regulators in biological networks. PLoS One 2019; 14:e0221463. [PMID: 31442253 PMCID: PMC6707611 DOI: 10.1371/journal.pone.0221463] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 08/07/2019] [Indexed: 12/27/2022] Open
Abstract
The topological characteristics of biological networks enable us to identify the key nodes in terms of modularity. However, due to a large size of the biological networks with many hubs and functional modules across intertwined layers within the network, it often becomes difficult to accomplish the task of identifying potential key regulators. We use for the first time a generalized formalism of Hamiltonian Energy (HE) with a recursive approach. The concept, when applied to the Apoptosis Regulatory Gene Network (ARGN), helped us identify 11 Motif hubs (MHs), which influenced the network up to motif levels. The approach adopted allowed to classify MHs into 5 significant motif hubs (S-MHs) and 6 non-significant motif hubs (NS-MHs). The significant motif hubs had a higher HE value and were considered as high-active key regulators; while the non-significant motif hubs had a relatively lower HE value and were considered as low-active key regulators, in network control mechanism. Further, we compared the results of the HE analyses with the topological characterization, after subjecting to the three conditions independently: (i) removing all MHs, (ii) removing only S-MHs, and (iii) removing only NS-MHs from the ARGN. This procedure allowed us to cross-validate the role of 5 S-MHs, NFk-B1, BRCA1, CEBPB, AR, and POU2F1 as the potential key regulators. The changes in HE calculations further showed that the removal of 5 S-MHs could cause perturbation at all levels of the network, a feature not discernible by topological analysis alone.
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Affiliation(s)
- Shazia Haider
- Department of Neurology, All India Institute of Medical Science (AIIMS), New Delhi, India
| | | | - R. K. Brojen Singh
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
- * E-mail: (RKBS); (AC); (RNKB)
| | - Anirban Chakraborti
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
- * E-mail: (RKBS); (AC); (RNKB)
| | - Rameshwar N. K. Bamezai
- Formerly at National Centre of Applied Human Genetics, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
- * E-mail: (RKBS); (AC); (RNKB)
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14
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Liu FY, Hsu TC, Choong P, Lin MH, Chuang YJ, Chen BS, Lin C. Uncovering the regeneration strategies of zebrafish organs: a comprehensive systems biology study on heart, cerebellum, fin, and retina regeneration. BMC SYSTEMS BIOLOGY 2018; 12:29. [PMID: 29560825 PMCID: PMC5861487 DOI: 10.1186/s12918-018-0544-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Background Regeneration is an important biological process for the restoration of organ mass, structure, and function after damage, and involves complex bio-physiological mechanisms including cell differentiation and immune responses. We constructed four regenerative protein-protein interaction (PPI) networks using dynamic models and AIC (Akaike’s Information Criterion), based on time-course microarray data from the regeneration of four zebrafish organs: heart, cerebellum, fin, and retina. We extracted core and organ-specific proteins, and proposed a recalled-blastema-like formation model to uncover regeneration strategies in zebrafish. Results It was observed that the core proteins were involved in TGF-β signaling for each step in the recalled-blastema-like formation model and TGF-β signaling may be vital for regeneration. Integrins, FGF, and PDGF accelerate hemostasis during heart injury, while Bdnf shields retinal neurons from secondary damage and augments survival during the injury response. Wnt signaling mediates the growth and differentiation of cerebellum and fin neural stem cells, potentially providing a signal to trigger differentiation. Conclusion Through our analysis of all four zebrafish regenerative PPI networks, we provide insights that uncover the underlying strategies of zebrafish organ regeneration.
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Affiliation(s)
- Fang-Yu Liu
- Department of Electrical Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Te-Cheng Hsu
- Department of Electrical Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Patrick Choong
- Department of Electrical Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Min-Hsuan Lin
- Department of Medical Science and Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Yung-Jen Chuang
- Department of Medical Science and Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Bor-Sen Chen
- Department of Electrical Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Che Lin
- Department of Electrical Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan.
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15
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Ribeiro AC, Ferreira R, Freitas R. Plant Lectins: Bioactivities and Bioapplications. STUDIES IN NATURAL PRODUCTS CHEMISTRY 2018. [DOI: 10.1016/b978-0-444-64056-7.00001-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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16
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Kathera C, Zhang J, Janardhan A, Sun H, Ali W, Zhou X, He L, Guo Z. Interacting partners of FEN1 and its role in the development of anticancer therapeutics. Oncotarget 2017; 8:27593-27602. [PMID: 28187440 PMCID: PMC5432360 DOI: 10.18632/oncotarget.15176] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 01/24/2017] [Indexed: 11/25/2022] Open
Abstract
Protein-protein interaction (PPI) plays a key role in cellular communication, Protein-protein interaction connected with each other with hubs and nods involved in signaling pathways. These interactions used to develop network based biomarkers for early diagnosis of cancer. FEN1(Flap endonuclease 1) is a central component in cellular metabolism, over expression and decrease of FEN1 levels may cause cancer, these regulation changes of Flap endonuclease 1reported in many cancer cells, to consider this data may needs to develop a network based biomarker. The current review focused on types of PPI, based on nature, detection methods and its role in cancer. Interacting partners of Flap endonuclease 1 role in DNA replication repair and development of anticancer therapeutics based on Protein-protein interaction data.
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Affiliation(s)
- Chandrasekhar Kathera
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jing Zhang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Avilala Janardhan
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Hongfang Sun
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Wajid Ali
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaolong Zhou
- The Laboratory of Animal Genetics, Breeding, and Reproduction, College of Animal Science and Technology, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Lingfeng He
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhigang Guo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
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Cardioprotection Effects of Sevoflurane by Regulating the Pathway of Neuroactive Ligand-Receptor Interaction in Patients Undergoing Coronary Artery Bypass Graft Surgery. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2017; 2017:3618213. [PMID: 28348638 PMCID: PMC5350303 DOI: 10.1155/2017/3618213] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 02/10/2017] [Accepted: 02/19/2017] [Indexed: 01/17/2023]
Abstract
This study was designed to identify attractor modules and further reveal the potential biological processes involving in sevoflurane-induced anesthesia in patients treated with coronary artery bypass graft (CABG) surgery. Microarray profile data (ID: E-GEOD-4386) on atrial samples obtained from patients receiving anesthetic gas sevoflurane prior to and following CABG procedure were downloaded from EMBL-EBI database for further analysis. Protein-protein interaction (PPI) networks of baseline and sevoflurane groups were inferred and reweighted according to Spearman correlation coefficient (SCC), followed by systematic modules inference using clique-merging approach. Subsequently, attract method was utilized to explore attractor modules. Finally, pathway enrichment analyses for genes in the attractor modules were implemented to illuminate the biological processes in sevoflurane group. Using clique-merging approach, 27 and 36 modules were obtained from the PPI networks of baseline and sevoflurane-treated samples, respectively. By comparing with the baseline condition, 5 module pairs with the same gene composition were identified. Subsequently, 1 out of 5 modules was identified as an attractor based on attract method. Additionally, pathway analysis indicated that genes in the attractor module were associated with neuroactive ligand-receptor interaction. Accordingly, sevoflurane might exert important functions in cardioprotection in patients following CABG, partially through regulating the pathway of neuroactive ligand-receptor interaction.
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18
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Identification of Novel Pathways in Plant Lectin-Induced Cancer Cell Apoptosis. Int J Mol Sci 2016; 17:228. [PMID: 26867193 PMCID: PMC4783960 DOI: 10.3390/ijms17020228] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 01/30/2016] [Accepted: 02/02/2016] [Indexed: 01/01/2023] Open
Abstract
Plant lectins have been investigated to elucidate their complicated mechanisms due to their remarkable anticancer activities. Although plant lectins seems promising as a potential anticancer agent for further preclinical and clinical uses, further research is still urgently needed and should include more focus on molecular mechanisms. Herein, a Naïve Bayesian model was developed to predict the protein-protein interaction (PPI), and thus construct the global human PPI network. Moreover, multiple sources of biological data, such as smallest shared biological process (SSBP), domain-domain interaction (DDI), gene co-expression profiles and cross-species interolog mapping were integrated to build the core apoptotic PPI network. In addition, we further modified it into a plant lectin-induced apoptotic cell death context. Then, we identified 22 apoptotic hub proteins in mesothelioma cells according to their different microarray expressions. Subsequently, we used combinational methods to predict microRNAs (miRNAs) which could negatively regulate the abovementioned hub proteins. Together, we demonstrated the ability of our Naïve Bayesian model-based network for identifying novel plant lectin-treated cancer cell apoptotic pathways. These findings may provide new clues concerning plant lectins as potential apoptotic inducers for cancer drug discovery.
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Wong YH, Wu CC, Wu JCC, Lai HY, Chen KY, Jheng BR, Chen MC, Chang TH, Chen BS. Temporal Genetic Modifications after Controlled Cortical Impact--Understanding Traumatic Brain Injury through a Systematic Network Approach. Int J Mol Sci 2016; 17:216. [PMID: 26861311 PMCID: PMC4783948 DOI: 10.3390/ijms17020216] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 12/10/2015] [Indexed: 02/05/2023] Open
Abstract
Traumatic brain injury (TBI) is a primary injury caused by external physical force and also a secondary injury caused by biological processes such as metabolic, cellular, and other molecular events that eventually lead to brain cell death, tissue and nerve damage, and atrophy. It is a common disease process (as opposed to an event) that causes disabilities and high death rates. In order to treat all the repercussions of this injury, treatment becomes increasingly complex and difficult throughout the evolution of a TBI. Using high-throughput microarray data, we developed a systems biology approach to explore potential molecular mechanisms at four time points post-TBI (4, 8, 24, and 72 h), using a controlled cortical impact (CCI) model. We identified 27, 50, 48, and 59 significant proteins as network biomarkers at these four time points, respectively. We present their network structures to illustrate the protein–protein interactions (PPIs). We also identified UBC (Ubiquitin C), SUMO1, CDKN1A (cyclindependent kinase inhibitor 1A), and MYC as the core network biomarkers at the four time points, respectively. Using the functional analytical tool MetaCore™, we explored regulatory mechanisms and biological processes and conducted a statistical analysis of the four networks. The analytical results support some recent findings regarding TBI and provide additional guidance and directions for future research.
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Affiliation(s)
- Yung-Hao Wong
- College of Mechanical and Electronic Engineering, Fujian Agriculture and Forestry University, Fujian 350002, China.
- Laboratory of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu 300, Taiwan.
- Institute of Biomedical Science, National Chung Hsing University, Taichung 402, Taiwan.
| | - Chia-Chou Wu
- Laboratory of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu 300, Taiwan.
| | - John Chung-Che Wu
- Department of Neurosurgery, Taipei Medical University Hospital, Taipei Medical University, Taipei 110, Taiwan.
| | - Hsien-Yong Lai
- Institution Review Board (IRB), Christian Mennonite Hospital, Hualien 970, Taiwan.
| | - Kai-Yun Chen
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan.
| | - Bo-Ren Jheng
- Laboratory of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu 300, Taiwan.
| | - Mien-Cheng Chen
- Division of Cardiology, Kaohsiung Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Kaohsiung City 833, Taiwan.
| | - Tzu-Hao Chang
- Graduate Institute of Biomedical Informatics, Taipei Medical University, Taipei 110, Taiwan.
| | - Bor-Sen Chen
- Laboratory of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu 300, Taiwan.
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Nacher JC, Akutsu T. Minimum dominating set-based methods for analyzing biological networks. Methods 2016; 102:57-63. [PMID: 26773457 DOI: 10.1016/j.ymeth.2015.12.017] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/16/2015] [Accepted: 12/16/2015] [Indexed: 12/24/2022] Open
Abstract
The fast increase of 'multi-omics' data does not only pose a computational challenge for its analysis but also requires novel algorithmic methodologies to identify complex biological patterns and decipher the ultimate roots of human disorders. To that end, the massive integration of omics data with disease phenotypes is offering a new window into the cell functionality. The minimum dominating set (MDS) approach has rapidly emerged as a promising algorithmic method to analyze complex biological networks integrated with human disorders, which can be composed of a variety of omics data, from proteomics and transcriptomics to metabolomics. Here we review the main theoretical foundations of the methodology and the key algorithms, and examine the recent applications in which biological systems are analyzed by using the MDS approach.
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Affiliation(s)
- Jose C Nacher
- Department of Information Science, Faculty of Science, Toho University, Miyama 2-2-1, Funabashi, Chiba 274-8510, Japan.
| | - Tatsuya Akutsu
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.
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21
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Nafis S, Ponnusamy K, Husain M, Singh RKB, Bamezai RNK. Identification of key regulators and their controlling mechanism in a combinatorial apoptosis network: a systems biology approach. MOLECULAR BIOSYSTEMS 2016; 12:3357-3369. [DOI: 10.1039/c6mb00526h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
NFKB1, SP1 and hsa-let-7a, were identified as key regulators of apoptosis, by network theory through probability of signal propagation, hub-removal and motif analysis.
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Affiliation(s)
- Shazia Nafis
- Department of Biotechnology
- Jamia Millia Islamia (Central University)
- New Delhi
- India
- School of Computational and Integrative Sciences
| | - Kalaiarasan Ponnusamy
- National Centre of Applied Human Genetics
- School of Life Sciences
- Jawaharlal Nehru University
- New Delhi
- India
| | - Mohammad Husain
- Department of Biotechnology
- Jamia Millia Islamia (Central University)
- New Delhi
- India
| | - R. K. Brojen Singh
- School of Computational and Integrative Sciences
- Jawaharlal Nehru University
- New Delhi
- India
| | - Rameshwar N. K. Bamezai
- School of Computational and Integrative Sciences
- Jawaharlal Nehru University
- New Delhi
- India
- National Centre of Applied Human Genetics
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22
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Wong YH, Lin CL, Chen TS, Chen CA, Jiang PS, Lai YH, Chu LJ, Li CW, Chen JJW, Chen BS. Multiple target drug cocktail design for attacking the core network markers of four cancers using ligand-based and structure-based virtual screening methods. BMC Med Genomics 2015; 8 Suppl 4:S4. [PMID: 26680552 PMCID: PMC4682379 DOI: 10.1186/1755-8794-8-s4-s4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Computer-aided drug design has a long history of being applied to discover new molecules to treat various cancers, but it has always been focused on single targets. The development of systems biology has let scientists reveal more hidden mechanisms of cancers, but attempts to apply systems biology to cancer therapies remain at preliminary stages. Our lab has successfully developed various systems biology models for several cancers. Based on these achievements, we present the first attempt to combine multiple-target therapy with systems biology. METHODS In our previous study, we identified 28 significant proteins--i.e., common core network markers--of four types of cancers as house-keeping proteins of these cancers. In this study, we ranked these proteins by summing their carcinogenesis relevance values (CRVs) across the four cancers, and then performed docking and pharmacophore modeling to do virtual screening on the NCI database for anti-cancer drugs. We also performed pathway analysis on these proteins using Panther and MetaCore to reveal more mechanisms of these cancer house-keeping proteins. RESULTS We designed several approaches to discover targets for multiple-target cocktail therapies. In the first one, we identified the top 20 drugs for each of the 28 cancer house-keeping proteins, and analyzed the docking pose to further understand the interaction mechanisms of these drugs. After screening for duplicates, we found that 13 of these drugs could target 11 proteins simultaneously. In the second approach, we chose the top 5 proteins with the highest summed CRVs and used them as the drug targets. We built a pharmacophore and applied it to do virtual screening against the Life-Chemical library for anti-cancer drugs. Based on these results, wet-lab bio-scientists could freely investigate combinations of these drugs for multiple-target therapy for cancers, in contrast to the traditional single target therapy. CONCLUSIONS Combination of systems biology with computer-aided drug design could help us develop novel drug cocktails with multiple targets. We believe this will enhance the efficiency of therapeutic practice and lead to new directions for cancer therapy.
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Affiliation(s)
- Yung-Hao Wong
- Laboratory of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
- Institute of Biomedical Science, National Chung Hsing University, Taiwan 40227, Republic of China
| | - Chih-Lung Lin
- Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu, Taiwan, ROC
| | - Ting-Shou Chen
- Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu, Taiwan, ROC
| | - Chien-An Chen
- Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu, Taiwan, ROC
| | - Pei-Shin Jiang
- Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu, Taiwan, ROC
| | - Yi-Hua Lai
- Institute of Biomedical Science, National Chung Hsing University, Taiwan 40227, Republic of China
| | - Lichieh Julie Chu
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan,ROC
| | - Cheng-Wei Li
- Laboratory of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Jeremy JW Chen
- Institute of Biomedical Science, National Chung Hsing University, Taiwan 40227, Republic of China
| | - Bor-Sen Chen
- Laboratory of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
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Chen D, Zhang Z, Meng Y. Systematic Tracking of Disrupted Modules Identifies Altered Pathways Associated with Congenital Heart Defects in Down Syndrome. Med Sci Monit 2015; 21:3334-42. [PMID: 26524729 PMCID: PMC4635630 DOI: 10.12659/msm.896001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND This work aimed to identify altered pathways in congenital heart defects (CHD) in Down syndrome (DS) by systematically tracking the dysregulated modules of reweighted protein-protein interaction (PPI) networks. MATERIAL AND METHODS We performed systematic identification and comparison of modules across normal and disease conditions by integrating PPI and gene-expression data. Based on Pearson correlation coefficient (PCC), normal and disease PPI networks were inferred and reweighted. Then, modules in the PPI network were explored by clique-merging algorithm; altered modules were identified via maximum weight bipartite matching and ranked in non-increasing order. Finally, pathways enrichment analysis of genes in altered modules was carried out based on Database for Annotation, Visualization, and Integrated Discovery (DAVID) to study the biological pathways in CHD in DS. RESULTS Our analyses revealed that 348 altered modules were identified by comparing modules in normal and disease PPI networks. Pathway functional enrichment analysis of disrupted module genes showed that the 4 most significantly altered pathways were: ECM-receptor interaction, purine metabolism, focal adhesion, and dilated cardiomyopathy. CONCLUSIONS We successfully identified 4 altered pathways and we predicted that these pathways would be good indicators for CHD in DS.
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Affiliation(s)
- Denghong Chen
- Department of Obstetrics, Jining No. 1 People's Hospital, Jining, Shandong, China (mainland)
| | - Zhenhua Zhang
- Department of Children's Health Prevention, Jining No. 1 People's Hospital, Jining, Shandong, China (mainland)
| | - Yuxiu Meng
- Department of Neonatology, Jining No. 1 People's Hospital, Jining, Shandong, China (mainland)
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Temporal Identification of Dysregulated Genes and Pathways in Clear Cell Renal Cell Carcinoma Based on Systematic Tracking of Disrupted Modules. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2015; 2015:313740. [PMID: 26543493 PMCID: PMC4620417 DOI: 10.1155/2015/313740] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 07/31/2015] [Accepted: 08/11/2015] [Indexed: 11/17/2022]
Abstract
Objective. The objective of this work is to identify dysregulated genes and pathways of ccRCC temporally according to systematic tracking of the dysregulated modules of reweighted Protein-Protein Interaction (PPI) networks. Methods. Firstly, normal and ccRCC PPI network were inferred and reweighted based on Pearson correlation coefficient (PCC). Then, we identified altered modules using maximum weight bipartite matching and ranked them in nonincreasing order. Finally, gene compositions of altered modules were analyzed, and pathways enrichment analyses of genes in altered modules were carried out based on Expression Analysis Systematic Explored (EASE) test. Results. We obtained 136, 576, 693, and 531 disrupted modules of ccRCC stages I, II, III, and IV, respectively. Gene composition analyses of altered modules revealed that there were 56 common genes (such as MAPK1, CCNA2, and GSTM3) existing in the four stages. Besides pathway enrichment analysis identified 5 common pathways (glutathione metabolism, cell cycle, alanine, aspartate, and glutamate metabolism, arginine and proline metabolism, and metabolism of xenobiotics by cytochrome P450) across stages I, II, III, and IV. Conclusions. We successfully identified dysregulated genes and pathways of ccRCC in different stages, and these might be potential biological markers and processes for treatment and etiology mechanism in ccRCC.
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Applying NGS Data to Find Evolutionary Network Biomarkers from the Early and Late Stages of Hepatocellular Carcinoma. BIOMED RESEARCH INTERNATIONAL 2015; 2015:391475. [PMID: 26366411 PMCID: PMC4558430 DOI: 10.1155/2015/391475] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 04/23/2015] [Accepted: 04/23/2015] [Indexed: 02/07/2023]
Abstract
Hepatocellular carcinoma (HCC) is a major liver tumor (~80%), besides hepatoblastomas, angiosarcomas, and cholangiocarcinomas. In this study, we used a systems biology approach to construct protein-protein interaction networks (PPINs) for early-stage and late-stage liver cancer. By comparing the networks of these two stages, we found that the two networks showed some common mechanisms and some significantly different mechanisms. To obtain differential network structures between cancer and noncancer PPINs, we constructed cancer PPIN and noncancer PPIN network structures for the two stages of liver cancer by systems biology method using NGS data from cancer cells and adjacent noncancer cells. Using carcinogenesis relevance values (CRVs), we identified 43 and 80 significant proteins and their PPINs (network markers) for early-stage and late-stage liver cancer. To investigate the evolution of network biomarkers in the carcinogenesis process, a primary pathway analysis showed that common pathways of the early and late stages were those related to ordinary cancer mechanisms. A pathway specific to the early stage was the mismatch repair pathway, while pathways specific to the late stage were the spliceosome pathway, lysine degradation pathway, and progesterone-mediated oocyte maturation pathway. This study provides a new direction for cancer-targeted therapies at different stages.
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Chen BS, Tsai KW, Li CW. Using Nonlinear Stochastic Evolutionary Game Strategy to Model an Evolutionary Biological Network of Organ Carcinogenesis Under a Natural Selection Scheme. Evol Bioinform Online 2015; 11:155-78. [PMID: 26244004 PMCID: PMC4509470 DOI: 10.4137/ebo.s26195] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 06/04/2015] [Accepted: 06/08/2015] [Indexed: 11/06/2022] Open
Abstract
Molecular biologists have long recognized carcinogenesis as an evolutionary process that involves natural selection. Cancer is driven by the somatic evolution of cell lineages. In this study, the evolution of somatic cancer cell lineages during carcinogenesis was modeled as an equilibrium point (ie, phenotype of attractor) shifting, the process of a nonlinear stochastic evolutionary biological network. This process is subject to intrinsic random fluctuations because of somatic genetic and epigenetic variations, as well as extrinsic disturbances because of carcinogens and stressors. In order to maintain the normal function (ie, phenotype) of an evolutionary biological network subjected to random intrinsic fluctuations and extrinsic disturbances, a network robustness scheme that incorporates natural selection needs to be developed. This can be accomplished by selecting certain genetic and epigenetic variations to modify the network structure to attenuate intrinsic fluctuations efficiently and to resist extrinsic disturbances in order to maintain the phenotype of the evolutionary biological network at an equilibrium point (attractor). However, during carcinogenesis, the remaining (or neutral) genetic and epigenetic variations accumulate, and the extrinsic disturbances become too large to maintain the normal phenotype at the desired equilibrium point for the nonlinear evolutionary biological network. Thus, the network is shifted to a cancer phenotype at a new equilibrium point that begins a new evolutionary process. In this study, the natural selection scheme of an evolutionary biological network of carcinogenesis was derived from a robust negative feedback scheme based on the nonlinear stochastic Nash game strategy. The evolvability and phenotypic robustness criteria of the evolutionary cancer network were also estimated by solving a Hamilton-Jacobi inequality - constrained optimization problem. The simulation revealed that the phenotypic shift of the lung cancer-associated cell network takes 54.5 years from a normal state to stage I cancer, 1.5 years from stage I to stage II cancer, and 2.5 years from stage II to stage III cancer, with a reasonable match for the statistical result of the average age of lung cancer. These results suggest that a robust negative feedback scheme, based on a stochastic evolutionary game strategy, plays a critical role in an evolutionary biological network of carcinogenesis under a natural selection scheme.
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Affiliation(s)
- Bor-Sen Chen
- Laboratory of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan
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Determination of Temporal Order among the Components of an Oscillatory System. PLoS One 2015; 10:e0124842. [PMID: 26151635 PMCID: PMC4495067 DOI: 10.1371/journal.pone.0124842] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 03/17/2015] [Indexed: 11/19/2022] Open
Abstract
Oscillatory systems in biology are tightly regulated process where the individual components (e.g. genes) express in an orderly manner by virtue of their functions. The temporal order among the components of an oscillatory system may potentially be disrupted for various reasons (e.g. environmental factors). As a result some components of the system may go out of order or even cease to participate in the oscillatory process. In this article, we develop a novel framework to evaluate whether the temporal order is unchanged in different populations (or experimental conditions). We also develop methodology to estimate the order among the components with a suitable notion of “confidence.” Using publicly available data on S. pombe, S. cerevisiae and Homo sapiens we discover that the temporal order among the genes cdc18; mik1; hhf1; hta2; fkh2 and klp5 is evolutionarily conserved from yeast to humans.
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Liu Z, Zhao J, Tan Y, Tang M, Li G. Systematic tracking of dysregulated modules identifies disrupted pathways in narcolepsy. Int J Clin Exp Med 2015; 8:9384-93. [PMID: 26309600 PMCID: PMC4538164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 05/25/2015] [Indexed: 06/04/2023]
Abstract
OBJECTIVE The objective of this work is to identify disrupted pathways in narcolepsy according to systematically tracking the dysregulated modules of reweighted Protein-Protein Interaction (PPI) networks. Here, we performed systematic identification and comparison of modules across normal and narcolepsy conditions by integrating PPI and gene-expression data. METHODS Firstly, normal and narcolepsy PPI network were inferred and reweighted based on Pearson correlation coefficient (PCC). Then, modules in PPI network were explored by clique-merging algorithm and we identified altered modules using a maximum weight bipartite matching and in non-increasing order. Finally, pathways enrichment analyses of genes in altered modules were carried out based on Expression Analysis Systematic Explored (EASE) test to illuminate the biological pathways in narcolepsy. RESULTS Our analyses revealed that 235 altered modules were identified by comparing modules in normal and narcolepsy PPI network. Pathway functional enrichment analysis of disrupted module genes showed 59 disrupted pathways within threshold P < 0.001. The most significant five disrupted pathways were: oxidative phosphorylation, T cell receptor signaling pathway, cell cycle, Alzheimer's disease and focal adhesion. CONCLUSIONS We successfully identified disrupted pathways and these pathways might be potential biological processes for treatment and etiology mechanism in narcolepsy.
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Affiliation(s)
- Zhenhua Liu
- Department of Neurology and Shandong Sleep Medical Center, Provincial Hospital Affiliated to Shandong UniversityJinan 250021, China
| | - Jiali Zhao
- Department of Neurology, Provincial Hospital Affiliated to Shandong UniversityJinan 250021, China
| | - Yinyin Tan
- Department of Neurology, Provincial Hospital Affiliated to Shandong UniversityJinan 250021, China
| | - Minglu Tang
- Shandong Sleep Medical Center, Provincial Hospital Affiliated to Shandong UniversityJinan 250021, China
| | - Guanzhen Li
- Shandong Sleep Medical Center, Provincial Hospital Affiliated to Shandong UniversityJinan 250021, China
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Li C, Wang J. Quantifying the underlying landscape and paths of cancer. J R Soc Interface 2015; 11:20140774. [PMID: 25232051 DOI: 10.1098/rsif.2014.0774] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Cancer is a disease regulated by the underlying gene networks. The emergence of normal and cancer states as well as the transformation between them can be thought of as a result of the gene network interactions and associated changes. We developed a global potential landscape and path framework to quantify cancer and associated processes. We constructed a cancer gene regulatory network based on the experimental evidences and uncovered the underlying landscape. The resulting tristable landscape characterizes important biological states: normal, cancer and apoptosis. The landscape topography in terms of barrier heights between stable state attractors quantifies the global stability of the cancer network system. We propose two mechanisms of cancerization: one is by the changes of landscape topography through the changes in regulation strengths of the gene networks. The other is by the fluctuations that help the system to go over the critical barrier at fixed landscape topography. The kinetic paths from least action principle quantify the transition processes among normal state, cancer state and apoptosis state. The kinetic rates provide the quantification of transition speeds among normal, cancer and apoptosis attractors. By the global sensitivity analysis of the gene network parameters on the landscape topography, we uncovered some key gene regulations determining the transitions between cancer and normal states. This can be used to guide the design of new anti-cancer tactics, through cocktail strategy of targeting multiple key regulation links simultaneously, for preventing cancer occurrence or transforming the early cancer state back to normal state.
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Affiliation(s)
- Chunhe Li
- Department of Chemistry, State University of New York at Stony Brook, Stony Brook, NY, USA Department of Physics, State University of New York at Stony Brook, Stony Brook, NY, USA
| | - Jin Wang
- Department of Chemistry, State University of New York at Stony Brook, Stony Brook, NY, USA Department of Physics, State University of New York at Stony Brook, Stony Brook, NY, USA State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, People's Republic of China
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Fu L, Zhang S, Zhang L, Tong X, Zhang J, Zhang Y, Ouyang L, Liu B, Huang J. Systems biology network-based discovery of a small molecule activator BL-AD008 targeting AMPK/ZIPK and inducing apoptosis in cervical cancer. Oncotarget 2015; 6:8071-88. [PMID: 25797270 PMCID: PMC4480736 DOI: 10.18632/oncotarget.3513] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 02/03/2015] [Indexed: 02/05/2023] Open
Abstract
The aim of this study was to discover a small molecule activator BL-AD008 targeting AMPK/ZIPK and inducing apoptosis in cervical cancer. In this study, we systematically constructed the global protein-protein interaction (PPI) network and predicted apoptosis-related protein connections by the Naïve Bayesian model. Then, we identified some classical apoptotic PPIs and other previously unrecognized PPIs between apoptotic kinases, such as AMPK and ZIPK. Subsequently, we screened a series of candidate compounds targeting AMPK/ZIPK, synthesized some compounds and eventually discovered a novel dual-target activator (BL-AD008). Moreover, we found BL-AD008 bear remarkable anti-proliferative activities toward cervical cancer cells and could induce apoptosis by death-receptor and mitochondrial pathways. Additionally, we found that BL-AD008-induced apoptosis was affected by the combination of AMPK and ZIPK. Then, we found that BL-AD008 bear its anti-tumor activities and induced apoptosis by targeting AMPK/ZIPK in vivo. In conclusion, these results demonstrate the ability of systems biology network to identify some key apoptotic kinase targets AMPK and ZIPK; thus providing a dual-target small molecule activator (BL-AD008) as a potential new apoptosis-modulating drug in future cervical cancer therapy.
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Affiliation(s)
- Leilei Fu
- State Key Laboratory of Biotherapy, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Shouyue Zhang
- State Key Laboratory of Biotherapy, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Lan Zhang
- State Key Laboratory of Biotherapy, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
| | - Xupeng Tong
- State Key Laboratory of Biotherapy, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
- School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Jin Zhang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
| | - Yonghui Zhang
- State Key Laboratory of Biotherapy, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
- Collaborative Innovation Center for Biotherapy, Department of Pharmacology & Pharmaceutical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Liang Ouyang
- State Key Laboratory of Biotherapy, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Bo Liu
- State Key Laboratory of Biotherapy, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Jian Huang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
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Bhat A, Dakna M, Mischak H. Integrating proteomics profiling data sets: a network perspective. Methods Mol Biol 2015; 1243:237-53. [PMID: 25384750 DOI: 10.1007/978-1-4939-1872-0_14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Understanding disease mechanisms often requires complex and accurate integration of cellular pathways and molecular networks. Systems biology offers the possibility to provide a comprehensive map of the cell's intricate wiring network, which can ultimately lead to decipher the disease phenotype. Here, we describe what biological pathways are, how they function in normal and abnormal cellular systems, limitations faced by databases for integrating data, and highlight how network models are emerging as a powerful integrative framework to understand and interpret the roles of proteins and peptides in diseases.
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Affiliation(s)
- Akshay Bhat
- Mosaiques-Diagnostics GmbH, Mellendorfer Straße 7-9, D-30625, Hannover, Germany,
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Srihari S, Madhamshettiwar PB, Song S, Liu C, Simpson PT, Khanna KK, Ragan MA. Complex-based analysis of dysregulated cellular processes in cancer. BMC SYSTEMS BIOLOGY 2014; 8 Suppl 4:S1. [PMID: 25521701 PMCID: PMC4290683 DOI: 10.1186/1752-0509-8-s4-s1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Background Differential expression analysis of (individual) genes is often used to study their roles in diseases. However, diseases such as cancer are a result of the combined effect of multiple genes. Gene products such as proteins seldom act in isolation, but instead constitute stable multi-protein complexes performing dedicated functions. Therefore, complexes aggregate the effect of individual genes (proteins) and can be used to gain a better understanding of cancer mechanisms. Here, we observe that complexes show considerable changes in their expression, in turn directed by the concerted action of transcription factors (TFs), across cancer conditions. We seek to gain novel insights into cancer mechanisms through a systematic analysis of complexes and their transcriptional regulation. Results We integrated large-scale protein-interaction (PPI) and gene-expression datasets to identify complexes that exhibit significant changes in their expression across different conditions in cancer. We devised a log-linear model to relate these changes to the differential regulation of complexes by TFs. The application of our model on two case studies involving pancreatic and familial breast tumour conditions revealed: (i) complexes in core cellular processes, especially those responsible for maintaining genome stability and cell proliferation (e.g. DNA damage repair and cell cycle) show considerable changes in expression; (ii) these changes include decrease and countering increase for different sets of complexes indicative of compensatory mechanisms coming into play in tumours; and (iii) TFs work in cooperative and counteractive ways to regulate these mechanisms. Such aberrant complexes and their regulating TFs play vital roles in the initiation and progression of cancer. Conclusions Complexes in core cellular processes display considerable decreases and countering increases in expression, strongly reflective of compensatory mechanisms in cancer. These changes are directed by the concerted action of cooperative and counteractive TFs. Our study highlights the roles of these complexes and TFs and presents several case studies of compensatory processes, thus providing novel insights into cancer mechanisms.
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Nafis S, Kalaiarasan P, Brojen Singh RK, Husain M, Bamezai RNK. Apoptosis regulatory protein-protein interaction demonstrates hierarchical scale-free fractal network. Brief Bioinform 2014; 16:675-99. [PMID: 25256288 DOI: 10.1093/bib/bbu036] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 08/21/2014] [Indexed: 12/29/2022] Open
Abstract
Dysregulation or inhibition of apoptosis favors cancer and many other diseases. Understanding of the network interaction of the genes involved in apoptotic pathway, therefore, is essential, to look for targets of therapeutic intervention. Here we used the network theory methods, using experimentally validated 25 apoptosis regulatory proteins and identified important genes for apoptosis regulation, which demonstrated a hierarchical scale-free fractal protein-protein interaction network. TP53, BRCA1, UBIQ and CASP3 were recognized as a four key regulators. BRCA1 and UBIQ were also individually found to control highly clustered modules and play an important role in the stability of the overall network. The connection among the BRCA1, UBIQ and TP53 proteins was found to be important for regulation, which controlled their own respective communities and the overall network topology. The feedback loop regulation motif was identified among NPM1, BRCA1 and TP53, and these crucial motif topologies were also reflected in high frequency. The propagation of the perturbed signal from hubs was found to be active upto some distance, after which propagation started decreasing and TP53 was the most efficient signal propagator. From the functional enrichment analysis, most of the apoptosis regulatory genes associated with cardiovascular diseases and highly expressed in brain tissues were identified. Apart from TP53, BRCA1 was observed to regulate apoptosis by influencing motif, propagation of signals and module regulation, reflecting their biological significance. In future, biochemical investigation of the observed hub-interacting partners could provide further understanding about their role in the pathophysiology of cancer.
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35
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Wong YH, Chen RH, Chen BS. Core and specific network markers of carcinogenesis from multiple cancer samples. J Theor Biol 2014; 362:17-34. [PMID: 25016045 DOI: 10.1016/j.jtbi.2014.05.045] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 05/19/2014] [Accepted: 05/28/2014] [Indexed: 01/07/2023]
Abstract
Cancer is the leading cause of death worldwide and is generally caused by mutations in multiple proteins or the dysregulation of pathways. Understanding the causes and the underlying carcinogenic mechanisms can help fight this disease. In this study, a systems biology approach was used to construct the protein-protein interaction (PPI) networks of four cancers and the non-cancers by their corresponding microarray data, PPI modeling and database-mining. By comparing PPI networks between cancer and non-cancer samples to find significant proteins with large PPI changes during carcinogenesis process, core and specific network markers were identified by the intersection and difference of significant proteins, respectively, with carcinogenesis relevance values (CRVs) for each cancer. A total of 28 significant proteins were identified as core network markers in the carcinogenesis of four types of cancer, two of which are novel cancer-related proteins (e.g., UBC and PSMA3). Moreover, seven crucial common pathways were found among these cancers based on their core network markers, and some specific pathways were particularly prominent based on the specific network markers of different cancers (e.g., the RIG-I-like receptor pathway in bladder cancer, the proteasome pathway and TCR pathway in liver cancer, and the HR pathway in lung cancer). Additional validation of these network markers using the literature and new tested datasets could strengthen our findings and confirm the proposed method. From these core and specific network markers, we could not only gain an insight into crucial common and specific pathways in the carcinogenesis, but also obtain a high promising PPI target for cancer therapy.
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Affiliation(s)
- Yung-Hao Wong
- Lab of Control and Systems Biology, Department of Electrical Engineering National Tsing Hua University, Hsinchu 30013, Taiwan.
| | - Ru-Hong Chen
- Lab of Control and Systems Biology, Department of Electrical Engineering National Tsing Hua University, Hsinchu 30013, Taiwan.
| | - Bor-Sen Chen
- Lab of Control and Systems Biology, Department of Electrical Engineering National Tsing Hua University, Hsinchu 30013, Taiwan.
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In-depth proteomic delineation of the colorectal cancer exoproteome: Mechanistic insight and identification of potential biomarkers. J Proteomics 2014; 103:121-36. [DOI: 10.1016/j.jprot.2014.03.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 03/07/2014] [Accepted: 03/18/2014] [Indexed: 12/30/2022]
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Frantzi M, Bhat A, Latosinska A. Clinical proteomic biomarkers: relevant issues on study design & technical considerations in biomarker development. Clin Transl Med 2014; 3:7. [PMID: 24679154 PMCID: PMC3994249 DOI: 10.1186/2001-1326-3-7] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 03/06/2014] [Indexed: 12/11/2022] Open
Abstract
Biomarker research is continuously expanding in the field of clinical proteomics. A combination of different proteomic-based methodologies can be applied depending on the specific clinical context of use. Moreover, current advancements in proteomic analytical platforms are leading to an expansion of biomarker candidates that can be identified. Specifically, mass spectrometric techniques could provide highly valuable tools for biomarker research. Ideally, these advances could provide with biomarkers that are clinically applicable for disease diagnosis and/ or prognosis. Unfortunately, in general the biomarker candidates fail to be implemented in clinical decision making. To improve on this current situation, a well-defined study design has to be established driven by a clear clinical need, while several checkpoints between the different phases of discovery, verification and validation have to be passed in order to increase the probability of establishing valid biomarkers. In this review, we summarize the technical proteomic platforms that are available along the different stages in the biomarker discovery pipeline, exemplified by clinical applications in the field of bladder cancer biomarker research.
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Affiliation(s)
- Maria Frantzi
- Mosaiques Diagnostics GmbH, Mellendorfer Strasse 7-9, D-30625 Hannover, Germany
- Biotechnology Division, Biomedical Research Foundation Academy of Athens, Soranou Ephessiou 4, 115 27 Athens, Greece
| | - Akshay Bhat
- Mosaiques Diagnostics GmbH, Mellendorfer Strasse 7-9, D-30625 Hannover, Germany
- Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Agnieszka Latosinska
- Biotechnology Division, Biomedical Research Foundation Academy of Athens, Soranou Ephessiou 4, 115 27 Athens, Greece
- Charité-Universitätsmedizin Berlin, Berlin, Germany
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Syafrizayanti, Betzen C, Hoheisel JD, Kastelic D. Methods for analyzing and quantifying protein–protein interaction. Expert Rev Proteomics 2014; 11:107-20. [DOI: 10.1586/14789450.2014.875857] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Srihari S, Raman V, Leong HW, Ragan MA. Evolution and Controllability of Cancer Networks: A Boolean Perspective. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2014; 11:83-94. [PMID: 26355510 DOI: 10.1109/tcbb.2013.128] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Cancer forms a robust system capable of maintaining stable functioning (cell sustenance and proliferation) despite perturbations. Cancer progresses as stages over time typically with increasing aggressiveness and worsening prognosis. Characterizing these stages and identifying the genes driving transitions between them is critical to understand cancer progression and to develop effective anti-cancer therapies. In this work, we propose a novel model for the `cancer system' as a Boolean state space in which a Boolean network, built from protein-interaction and gene-expression data from different stages of cancer, transits between Boolean satisfiability states by "editing" interactions and "flipping" genes. Edits reflect rewiring of the PPI network while flipping of genes reflect activation or silencing of genes between stages. We formulate a minimization problem min flip to identify these genes driving the transitions. The application of our model (called BoolSpace) on three case studies-pancreatic and breast tumours in human and post spinal-cord injury (SCI) in rats-reveals valuable insights into the phenomenon of cancer progression: (i) interactions involved in core cell-cycle and DNA-damage repair pathways are significantly rewired in tumours, indicating significant impact to key genome-stabilizing mechanisms; (ii) several of the genes flipped are serine/threonine kinases which act as biological switches, reflecting cellular switching mechanisms between stages; and (iii) different sets of genes are flipped during the initial and final stages indicating a pattern to tumour progression. Based on these results, we hypothesize that robustness of cancer partly stems from "passing of the baton" between genes at different stages-genes from different biological processes and/or cellular components are involved in different stages of tumour progression thereby allowing tumour cells to evade targeted therapy, and therefore an effective therapy should target a "cover set" of these genes. A C/C++ implementation of BoolSpace is freely available at: http://www.bioinformatics.org.au/tools-data.
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Randhawa V, Sharma P, Bhushan S, Bagler G. Identification of key nodes of type 2 diabetes mellitus protein interactome and study of their interactions with phloridzin. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2013; 17:302-17. [PMID: 23692363 DOI: 10.1089/omi.2012.0115] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Network biology-inspired approaches could be used effectively in probing regulatory processes by which small molecules intervene with disease mechanisms. The present study aims at identification of key targets of type 2 diabetes mellitus (T2DM) by network analysis of the underlying protein interactome, and probing for mechanisms by which phloridzin could be critical at altering the disease phenotype. Towards this goal, we constructed a protein-protein interaction network associated with T2DM, starting from candidate genes and systems-level interactions data available. The relevance of the network constructed was verified with the help of gene ontology, node deletion, and biological essentiality studies. Using a network analysis method, MAPK1, EP300, and SMAD2 were identified as the most central proteins of potential therapeutic value. Phloridzin, a known antidiabetic agent, potentially interacts with proteins central to T2DM mechanisms. The structural understanding of interaction of phloridzin with these proteins of relevance to T2DM could provide better insight into its regulatory mechanisms and help in developing better therapeutic agents. The molecular docking results suggest that phloridzin is potentially involved in making critical interactions with MAPK1. These results could further be validated by experimental studies and could be used to design therapeutic agents for T2DM intervention.
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Affiliation(s)
- Vinay Randhawa
- Biotechnology Division, Institute of Himalayan Bioresource Technology, Council of Scientific and Industrial Research (CSIR-IHBT), Palampur, India
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Systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering. Cells 2013; 2:635-88. [PMID: 24709875 PMCID: PMC3972654 DOI: 10.3390/cells2040635] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 09/12/2013] [Accepted: 09/19/2013] [Indexed: 01/11/2023] Open
Abstract
Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i) system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii) system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii) system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv) systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering.
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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: 506] [Impact Index Per Article: 46.0] [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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Srihari S, Ragan MA. Systematic tracking of dysregulated modules identifies novel genes in cancer. Bioinformatics 2013; 29:1553-61. [DOI: 10.1093/bioinformatics/btt191] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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Abstract
Complex diseases are caused by a combination of genetic and environmental factors. Uncovering the molecular pathways through which genetic factors affect a phenotype is always difficult, but in the case of complex diseases this is further complicated since genetic factors in affected individuals might be different. In recent years, systems biology approaches and, more specifically, network based approaches emerged as powerful tools for studying complex diseases. These approaches are often built on the knowledge of physical or functional interactions between molecules which are usually represented as an interaction network. An interaction network not only reports the binary relationships between individual nodes but also encodes hidden higher level organization of cellular communication. Computational biologists were challenged with the task of uncovering this organization and utilizing it for the understanding of disease complexity, which prompted rich and diverse algorithmic approaches to be proposed. We start this chapter with a description of the general characteristics of complex diseases followed by a brief introduction to physical and functional networks. Next we will show how these networks are used to leverage genotype, gene expression, and other types of data to identify dysregulated pathways, infer the relationships between genotype and phenotype, and explain disease heterogeneity. We group the methods by common underlying principles and first provide a high level description of the principles followed by more specific examples. We hope that this chapter will give readers an appreciation for the wealth of algorithmic techniques that have been developed for the purpose of studying complex diseases as well as insight into their strengths and limitations.
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Affiliation(s)
- Dong-Yeon Cho
- National Center for Biotechnology Information, NLM, NIH, Bethesda, Maryland, United States of America
| | - Yoo-Ah Kim
- National Center for Biotechnology Information, NLM, NIH, Bethesda, Maryland, United States of America
| | - Teresa M. Przytycka
- National Center for Biotechnology Information, NLM, NIH, Bethesda, Maryland, United States of America
- * E-mail:
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Cheng TMK, Gulati S, Agius R, Bates PA. Understanding cancer mechanisms through network dynamics. Brief Funct Genomics 2012; 11:543-60. [PMID: 22811516 DOI: 10.1093/bfgp/els025] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2024] Open
Abstract
Cancer is a complex, multifaceted disease. Cellular systems are perturbed both during the onset and development of cancer, and the behavioural change of tumour cells usually involves a broad range of dynamic variations. To an extent, the difficulty of monitoring the systemic change has been alleviated by recent developments in the high-throughput technologies. At both the genomic as well as proteomic levels, the technological advances in microarray and mass spectrometry, in conjunction with computational simulations and the construction of human interactome maps have facilitated the progress of identifying disease-associated genes. On a systems level, computational approaches developed for network analysis are becoming especially useful for providing insights into the mechanism behind tumour development and metastasis. This review emphasizes network approaches that have been developed to study cancer and provides an overview of our current knowledge of protein-protein interaction networks, and how their systemic perturbation can be analysed by two popular network simulation methods: Boolean network and ordinary differential equations.
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Affiliation(s)
- Tammy M K Cheng
- Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln's Inn Fields, London WC2A 3LY, UK
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Wang N, Xu HL, Zhao X, Wen X, Wang FT, Wang SY, Fu LL, Liu B, Bao JK. Network-based identification of novel connections among apoptotic signaling pathways in cancer. Appl Biochem Biotechnol 2012; 167:621-31. [PMID: 22581077 DOI: 10.1007/s12010-012-9704-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Accepted: 04/23/2012] [Indexed: 02/05/2023]
Abstract
MicroRNAs (miRNAs), highly conserved, non-coding endogenous RNA and nearly ~22 nucleotides (nt) in length, are well-known to regulate several apoptotic pathways in cancer. In this study, we computationally constructed the initial human apoptotic PPI network by several online databases, and further integrated these high-throughput datasets into a Naïve Bayesian model to predict protein functional connections. Based on the modified apoptotic network, we identified several apoptotic hub proteins such as TP53, SRC, M3K3/5/8, cyclin-dependent kinase2/6, TNFR16/19, and TGF-β receptor 1/2. Subsequently, we identified some microRNAs that could target the aforementioned apoptotic hub proteins by using TargetScan, PicTar, and Diana-MicroH. In conclusion, these results demonstrate the PPI network-based identification of new connections amongst apoptotic pathways in cancer, which may shed new light on the intricate relationships between core apoptotic pathways and some targeted miRNAs in human cancers.
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Affiliation(s)
- Nan Wang
- School of Life Sciences and The State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China
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Pathway-pathway network-based study of the therapeutic mechanisms by which salvianolic acid B regulates cardiovascular diseases. ACTA ACUST UNITED AC 2012. [DOI: 10.1007/s11434-012-5142-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Laezza F. An interview with Fernanda Laezza, MD, PhD, by Vicki Glaser. Assay Drug Dev Technol 2012; 10:105-10. [PMID: 22497607 DOI: 10.1089/adt.2012.1002.pr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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49
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Zhao S, Li S. A co-module approach for elucidating drug-disease associations and revealing their molecular basis. ACTA ACUST UNITED AC 2012; 28:955-61. [PMID: 22285830 DOI: 10.1093/bioinformatics/bts057] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
MOTIVATION Understanding how drugs and diseases are associated in the molecular level is of critical importance to unveil disease mechanisms and treatments. Until recently, few studies attempt end to discover important gene modules shared by both drugs and diseases. RESULTS Here, we propose a novel presentation of drug-gene-disease relationship, a 'co-module', which is characterized by closely related drugs, diseases and genes. We first define a network-based gene closeness profile to relate drug to disease. Then, we develop a Bayesian partition method to identify drug-gene-disease co-modules underlying the gene closeness data. Genes share similar notable patterns with respect not only to the drugs but also the diseases within a co-module. Simulations show that our method, comCIPHER, achieves a better performance compared with a popular co-module detection method, PPA. We apply comCIPHER to a set consisting of 723 drugs, 275 diseases and 1442 genes and demonstrate that our co-module approach is able to identify new drug-disease associations and highlight their molecular basis. Disease co-morbidity emerges as well. Three co-modules are further illustrated in which new drug applications, including the anti-cancer metastasis activity of an anti-asthma drug Pranlukast, and a cardiovascular stress-testing agent Arbutamine for obesity, as well as potential side-effects, e.g. hypotension for Triamterene, are computationally identified. AVAILABILITY The compiled version of comCIPHER can be found at http://bioinfo.au.tsinghua.edu.cn/comCIPHER/. The 86 co-modules can be downloaded from http://bioinfo.au.tsinghua.edu.cn/comCIPHER/Co_Module_Results.zip. CONTACT shaoli@mail.tsinghua.edu.cn SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Shiwen Zhao
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST/Department of Automation, Tsinghua University, Beijing, China
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Yao CW, Hsu BD, Chen BS. Constructing gene regulatory networks for long term photosynthetic light acclimation in Arabidopsis thaliana. BMC Bioinformatics 2011; 12:335. [PMID: 21834997 PMCID: PMC3162938 DOI: 10.1186/1471-2105-12-335] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Accepted: 08/11/2011] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Photosynthetic light acclimation is an important process that allows plants to optimize the efficiency of photosynthesis, which is the core technology for green energy. However, currently little is known about the molecular mechanisms behind the regulation of the photosynthetic light acclimation response. In this study, a systematic method is proposed to investigate this mechanism by constructing gene regulatory networks from microarray data of Arabidopsis thaliana. METHODS The potential TF-gene regulatory pairs of photosynthetic light acclimation have been obtained by data mining of literature and databases. Following the identification of these potential TF-gene pairs, they have been refined using Pearson's correlation, allowing the construction of a rough gene regulatory network. This rough gene regulatory network is then pruned using time series microarray data of Arabidopsis thaliana via the maximum likelihood system identification method and Akaike's system order detection method to approach the real gene regulatory network of photosynthetic light acclimation. RESULTS By comparing the gene regulatory networks under the PSI-to-PSII light shift and the PSII-to-PSI light shift, it is possible to identify important transcription factors for the different light shift conditions. Furthermore, the robustness of the gene network, in particular the hubs and weak linkage points, are also discussed under the different light conditions to gain further insight into the mechanisms of photosynthesis. CONCLUSIONS This study investigates the molecular mechanisms of photosynthetic light acclimation for Arabidopsis thaliana from the physiological level. This has been achieved through the construction of gene regulatory networks from the limited data sources and literature via an efficient computation method. If more experimental data for whole-genome ChIP-chip data and microarray data with multiple sampling points becomes available in the future, the proposed method will be improved on by constructing the whole-genome gene regulatory network. These advances will greatly improve our understanding of the mechanisms of the photosynthetic system.
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Affiliation(s)
- Cheng-Wei Yao
- Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsin-Chu, 300, Taiwan
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