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Stephan S, Galland S, Labbani Narsis O, Shoji K, Vachenc S, Gerart S, Nicolle C. Agent-based approaches for biological modeling in oncology: A literature review. Artif Intell Med 2024; 152:102884. [PMID: 38703466 DOI: 10.1016/j.artmed.2024.102884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/06/2024]
Abstract
CONTEXT Computational modeling involves the use of computer simulations and models to study and understand real-world phenomena. Its application is particularly relevant in the study of potential interactions between biological elements. It is a promising approach to understand complex biological processes and predict their behavior under various conditions. METHODOLOGY This paper is a review of the recent literature on computational modeling of biological systems. Our study focuses on the field of oncology and the use of artificial intelligence (AI) and, in particular, agent-based modeling (ABM), between 2010 and May 2023. RESULTS Most of the articles studied focus on improving the diagnosis and understanding the behaviors of biological entities, with metaheuristic algorithms being the models most used. Several challenges are highlighted regarding increasing and structuring knowledge about biological systems, developing holistic models that capture multiple scales and levels of organization, reproducing emergent behaviors of biological systems, validating models with experimental data, improving computational performance of models and algorithms, and ensuring privacy and personal data protection are discussed.
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Affiliation(s)
- Simon Stephan
- UTBM, CIAD UMR 7533, Belfort, F-90010, France; Université de Bourgogne, CIAD UMR 7533, Dijon, F-21000, France.
| | | | | | - Kenji Shoji
- Oncodesign Precision Medicine (OPM), 18 Rue Jean Mazen, Dijon, F-21000, France
| | - Sébastien Vachenc
- Oncodesign Precision Medicine (OPM), 18 Rue Jean Mazen, Dijon, F-21000, France
| | - Stéphane Gerart
- Oncodesign Precision Medicine (OPM), 18 Rue Jean Mazen, Dijon, F-21000, France
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Manuel AM, Gottlieb A, Freeman L, Zhao Z. Montelukast as a repurposable additive drug for standard-efficacy multiple sclerosis treatment: Emulating clinical trials with retrospective administrative health claims data. Mult Scler 2024; 30:696-706. [PMID: 38660773 PMCID: PMC11073911 DOI: 10.1177/13524585241240398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
BACKGROUND Effective and safe treatment options for multiple sclerosis (MS) are still needed. Montelukast, a leukotriene receptor antagonist (LTRA) currently indicated for asthma or allergic rhinitis, may provide an additional therapeutic approach. OBJECTIVE The study aimed to evaluate the effects of montelukast on the relapses of people with MS (pwMS). METHODS In this retrospective case-control study, two independent longitudinal claims datasets were used to emulate randomized clinical trials (RCTs). We identified pwMS aged 18-65 years, on MS disease-modifying therapies concomitantly, in de-identified claims from Optum's Clinformatics® Data Mart (CDM) and IQVIA PharMetrics® Plus for Academics. Cases included 483 pwMS on montelukast and with medication adherence in CDM and 208 in PharMetrics Plus for Academics. We randomly sampled controls from 35,330 pwMS without montelukast prescriptions in CDM and 10,128 in PharMetrics Plus for Academics. Relapses were measured over a 2-year period through inpatient hospitalization and corticosteroid claims. A doubly robust causal inference model estimated the effects of montelukast, adjusting for confounders and censored patients. RESULTS pwMS treated with montelukast demonstrated a statistically significant 23.6% reduction in relapses compared to non-users in 67.3% of emulated RCTs. CONCLUSION Real-world evidence suggested that montelukast reduces MS relapses, warranting future clinical trials and further research on LTRAs' potential mechanism in MS.
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Affiliation(s)
- Astrid M Manuel
- Center for Precision Health, McWilliams School of Biomedical Informatics, University of Texas Health Science Center at Houston, TX
| | - Assaf Gottlieb
- Center for Precision Health, McWilliams School of Biomedical Informatics, University of Texas Health Science Center at Houston, TX
| | - Leorah Freeman
- Neurology Department, Dell Medical School, The University of Texas at Austin, TX
| | - Zhongming Zhao
- Center for Precision Health, McWilliams School of Biomedical Informatics, University of Texas Health Science Center at Houston, TX
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, TX
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Mahmoudi A, Hajihasani MM, Majeed M, Jamialahmadi T, Sahebkar A. Effect of Calebin-A on Critical Genes Related to NAFLD: A Protein-Protein Interaction Network and Molecular Docking Study. Curr Genomics 2024; 25:120-139. [PMID: 38751599 PMCID: PMC11092913 DOI: 10.2174/0113892029280454240214072212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 01/12/2024] [Accepted: 02/01/2024] [Indexed: 05/18/2024] Open
Abstract
Background Calebin-A is a minor phytoconstituent of turmeric known for its activity against inflammation, oxidative stress, cancerous, and metabolic disorders like Non-alcoholic fatty liver disease(NAFLD). Based on bioinformatic tools. Subsequently, the details of the interaction of critical proteins with Calebin-A were investigated using the molecular docking technique. Methods We first probed the intersection of genes/ proteins between NAFLD and Calebin-A through online databases. Besides, we performed an enrichment analysis using the ClueGO plugin to investigate signaling pathways and gene ontology. Next, we evaluate the possible interaction of Calebin-A with significant hub proteins involved in NAFLD through a molecular docking study. Results We identified 87 intersection genes Calebin-A targets associated with NAFLD. PPI network analysis introduced 10 hub genes (TP53, TNF, STAT3, HSP90AA1, PTGS2, HDAC6, ABCB1, CCT2, NR1I2, and GUSB). In KEGG enrichment, most were associated with Sphingolipid, vascular endothelial growth factor A (VEGFA), C-type lectin receptor, and mitogen-activated protein kinase (MAPK) signaling pathways. The biological processes described in 87 intersection genes are mostly concerned with regulating the apoptotic process, cytokine production, and intracellular signal transduction. Molecular docking results also directed that Calebin-A had a high affinity to bind hub proteins linked to NAFLD. Conclusion Here, we showed that Calebin-A, through its effect on several critical genes/ proteins and pathways, might repress the progression of NAFLD.
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Affiliation(s)
- Ali Mahmoudi
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Mahdi Hajihasani
- Department of Pharmaceutical Control, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Muhammed Majeed
- Department of Chemistry, Sabinsa Corporation, 20 Lake Drive, East Windsor, NJ, 08520, USA
| | - Tannaz Jamialahmadi
- Medical Toxicology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran;
| | - Amirhossein Sahebkar
- Department of Medical Biotechnology, Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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Israr J, Alam S, Kumar A. System biology approaches for drug repurposing. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 205:221-245. [PMID: 38789180 DOI: 10.1016/bs.pmbts.2024.03.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
Drug repurposing, or drug repositioning, refers to the identification of alternative therapeutic applications for established medications that go beyond their initial indications. This strategy has becoming increasingly popular since it has the potential to significantly reduce the overall costs of drug development by around $300 million. System biology methodologies have been employed to facilitate medication repurposing, encompassing computational techniques such as signature matching and network-based strategies. These techniques utilize pre-existing drug-related data types and databases to find prospective repurposed medications that have minimal or acceptable harmful effects on patients. The primary benefit of medication repurposing in comparison to drug development lies in the fact that approved pharmaceuticals have already undergone multiple phases of clinical studies, thereby possessing well-established safety and pharmacokinetic properties. Utilizing system biology methodologies in medication repurposing offers the capacity to expedite the discovery of viable candidates for drug repurposing and offer novel perspectives for structure-based drug design.
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Affiliation(s)
- Juveriya Israr
- Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Lucknow-Deva Road, Barabanki, Uttar Pradesh, India; Department of Biotechnology Era University, Lucknow, Uttar Pradesh, India
| | - Shabroz Alam
- Department of Biotechnology Era University, Lucknow, Uttar Pradesh, India
| | - Ajay Kumar
- Department of Biotechnology, Faculty of Engineering and Technology, Rama University, Mandhana, Kanpur, Uttar Pradesh, India.
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Wu L, Jin W, Yu H, Liu B. Modulating autophagy to treat diseases: A revisited review on in silico methods. J Adv Res 2024; 58:175-191. [PMID: 37192730 PMCID: PMC10982871 DOI: 10.1016/j.jare.2023.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 05/18/2023] Open
Abstract
BACKGROUND Autophagy refers to the conserved cellular catabolic process relevant to lysosome activity and plays a vital role in maintaining the dynamic equilibrium of intracellular matter by degrading harmful and abnormally accumulated cellular components. Accumulating evidence has recently revealed that dysregulation of autophagy by genetic and exogenous interventions may disrupt cellular homeostasis in human diseases. In silico approaches as powerful aids to experiments have also been extensively reported to play their critical roles in the storage, prediction, and analysis of massive amounts of experimental data. Thus, modulating autophagy to treat diseases by in silico methods would be anticipated. AIM OF REVIEW Here, we focus on summarizing the updated in silico approaches including databases, systems biology network approaches, omics-based analyses, mathematical models, and artificial intelligence (AI) methods that sought to modulate autophagy for potential therapeutic purposes, which will provide a new insight into more promising therapeutic strategies. KEY SCIENTIFIC CONCEPTS OF REVIEW Autophagy-related databases are the data basis of the in silico method, storing a large amount of information about DNA, RNA, proteins, small molecules and diseases. The systems biology approach is a method to systematically study the interrelationships among biological processes including autophagy from a macroscopic perspective. Omics-based analyses are based on high-throughput data to analyze gene expression at different levels of biological processes involving autophagy. mathematical models are visualization methods to describe the dynamic process of autophagy, and its accuracy is related to the selection of parameters. AI methods use big data related to autophagy to predict autophagy targets, design targeted small molecules, and classify diverse human diseases for potential therapeutic applications.
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Affiliation(s)
- Lifeng Wu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Wenke Jin
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Haiyang Yu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China.
| | - Bo Liu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.
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Pathak RK, Kim JM. Veterinary systems biology for bridging the phenotype-genotype gap via computational modeling for disease epidemiology and animal welfare. Brief Bioinform 2024; 25:bbae025. [PMID: 38343323 PMCID: PMC10859662 DOI: 10.1093/bib/bbae025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/02/2024] [Accepted: 01/15/2024] [Indexed: 02/15/2024] Open
Abstract
Veterinary systems biology is an innovative approach that integrates biological data at the molecular and cellular levels, allowing for a more extensive understanding of the interactions and functions of complex biological systems in livestock and veterinary science. It has tremendous potential to integrate multi-omics data with the support of vetinformatics resources for bridging the phenotype-genotype gap via computational modeling. To understand the dynamic behaviors of complex systems, computational models are frequently used. It facilitates a comprehensive understanding of how a host system defends itself against a pathogen attack or operates when the pathogen compromises the host's immune system. In this context, various approaches, such as systems immunology, network pharmacology, vaccinology and immunoinformatics, can be employed to effectively investigate vaccines and drugs. By utilizing this approach, we can ensure the health of livestock. This is beneficial not only for animal welfare but also for human health and environmental well-being. Therefore, the current review offers a detailed summary of systems biology advancements utilized in veterinary sciences, demonstrating the potential of the holistic approach in disease epidemiology, animal welfare and productivity.
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Affiliation(s)
- Rajesh Kumar Pathak
- Department of Animal Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi-do 17546, Republic of Korea
| | - Jun-Mo Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi-do 17546, Republic of Korea
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Tafti A, Shojaei S, Zali H, Karima S, Mohammadi-Yeganeh S, Mondanizadeh M. A systems biology approach and in vitro experiment indicated Rapamycin targets key cancer and cell cycle-related genes and miRNAs in triple-negative breast cancer cells. Mol Carcinog 2023; 62:1960-1973. [PMID: 37787375 DOI: 10.1002/mc.23628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 07/29/2023] [Accepted: 08/22/2023] [Indexed: 10/04/2023]
Abstract
An anticancer drug known as Rapamycin acts by inhibiting the mammalian target of the Rapamycin pathway. This agent has recently been investigated for its potential therapeutic benefits in sensitizing drug-resistant breast cancer (BC) treatment. The molecular mechanism underlying these effects, however, is still a mystery. Using a systems biology method and in vitro experiment, this study sought to discover essential genes and microRNAs (miRNAs) targeted by Rapamycin in triple-negative BC (TNBC) cells to aid prospective new medications with less adverse effects in BC treatment. We developed the transcription factor-miRNA-gene and protein-protein interaction networks using the freely accessible microarray data sets. FANMOD and MCODE were utilized to identify critical regulatory motifs, clusters, and seeds. Then, functional enrichment analyses were conducted. Using topological analysis and motif detection, the most important genes and miRNAs were discovered. We used quantitative real-time polymerase chain reaction (qRT-PCR) to examine the effect of Rapamycin on the expression of the selected genes and miRNAs to verify our findings. We performed flow cytometry to investigate Rapamycin's impact on cell cycle and apoptosis. Furthermore, wound healing and migration assays were done. Three downregulated (PTGS2, EGFR, VEGFA) and three upregulated (c-MYC, MAPK1, PIK3R1) genes were chosen as candidates for additional experimental verification. There were also three upregulated miRNAs (miR-92a, miR-16, miR-20a) and three downregulated miRNAs (miR-146a, miR-145, miR-27a) among the six selected miRNAs. The qRT-PCR findings in MDA-MB-231 cells indicated that c-MYC, MAPK1, PIK3R1, miR-92a, miR-16, and miR-20a expression levels were considerably elevated following Rapamycin treatment, whereas PTGS2, EGFR, VEGFA, miR-146a, and miR-145 expression levels were dramatically lowered (p < 0.05). These genes are engaged in cancer pathways, transcriptional dysregulation in cancer, and cell cycle, according to the top pathway enrichment findings. Migration and wound healing abilities of the cells declined after Rapamycin treatment, and the number of apoptotic cells increased. We demonstrated that Rapamycin suppresses cell migration and metastasis in the TNBC cell line. In addition, our data indicated that Rapamycin induces apoptosis in this cell line. The discovered vital genes and miRNAs affected by Rapamycin are anticipated to have crucial roles in the pathogenesis of TNBC and its therapeutic resistance.
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Affiliation(s)
- Ali Tafti
- Department of Biotechnology and Molecular Medicine, Faculty of Medicine, Arak University of Medical Sciences, Arak, Iran
| | - Samaneh Shojaei
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hakimeh Zali
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Saeed Karima
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Samira Mohammadi-Yeganeh
- Medical Nanotechnology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mahdieh Mondanizadeh
- Department of Biotechnology and Molecular Medicine, Faculty of Medicine, Arak University of Medical Sciences, Arak, Iran
- Molecular and Medicine Research Center, Arak University of Medical Sciences, Arak, Iran
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Ruan H, Zhang H, Feng J, Luo H, Fu F, Yao S, Zhou C, Zhang Z, Bian Y, Jin H, Zhang Y, Wu C, Tong P. Inhibition of Caspase-1-mediated pyroptosis promotes osteogenic differentiation, offering a therapeutic target for osteoporosis. Int Immunopharmacol 2023; 124:110901. [PMID: 37839278 DOI: 10.1016/j.intimp.2023.110901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/20/2023] [Accepted: 09/03/2023] [Indexed: 10/17/2023]
Abstract
BACKGROUND Pyroptosis, an emerging inflammatory form of cell death, has been previously demonstrated to stimulate a massive inflammatory response, thus hindering the osteogenic differentiation of bone marrow mesenchymal stem cells (BMSCs). Nevertheless, the impact of pyroptosis in thwarting osteogenic differentiation and exacerbating the advancement of osteoporosis (OP) remains enigmatic. METHODS We evaluated the expression levels of pyroptosis-associated indicators, including NOD-like receptor family pyrin domain-containing protein 3 (NLRP3), CASPASE-1, IL-1β, and IL-18, in specimens obtained from femoral heads of OP patients, as well as in an ovariectomy-induced mouse model of OP. Subsequently, the precise roles of pyroptosis in osteogenic differentiation were investigated using bioinformatics analysis, alongside morphological and biochemical assessments. RESULTS The pivotal pyroptotic proteins, including NLRP3, Caspase-1, IL-1β, and IL-18, exhibited significant upregulation within the bone tissue samples of clinical OP cases, as well as in the femoral tissues of ovariectomy (OVX)-induced mouse OP model, displaying a negatively associated with compromised osteogenic capacity, as represented by lessened bone mass, suppressed expression of osteogenic proteins such as Runt-related transcription factor 2 (RUNX2), Alkaline phosphatase (ALP), Osterix (OSX), and Osteopontin (OPN), and increased lipid droplets. Moreover, bioinformatics analysis substantiated shared gene expression patterns between pyroptosis and OP pathology, encompassing NLRP3, Caspase-1, IL-1β, IL-18, etc. Furthermore, our in vitro investigation using ST2 cells revealed that dexamethasone treatment prominently induced pyroptosis while impeding osteogenic differentiation. Notably, gene silencing of Caspase-1 effectively counteracted the inhibitory effects of dexamethasone on osteogenic differentiation, as manifested by increased ALP activity and enhanced expression of RUNX2, ALP, OSX, and OPN. CONCLUSION Our findings unequivocally underscore that inhibition of Caspase-1-mediated pyroptosis promotes osteogenic differentiation, providing a promising therapeutic target for managing OP.
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Affiliation(s)
- Hongfeng Ruan
- Institute of Orthopaedics and Traumatology, the First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Huihao Zhang
- Department of Orthopaedics, First Hospital of Wuhan, Wuhan, Hubei, China; Hangzhou Fuyang Hospital of TCM Orthopedics and Traumatology, Hangzhou, Zhejiang, China
| | - Jing Feng
- Department of Orthopaedics, First Hospital of Wuhan, Wuhan, Hubei, China
| | - Huan Luo
- Department of Pharmacy, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Fangda Fu
- Institute of Orthopaedics and Traumatology, the First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Sai Yao
- Institute of Orthopaedics and Traumatology, the First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Chengcong Zhou
- Institute of Orthopaedics and Traumatology, the First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Zhiguo Zhang
- Institute of Orthopaedics and Traumatology, the First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Yishan Bian
- Institute of Orthopaedics and Traumatology, the First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Hongting Jin
- Institute of Orthopaedics and Traumatology, the First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Yuliang Zhang
- Hangzhou Fuyang Hospital of TCM Orthopedics and Traumatology, Hangzhou, Zhejiang, China.
| | - Chengliang Wu
- Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China.
| | - Peijian Tong
- Institute of Orthopaedics and Traumatology, the First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China.
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Wu Y, Qian B, Wang A, Dong H, Zhu E, Ma B. iLSGRN: inference of large-scale gene regulatory networks based on multi-model fusion. Bioinformatics 2023; 39:btad619. [PMID: 37851379 PMCID: PMC10589915 DOI: 10.1093/bioinformatics/btad619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 10/04/2023] [Accepted: 10/17/2023] [Indexed: 10/19/2023] Open
Abstract
MOTIVATION Gene regulatory networks (GRNs) are a way of describing the interaction between genes, which contribute to revealing the different biological mechanisms in the cell. Reconstructing GRNs based on gene expression data has been a central computational problem in systems biology. However, due to the high dimensionality and non-linearity of large-scale GRNs, accurately and efficiently inferring GRNs is still a challenging task. RESULTS In this article, we propose a new approach, iLSGRN, to reconstruct large-scale GRNs from steady-state and time-series gene expression data based on non-linear ordinary differential equations. Firstly, the regulatory gene recognition algorithm calculates the Maximal Information Coefficient between genes and excludes redundant regulatory relationships to achieve dimensionality reduction. Then, the feature fusion algorithm constructs a model leveraging the feature importance derived from XGBoost (eXtreme Gradient Boosting) and RF (Random Forest) models, which can effectively train the non-linear ordinary differential equations model of GRNs and improve the accuracy and stability of the inference algorithm. The extensive experiments on different scale datasets show that our method makes sensible improvement compared with the state-of-the-art methods. Furthermore, we perform cross-validation experiments on the real gene datasets to validate the robustness and effectiveness of the proposed method. AVAILABILITY AND IMPLEMENTATION The proposed method is written in the Python language, and is available at: https://github.com/lab319/iLSGRN.
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Affiliation(s)
- Yiming Wu
- School of Information Science and Technology, Dalian Maritime University, Dalian 116026, China
| | - Bing Qian
- School of Information Science and Technology, Dalian Maritime University, Dalian 116026, China
| | - Anqi Wang
- Department of Statistics and Actuarial Science, The University of Hong Kong, Hong Kong 999077, China
| | - Heng Dong
- School of Information Science and Technology, Dalian Maritime University, Dalian 116026, China
| | - Enqiang Zhu
- Institution of Computing Science and Technology, Guangzhou University, Guangzhou 510006, China
| | - Baoshan Ma
- School of Information Science and Technology, Dalian Maritime University, Dalian 116026, China
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Li C, Wang T, Lin X. Analyzing omics data by feature combinations based on kernel functions. J Bioinform Comput Biol 2023; 21:2350021. [PMID: 37852788 DOI: 10.1142/s021972002350021x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
Defining meaningful feature (molecule) combinations can enhance the study of disease diagnosis and prognosis. However, feature combinations are complex and various in biosystems, and the existing methods examine the feature cooperation in a single, fixed pattern for all feature pairs, such as linear combination. To identify the appropriate combination between two features and evaluate feature combination more comprehensively, this paper adopts kernel functions to study feature relationships and proposes a new omics data analysis method KF-[Formula: see text]-TSP. Besides linear combination, KF-[Formula: see text]-TSP also explores the nonlinear combination of features, and allows hybridizing multiple kernel functions to evaluate feature interaction from multiple views. KF-[Formula: see text]-TSP selects [Formula: see text] > 0 top-scoring pairs to build an ensemble classifier. Experimental results show that KF-[Formula: see text]-TSP with multiple kernel functions which evaluates feature combinations from multiple views is better than that with only one kernel function. Meanwhile, KF-[Formula: see text]-TSP performs better than TSP family algorithms and the previous methods based on conversion strategy in most cases. It performs similarly to the popular machine learning methods in omics data analysis, but involves fewer feature pairs. In the procedure of physiological and pathological changes, molecular interactions can be both linear and nonlinear. Hence, KF-[Formula: see text]-TSP, which can measure molecular combination from multiple perspectives, can help to mine information closely related to physiological and pathological changes and study disease mechanism.
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Affiliation(s)
- Chao Li
- School of Computer Science and Technology, Dalian University of Technology, No. 2 Linggong Road, Dalian, Liaoning 116024, P. R. China
| | - Tianxiang Wang
- School of Computer Science and Technology, Dalian University of Technology, No. 2 Linggong Road, Dalian, Liaoning 116024, P. R. China
| | - Xiaohui Lin
- School of Computer Science and Technology, Dalian University of Technology, No. 2 Linggong Road, Dalian, Liaoning 116024, P. R. China
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Nelson LM, Spencer H, Hijane K, Thinuan P, Nelson CW, Vincent AJ, Gordon CM, Plant TM, Fazeli PK. My 28 Days - a global digital women's health initiative for evaluation and management of secondary amenorrhea: case report and literature review. Front Endocrinol (Lausanne) 2023; 14:1227253. [PMID: 37772077 PMCID: PMC10523024 DOI: 10.3389/fendo.2023.1227253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/18/2023] [Indexed: 09/30/2023] Open
Abstract
There is a need to close the gap between knowledge and action in health care. Effective care requires a convenient and reliable distribution process. As global internet and mobile communication increase capacity, innovative approaches to digital health education platforms and care delivery are feasible. We report the case of a young African woman who developed acute secondary amenorrhea at age 18. Subsequently, she experienced a 10-year delay in the diagnosis of the underlying cause. A global digital medical hub focused on women's health and secondary amenorrhea could reduce the chance of such mismanagement. Such a hub would establish more efficient information integration and exchange processes to better serve patients, family caregivers, health care providers, and investigators. Here, we show proof of concept for a global digital medical hub for women's health. First, we describe the physiological control systems that govern the normal menstrual cycle, and review the pathophysiology and management of secondary amenorrhea. The symptom may lead to broad and profound health implications for the patient and extended family members. In specific situations, there may be significant morbidity related to estradiol deficiency: (1) reduced bone mineral density, 2) cardiovascular disease, and 3) cognitive decline. Using primary ovarian insufficiency (POI) as the paradigm condition, the Mary Elizabeth Conover Foundation has been able to address the specific global educational needs of these women. The Foundation did this by creating a professionally managed Facebook group specifically for these women. POI most commonly presents with secondary amenorrhea. Here we demonstrate the feasibility of conducting a natural history study on secondary amenorrhea with international reach to be coordinated by a global digital medical hub. Such an approach takes full advantage of internet and mobile device communication systems. We refer to this global digital women's health initiative as My 28 Days®.
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Affiliation(s)
- Lawrence M. Nelson
- Digital Women's Health Initiative, Mary Elizabeth Conover Foundation, Tysons, VA, United States
| | - Hillary Spencer
- Digital Women's Health Initiative, Mary Elizabeth Conover Foundation, Tysons, VA, United States
| | - Karima Hijane
- Digital Women's Health Initiative, Mary Elizabeth Conover Foundation, Tysons, VA, United States
| | - Payom Thinuan
- Faculty of Nursing, Boromarajonani College of Nursing Nakhon, Lampang, Thailand
| | - Chaninan W. Nelson
- Digital Women's Health Initiative, Mary Elizabeth Conover Foundation, Tysons, VA, United States
| | - Amanda J. Vincent
- Monash Centre for Health Research and Implementation (MCHRI), Monash University, Clayton, VIC, Australia
| | - Catherine M. Gordon
- Endocrinology and Metabolism, Baylor College of Medicine, Houston, TX, United States
| | - Tony M. Plant
- Endocrinology and Metabolism, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Pouneh K. Fazeli
- Endocrinology and Metabolism, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
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12
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O'Connor LM, O'Connor BA, Lim SB, Zeng J, Lo CH. Integrative multi-omics and systems bioinformatics in translational neuroscience: A data mining perspective. J Pharm Anal 2023; 13:836-850. [PMID: 37719197 PMCID: PMC10499660 DOI: 10.1016/j.jpha.2023.06.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 06/20/2023] [Accepted: 06/25/2023] [Indexed: 09/19/2023] Open
Abstract
Bioinformatic analysis of large and complex omics datasets has become increasingly useful in modern day biology by providing a great depth of information, with its application to neuroscience termed neuroinformatics. Data mining of omics datasets has enabled the generation of new hypotheses based on differentially regulated biological molecules associated with disease mechanisms, which can be tested experimentally for improved diagnostic and therapeutic targeting of neurodegenerative diseases. Importantly, integrating multi-omics data using a systems bioinformatics approach will advance the understanding of the layered and interactive network of biological regulation that exchanges systemic knowledge to facilitate the development of a comprehensive human brain profile. In this review, we first summarize data mining studies utilizing datasets from the individual type of omics analysis, including epigenetics/epigenomics, transcriptomics, proteomics, metabolomics, lipidomics, and spatial omics, pertaining to Alzheimer's disease, Parkinson's disease, and multiple sclerosis. We then discuss multi-omics integration approaches, including independent biological integration and unsupervised integration methods, for more intuitive and informative interpretation of the biological data obtained across different omics layers. We further assess studies that integrate multi-omics in data mining which provide convoluted biological insights and offer proof-of-concept proposition towards systems bioinformatics in the reconstruction of brain networks. Finally, we recommend a combination of high dimensional bioinformatics analysis with experimental validation to achieve translational neuroscience applications including biomarker discovery, therapeutic development, and elucidation of disease mechanisms. We conclude by providing future perspectives and opportunities in applying integrative multi-omics and systems bioinformatics to achieve precision phenotyping of neurodegenerative diseases and towards personalized medicine.
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Affiliation(s)
- Lance M. O'Connor
- College of Biological Sciences, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Blake A. O'Connor
- School of Pharmacy, University of Wisconsin, Madison, WI, 53705, USA
| | - Su Bin Lim
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, 16499, South Korea
| | - Jialiu Zeng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| | - Chih Hung Lo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
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13
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Rathore D, Marino MJ, Nita-Lazar A. Omics and systems view of innate immune pathways. Proteomics 2023; 23:e2200407. [PMID: 37269203 DOI: 10.1002/pmic.202200407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/16/2023] [Accepted: 05/23/2023] [Indexed: 06/04/2023]
Abstract
Multiomics approaches to studying systems biology are very powerful techniques that can elucidate changes in the genomic, transcriptomic, proteomic, and metabolomic levels within a cell type in response to an infection. These approaches are valuable for understanding the mechanisms behind disease pathogenesis and how the immune system responds to being challenged. With the emergence of the COVID-19 pandemic, the importance and utility of these tools have become evident in garnering a better understanding of the systems biology within the innate and adaptive immune response and for developing treatments and preventative measures for new and emerging pathogens that pose a threat to human health. In this review, we focus on state-of-the-art omics technologies within the scope of innate immunity.
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Affiliation(s)
- Deepali Rathore
- Functional Cellular Networks Section, Laboratory of Immune Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Matthew J Marino
- Functional Cellular Networks Section, Laboratory of Immune Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Aleksandra Nita-Lazar
- Functional Cellular Networks Section, Laboratory of Immune Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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14
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Nelson AR, Bugg D, Davis J, Saucerman JJ. Network model integrated with multi-omic data predicts MBNL1 signals that drive myofibroblast activation. iScience 2023; 26:106502. [PMID: 37091233 PMCID: PMC10119756 DOI: 10.1016/j.isci.2023.106502] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 01/09/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
RNA-binding protein muscleblind-like1 (MBNL1) was recently identified as a central regulator of cardiac wound healing and myofibroblast activation. To identify putative MBNL1 targets, we integrated multiple genome-wide screens with a fibroblast network model. We expanded the model to include putative MBNL1-target interactions and recapitulated published experimental results to validate new signaling modules. We prioritized 14 MBNL1 targets and developed novel fibroblast signaling modules for p38 MAPK, Hippo, Runx1, and Sox9 pathways. We experimentally validated MBNL1 regulation of p38 expression in mouse cardiac fibroblasts. Using the expanded fibroblast model, we predicted a hierarchy of MBNL1 regulated pathways with strong influence on αSMA expression. This study lays a foundation to explore the network mechanisms of MBNL1 signaling central to fibrosis.
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Affiliation(s)
- Anders R. Nelson
- Department of Pharmacology, University of Virginia, 1340 Jefferson Park Avenue, Pinn Hall, 5th Floor, PO Box 800735, Charlottesville, VA 22908-0735, USA
| | - Darrian Bugg
- Department of Lab Medicine & Pathology, University of Washington, 1959 NE Pacific Street Box 357470, Seattle, WA 98195, USA
| | - Jennifer Davis
- Department of Lab Medicine & Pathology, University of Washington, 1959 NE Pacific Street Box 357470, Seattle, WA 98195, USA
- Department of Bioengineering, University of Washington, PO Box 355061, Seattle, WA 98195-5061, USA
- Institute for Stem Cell & Regenerative Medicine, University of Washington, 850 Republican Street, PO Box 358056, Seattle, WA 98109, USA
| | - Jeffrey J. Saucerman
- Department of Biomedical Engineering, University of Virginia, PO Box 800759, Charlottesville, VA 22903 , USA
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15
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Merseal HM, Beaty RE, Kenett YN, Lloyd-Cox J, de Manzano Ö, Norgaard M. Representing melodic relationships using network science. Cognition 2023; 233:105362. [PMID: 36628852 DOI: 10.1016/j.cognition.2022.105362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 11/13/2022] [Accepted: 12/18/2022] [Indexed: 01/11/2023]
Abstract
Music is a complex system consisting of many dimensions and hierarchically organized information-the organization of which, to date, we do not fully understand. Network science provides a powerful approach to representing such complex systems, from the social networks of people to modelling the underlying network structures of different cognitive mechanisms. In the present research, we explored whether network science methodology can be extended to model the melodic patterns underlying expert improvised music. Using a large corpus of transcribed improvisations, we constructed a network model in which 5-pitch sequences were linked depending on consecutive occurrences, constituting 116,403 nodes (sequences) and 157,429 edges connecting them. We then investigated whether mathematical graph modelling relates to musical characteristics in real-world listening situations via a behavioral experiment paralleling those used to examine language. We found that as melodic distance within the network increased, participants judged melodic sequences as less related. Moreover, the relationship between distance and reaction time (RT) judgements was quadratic: participants slowed in RT up to distance four, then accelerated; a parallel finding to research in language networks. This study offers insights into the hidden network structure of improvised tonal music and suggests that humans are sensitive to the property of melodic distance in this network. More generally, our work demonstrates the similarity between music and language as complex systems, and how network science methods can be used to quantify different aspects of its complexity.
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Affiliation(s)
- Hannah M Merseal
- Department of Psychology, Pennsylvania State University, United States.
| | - Roger E Beaty
- Department of Psychology, Pennsylvania State University, United States
| | - Yoed N Kenett
- Faculty of Data and Decisions Sciences, Technion Institute of Technology, Israel
| | - James Lloyd-Cox
- Department of Cognitive Neuroscience, Goldsmiths, University of London, England, United Kingdom
| | - Örjan de Manzano
- Department of Cognitive Neuropsychology, Max Planck Institute for Empirical Aesthetics, Germany
| | - Martin Norgaard
- Department of Music Education, Georgia State University, United States
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16
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Integrated Bioinformatics Analysis of Shared Genes, miRNA, Biological Pathways and Their Potential Role as Therapeutic Targets in Huntington's Disease Stages. Int J Mol Sci 2023; 24:ijms24054873. [PMID: 36902304 PMCID: PMC10003639 DOI: 10.3390/ijms24054873] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/24/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023] Open
Abstract
Huntington's Disease (HD) is a progressive neurodegenerative disease caused by CAG repeat expansion in the huntingtin gene (HTT). The HTT gene was the first disease-associated gene mapped to a chromosome, but the pathophysiological mechanisms, genes, proteins or miRNAs involved in HD remain poorly understood. Systems bioinformatics approaches can divulge the synergistic relationships of multiple omics data and their integration, and thus provide a holistic approach to understanding diseases. The purpose of this study was to identify the differentially expressed genes (DEGs), HD-related gene targets, pathways and miRNAs in HD and, more specifically, between the pre-symptomatic and symptomatic HD stages. Three publicly available HD datasets were analysed to obtain DEGs for each HD stage from each dataset. In addition, three databases were used to obtain HD-related gene targets. The shared gene targets between the three public databases were compared, and clustering analysis was performed on the common shared genes. Enrichment analysis was performed on (i) DEGs identified for each HD stage in each dataset, (ii) gene targets from the public databases and (iii) the clustering analysis results. Furthermore, the hub genes shared between the public databases and the HD DEGs were identified, and topological network parameters were applied. Identification of HD-related miRNAs and their gene targets was obtained, and a miRNA-gene network was constructed. Enriched pathways identified for the 128 common genes revealed pathways linked to multiple neurodegeneration diseases (HD, Parkinson's disease, Spinocerebellar ataxia), MAPK and HIF-1 signalling pathways. Eighteen HD-related hub genes were identified based on network topological analysis of MCC, degree and closeness. The highest-ranked genes were FoxO3 and CASP3, CASP3 and MAP2 were found for betweenness and eccentricity and CREBBP and PPARGC1A were identified for the clustering coefficient. The miRNA-gene network identified eleven miRNAs (mir-19a-3p, mir-34b-3p, mir-128-5p, mir-196a-5p, mir-34a-5p, mir-338-3p, mir-23a-3p and mir-214-3p) and eight genes (ITPR1, CASP3, GRIN2A, FoxO3, TGM2, CREBBP, MTHFR and PPARGC1A). Our work revealed that various biological pathways seem to be involved in HD either during the pre-symptomatic or symptomatic stages of HD. This may offer some clues for the molecular mechanisms, pathways and cellular components underlying HD and how these may act as potential therapeutic targets for HD.
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Huang X, Su B, Zhu C, He X, Lin X. Dynamic Network Construction for Identifying Early Warning Signals Based On a Data-Driven Approach: Early Diagnosis Biomarker Discovery for Gastric Cancer. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:923-931. [PMID: 35594220 DOI: 10.1109/tcbb.2022.3176319] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
During the development of complex diseases, there is a critical transition from one status to another at a tipping point, which can be an early indicator of disease deterioration. To effectively enhance the performance of early risk identification, a novel dynamic network construction algorithm for identifying early warning signals based on a data-driven approach (EWS-DDA) was proposed. In EWS-DDA, the shrunken centroid was introduced to measure dynamic expression changes in assumed pathway reactions during the progression of complex disease for network construction and to define early warning signals by means of a data-driven approach. We applied EWS-DDA to perform a comprehensive analysis of gene expression profiles of gastric cancer (GC) from The Cancer Genome Atlas database and the Gene Expression Omnibus database. Six crucial genes were selected as potential biomarkers for the early diagnosis of GC. The experimental results of statistical analysis and biological analysis suggested that the six genes play important roles in GC occurrence and development. Then, EWS-DDA was compared with other state-of-the-art network methods to validate its performance. The theoretical analysis and comparison results suggested that EWS-DDA has great potential for a more complete presentation of disease deterioration and effective extraction of early warning information.
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18
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Lu Z, Xu J, Cao B, Jin C. Screening and identification of susceptibility genes for osteosarcoma based on bioinformatics analysis. ANNALS OF TRANSLATIONAL MEDICINE 2023; 11:87. [PMID: 36819543 PMCID: PMC9929789 DOI: 10.21037/atm-22-6369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/10/2023] [Indexed: 01/30/2023]
Abstract
Background Gene play an important role in malignant tumors. However, there is still insufficient research on genetic variations in osteosarcoma (OS) patients. Therefore, we aimed to analyze the gene expression profile of OS using bioinformatics and to explore the pathogenesis of OS at the molecular level. Methods The gene chip dataset of OS samples was downloaded from the Gene Expression Omnibus (GEO) database for screening differentially expressed genes (DEGs). The R language clusterProfiler software package was used to perform Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis for DEGs. The central node proteins of the protein interaction network were analyzed by the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database, Cytoscape, and its plug-ins cytoHubba and NetworkAnalyzer to find the key genes. Results A total of 631 DEGs were obtained, including 362 upregulated genes and 269 downregulated genes. DEGs were mainly involved in the regulation of leukocyte chemotaxis and migration, vascular development, and other biological processes (BPs); mediation of receptor ligand activity, growth factor binding, growth factor activity, integrin binding, and other molecular functions (MFs); and were enriched in the extracellular matrix (ECM). Conclusions DEGs in the ECM and growth factors play a key role in the development of OS. The leukocyte transendothelial migration pathway and the PI3K-AKT pathway are closely related to OS, and the related molecular mechanism is worthy of further study.
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Affiliation(s)
- Zhengyu Lu
- Department of Orthopedics, Taizhou First People’s Hospital, Huangyan Hospital of Wenzhou Medical University, Taizhou, China
| | - Jin Xu
- Department of Orthopedics, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, China
| | - Binhao Cao
- Department of Orthopedics, Taizhou First People’s Hospital, Huangyan Hospital of Wenzhou Medical University, Taizhou, China
| | - Chongqiang Jin
- Department of Orthopedics, Taizhou First People’s Hospital, Huangyan Hospital of Wenzhou Medical University, Taizhou, China
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Hasija Y. Editorial: Data integration and physiological modelling. Front Physiol 2023; 13:1116488. [PMID: 36685172 PMCID: PMC9848393 DOI: 10.3389/fphys.2022.1116488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 12/14/2022] [Indexed: 01/06/2023] Open
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20
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Zhang W, Liu L, Xiao X, Zhou H, Peng Z, Wang W, Huang L, Xie Y, Xu H, Tao L, Nie W, Yuan X, Liu F, Yuan Q. Identification of common molecular signatures of SARS-CoV-2 infection and its influence on acute kidney injury and chronic kidney disease. Front Immunol 2023; 14:961642. [PMID: 37026010 PMCID: PMC10070855 DOI: 10.3389/fimmu.2023.961642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 03/07/2023] [Indexed: 04/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the main cause of COVID-19, causing hundreds of millions of confirmed cases and more than 18.2 million deaths worldwide. Acute kidney injury (AKI) is a common complication of COVID-19 that leads to an increase in mortality, especially in intensive care unit (ICU) settings, and chronic kidney disease (CKD) is a high risk factor for COVID-19 and its related mortality. However, the underlying molecular mechanisms among AKI, CKD, and COVID-19 are unclear. Therefore, transcriptome analysis was performed to examine common pathways and molecular biomarkers for AKI, CKD, and COVID-19 in an attempt to understand the association of SARS-CoV-2 infection with AKI and CKD. Three RNA-seq datasets (GSE147507, GSE1563, and GSE66494) from the GEO database were used to detect differentially expressed genes (DEGs) for COVID-19 with AKI and CKD to search for shared pathways and candidate targets. A total of 17 common DEGs were confirmed, and their biological functions and signaling pathways were characterized by enrichment analysis. MAPK signaling, the structural pathway of interleukin 1 (IL-1), and the Toll-like receptor pathway appear to be involved in the occurrence of these diseases. Hub genes identified from the protein-protein interaction (PPI) network, including DUSP6, BHLHE40, RASGRP1, and TAB2, are potential therapeutic targets in COVID-19 with AKI and CKD. Common genes and pathways may play pathogenic roles in these three diseases mainly through the activation of immune inflammation. Networks of transcription factor (TF)-gene, miRNA-gene, and gene-disease interactions from the datasets were also constructed, and key gene regulators influencing the progression of these three diseases were further identified among the DEGs. Moreover, new drug targets were predicted based on these common DEGs, and molecular docking and molecular dynamics (MD) simulations were performed. Finally, a diagnostic model of COVID-19 was established based on these common DEGs. Taken together, the molecular and signaling pathways identified in this study may be related to the mechanisms by which SARS-CoV-2 infection affects renal function. These findings are significant for the effective treatment of COVID-19 in patients with kidney diseases.
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Affiliation(s)
- Weiwei Zhang
- Department of Nephrology, Xiangya Hospital of Central South University, Changsha, China
| | - Leping Liu
- Department of Pediatrics, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Xiangcheng Xiao
- Department of Nephrology, Xiangya Hospital of Central South University, Changsha, China
| | - Hongshan Zhou
- Department of Nephrology, Xiangya Hospital of Central South University, Changsha, China
| | - Zhangzhe Peng
- Department of Nephrology, Xiangya Hospital of Central South University, Changsha, China
- Organ Fibrosis Key Lab of Hunan Province, Central South University, Changsha, China
| | - Wei Wang
- Department of Nephrology, Xiangya Hospital of Central South University, Changsha, China
- Organ Fibrosis Key Lab of Hunan Province, Central South University, Changsha, China
| | - Ling Huang
- Department of Nephrology, Xiangya Hospital of Central South University, Changsha, China
- Organ Fibrosis Key Lab of Hunan Province, Central South University, Changsha, China
| | - Yanyun Xie
- Department of Nephrology, Xiangya Hospital of Central South University, Changsha, China
- Organ Fibrosis Key Lab of Hunan Province, Central South University, Changsha, China
| | - Hui Xu
- Department of Nephrology, Xiangya Hospital of Central South University, Changsha, China
- Organ Fibrosis Key Lab of Hunan Province, Central South University, Changsha, China
| | - Lijian Tao
- Department of Nephrology, Xiangya Hospital of Central South University, Changsha, China
- Organ Fibrosis Key Lab of Hunan Province, Central South University, Changsha, China
| | - Wannian Nie
- Department of Nephrology, Xiangya Hospital of Central South University, Changsha, China
| | - Xiangning Yuan
- Department of Nephrology, Xiangya Hospital of Central South University, Changsha, China
- Organ Fibrosis Key Lab of Hunan Province, Central South University, Changsha, China
| | - Fang Liu
- Health Management Center, Xiangya Hospital of Central South University, Changsha, China
- *Correspondence: Fang Liu, ; Qiongjing Yuan,
| | - Qiongjing Yuan
- Department of Nephrology, Xiangya Hospital of Central South University, Changsha, China
- Organ Fibrosis Key Lab of Hunan Province, Central South University, Changsha, China
- National Clinical Medical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, China
- Research Center for Medical Metabolomics, Xiangya Hospital of Central South University, Changsha, China
- *Correspondence: Fang Liu, ; Qiongjing Yuan,
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Translational Bioinformatics for Human Reproductive Biology Research: Examples, Opportunities and Challenges for a Future Reproductive Medicine. Int J Mol Sci 2022; 24:ijms24010004. [PMID: 36613446 PMCID: PMC9819745 DOI: 10.3390/ijms24010004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Since 1978, with the first IVF (in vitro fertilization) baby birth in Manchester (England), more than eight million IVF babies have been born throughout the world, and many new techniques and discoveries have emerged in reproductive medicine. To summarize the modern technology and progress in reproductive medicine, all scientific papers related to reproductive medicine, especially papers related to reproductive translational medicine, were fully searched, manually curated and reviewed. Results indicated whether male reproductive medicine or female reproductive medicine all have made significant progress, and their markers have experienced the progress from karyotype analysis to single-cell omics. However, due to the lack of comprehensive databases, especially databases collecting risk exposures, disease markers and models, prevention drugs and effective treatment methods, the application of the latest precision medicine technologies and methods in reproductive medicine is limited.
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22
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Xie E, Nadeem U, Xie B, D’Souza M, Sulakhe D, Skondra D. Using Computational Drug-Gene Analysis to Identify Novel Therapeutic Candidates for Retinal Neuroprotection. Int J Mol Sci 2022; 23:ijms232012648. [PMID: 36293505 PMCID: PMC9604082 DOI: 10.3390/ijms232012648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/11/2022] [Accepted: 10/18/2022] [Indexed: 01/24/2023] Open
Abstract
Retinal cell death is responsible for irreversible vision loss in many retinal disorders. No commercially approved treatments are currently available to attenuate retinal cell loss and preserve vision. We seek to identify chemicals/drugs with thoroughly-studied biological functions that possess neuroprotective effects in the retina using a computational bioinformatics approach. We queried the National Center for Biotechnology Information (NCBI) to identify genes associated with retinal neuroprotection. Enrichment analysis was performed using ToppGene to identify compounds related to the identified genes. This analysis constructs a Pharmacome from multiple drug-gene interaction databases to predict compounds with statistically significant associations to genes involved in retinal neuroprotection. Compounds with known deleterious effects (e.g., asbestos, ethanol) or with no clinical indications (e.g., paraquat, ozone) were manually filtered. We identified numerous drug/chemical classes associated to multiple genes implicated in retinal neuroprotection using a systematic computational approach. Anti-diabetics, lipid-lowering medicines, and antioxidants are among the treatments anticipated by this analysis, and many of these drugs could be readily repurposed for retinal neuroprotection. Our technique serves as an unbiased tool that can be utilized in the future to lead focused preclinical and clinical investigations for complex processes such as neuroprotection, as well as a wide range of other ocular pathologies.
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Affiliation(s)
- Edward Xie
- Chicago Medical School at Rosalind, Franklin University of Medicine and Science, Chicago, IL 60064, USA
| | - Urooba Nadeem
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Bingqing Xie
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Mark D’Souza
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
| | - Dinanath Sulakhe
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
| | - Dimitra Skondra
- Department of Ophthalmology and Visual Science, University of Chicago, Chicago, IL 60637, USA
- Correspondence:
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Onisiforou A, Spyrou GM. Systems Bioinformatics Reveals Possible Relationship between COVID-19 and the Development of Neurological Diseases and Neuropsychiatric Disorders. Viruses 2022; 14:v14102270. [PMID: 36298824 PMCID: PMC9611753 DOI: 10.3390/v14102270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 11/23/2022] Open
Abstract
Coronavirus Disease 2019 (COVID-19) is associated with increased incidence of neurological diseases and neuropsychiatric disorders after infection, but how it contributes to their development remains under investigation. Here, we investigate the possible relationship between COVID-19 and the development of ten neurological disorders and three neuropsychiatric disorders by exploring two pathological mechanisms: (i) dysregulation of host biological processes via virus-host protein-protein interactions (PPIs), and (ii) autoreactivity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epitopes with host "self" proteins via molecular mimicry. We also identify potential genetic risk factors which in combination with SARS-CoV-2 infection might lead to disease development. Our analysis indicated that neurodegenerative diseases (NDs) have a higher number of disease-associated biological processes that can be modulated by SARS-CoV-2 via virus-host PPIs than neuropsychiatric disorders. The sequence similarity analysis indicated the presence of several matching 5-mer and/or 6-mer linear motifs between SARS-CoV-2 epitopes with autoreactive epitopes found in Alzheimer's Disease (AD), Parkinson's Disease (PD), Myasthenia Gravis (MG) and Multiple Sclerosis (MS). The results include autoreactive epitopes that recognize amyloid-beta precursor protein (APP), microtubule-associated protein tau (MAPT), acetylcholine receptors, glial fibrillary acidic protein (GFAP), neurofilament light polypeptide (NfL) and major myelin proteins. Altogether, our results suggest that there might be an increased risk for the development of NDs after COVID-19 both via autoreactivity and virus-host PPIs.
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Dimitrova A, Sferra G, Scippa GS, Trupiano D. Network-Based Analysis to Identify Hub Genes Involved in Spatial Root Response to Mechanical Constrains. Cells 2022; 11:cells11193121. [PMID: 36231084 PMCID: PMC9564363 DOI: 10.3390/cells11193121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/16/2022] Open
Abstract
Previous studies report that the asymmetric response, observed along the main poplar woody bent root axis, was strongly related to both the type of mechanical forces (compression or tension) and the intensity of force displacement. Despite a large number of targets that have been proposed to trigger this asymmetry, an understanding of the comprehensive and synergistic effect of the antistress spatially related pathways is still lacking. Recent progress in the bioinformatics area has the potential to fill these gaps through the use of in silico studies, able to investigate biological functions and pathway overlaps, and to identify promising targets in plant responses. Presently, for the first time, a comprehensive network-based analysis of proteomic signatures was used to identify functions and pivotal genes involved in the coordinated signalling pathways and molecular activities that asymmetrically modulate the response of different bent poplar root sectors and sides. To accomplish this aim, 66 candidate proteins, differentially represented across the poplar bent root sides and sectors, were grouped according to their abundance profile patterns and mapped, together with their first neighbours, on a high-confidence set of interactions from STRING to compose specific cluster-related subnetworks (I–VI). Successively, all subnetworks were explored by a functional gene set enrichment analysis to identify enriched gene ontology terms. Subnetworks were then analysed to identify the genes that are strongly interconnected with other genes (hub gene) and, thus, those that have a pivotal role in the bent root asymmetric response. The analysis revealed novel information regarding the response coordination, communication, and potential signalling pathways asymmetrically activated along the main root axis, delegated mainly to Ca2+ (for new lateral root formation) and ROS (for gravitropic response and lignin accumulation) signatures. Furthermore, some of the data indicate that the concave side of the bent sector, where the mechanical forces are most intense, communicates to the other (neighbour and distant) sectors, inducing spatially related strategies to ensure water uptake and accompanying cell modification. This information could be critical for understanding how plants maintain and improve their structural integrity—whenever and wherever it is necessary—in natural mechanical stress conditions.
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Zhang Z, Zhang Y, Yang D, Luo Y, Luo Y, Ru Y, Song J, Fei X, Chen Y, Li B, Jiang J, Kuai L. Characterisation of key biomarkers in diabetic ulcers via systems bioinformatics. Int Wound J 2022; 20:529-542. [PMID: 36181454 PMCID: PMC9885479 DOI: 10.1111/iwj.13900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 07/02/2022] [Accepted: 07/04/2022] [Indexed: 02/03/2023] Open
Abstract
Diabetic ulcers (DUs) are characterised by a high incidence and disability rate. However, its pathogenesis remains elusive. Thus, a deep understanding of the underlying mechanisms for the pathogenesis of DUs has vital implications. The weighted gene co-expression network analysis was performed on the main data from the Gene Expression Omnibus database. Gene Ontology (GO) terms, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were adopted to analyse the potential biological function of the most relevant module. Furthermore, we utilised CytoHubba and protein-protein interaction network to identify the hub genes. Finally, the hub genes were validated by animal experiments in diabetic ulcer mice models. The expression of genes from the turquoise module was found to be strongly related to DUs. GO terms, KEGG analysis showed that biological functions are closely related to immune response. The hub genes included IFI35, IFIT2, MX2, OASL, RSAD2, and XAF1, which were higher in wounds of DUs mice than that in normal lesions. Additionally, we also demonstrated that the expression of hub genes was correlated with the immune response using immune checkpoint, immune cell infiltration, and immune scores. These data suggests that IFI35, IFIT2, MX2, OASL, RSAD2, and XAF1 are crucial for DUs.
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Affiliation(s)
- Zhan Zhang
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western MedicineShanghai University of Traditional Chinese MedicineShanghaiChina,Institute of DermatologyShanghai Academy of Traditional Chinese MedicineShanghaiChina
| | - Ying Zhang
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western MedicineShanghai University of Traditional Chinese MedicineShanghaiChina,Institute of DermatologyShanghai Academy of Traditional Chinese MedicineShanghaiChina
| | - Dan Yang
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western MedicineShanghai University of Traditional Chinese MedicineShanghaiChina,Institute of DermatologyShanghai Academy of Traditional Chinese MedicineShanghaiChina
| | - Yue Luo
- Department of Integrated TCM and Western Medicine, Shanghai Skin Disease HospitalTongji UniversityShanghaiChina
| | - Ying Luo
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western MedicineShanghai University of Traditional Chinese MedicineShanghaiChina,Institute of DermatologyShanghai Academy of Traditional Chinese MedicineShanghaiChina
| | - Yi Ru
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western MedicineShanghai University of Traditional Chinese MedicineShanghaiChina,Institute of DermatologyShanghai Academy of Traditional Chinese MedicineShanghaiChina
| | - Jiankun Song
- Department of Integrated TCM and Western Medicine, Shanghai Skin Disease HospitalTongji UniversityShanghaiChina
| | - Xiaoya Fei
- Department of Integrated TCM and Western Medicine, Shanghai Skin Disease HospitalTongji UniversityShanghaiChina
| | - Yiran Chen
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western MedicineShanghai University of Traditional Chinese MedicineShanghaiChina,Institute of DermatologyShanghai Academy of Traditional Chinese MedicineShanghaiChina
| | - Bin Li
- Institute of DermatologyShanghai Academy of Traditional Chinese MedicineShanghaiChina,Department of Integrated TCM and Western Medicine, Shanghai Skin Disease HospitalTongji UniversityShanghaiChina
| | - Jingsi Jiang
- Department of Skin and Cosmetics Research, Shanghai Skin Disease HospitalTongji UniversityShanghaiChina
| | - Le Kuai
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western MedicineShanghai University of Traditional Chinese MedicineShanghaiChina,Institute of DermatologyShanghai Academy of Traditional Chinese MedicineShanghaiChina
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Long F, Tian L, Chai Z, Li J, Tang Y, Liu M. Identification of stage-associated exosome miRNAs in colorectal cancer by improved robust and corroborative approach embedded miRNA-target network. Front Med (Lausanne) 2022; 9:881788. [PMID: 36237545 PMCID: PMC9551196 DOI: 10.3389/fmed.2022.881788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 09/09/2022] [Indexed: 12/24/2022] Open
Abstract
Background Colorectal cancer (CRC) is a common gastrointestinal tumor with high morbidity and mortality. At the molecular level, patients at different stages present considerable heterogeneity. Although the miRNA in exosome is an effective biomarker to reveal tumor progression, studies based on stage-associated exosome miRNA regulatory network analysis still lacking. This study aims to identify CRC stage-associated exosome miRNAs and reveal their potential function in tumor progression. Methods In this study, serum and cellular exosome miRNA expression microarrays associated with CRC were downloaded from GEO database. Stage-common (SC) and stage-specific (SS) differentially expressed miRNAs were extracted and their targets were identified based on 11 databases. Furthermore, miRNA SC and SS regulatory function networks were built based on the CRC phenotypic relevance of miRNA targets, and the corresponding transcription factors were identified. Concurrently, the potential stage-associated miRNAs were identified by receiver-operating characteristic (ROC) curve analysis, survival analysis, drug response analysis, ceRNA analysis, pathway analysis and a comprehensive investigation of 159 publications. Results Ten candidate stage-associated miRNAs were identified, with three SC (miR-146a-5p, miR-22-3p, miR-23b-3p) and seven SS (I: miR-301a-3p, miR-548i; IIIA: miR-23a-3p; IV: miR-194-3p, miR-33a-3p, miR-485-3p, miR-194-5p) miRNAs. Additionally, their targets were enriched in several vital cancer-associated pathways such as TGF-beta, p53, and hippo signaling pathways. Moreover, five key hotspot target genes (CCNA2, MAPK1, PTPRD, MET, and CDKN1A) were demonstrated to associated with better overall survival in CRC patients. Finally, miR-23b-3p, miR-301a-3p and miR-194-3p were validated being the most stably expressed stage-associated miRNAs in CRC serum exosomes, cell exosomes and tissues. Conclusions These CRC stage-associated exosome miRNAs aid to further mechanism research of tumor progression and provide support for better clinical management in patients with different stages.
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Nadeem U, Xie B, Xie EF, D'Souza M, Dao D, Sulakhe D, Skondra D. Using Advanced Bioinformatics Tools to Identify Novel Therapeutic Candidates for Age-Related Macular Degeneration. Transl Vis Sci Technol 2022; 11:10. [PMID: 35972434 PMCID: PMC9396676 DOI: 10.1167/tvst.11.8.10] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose Age-related macular degeneration (AMD) is the most common cause of aging-related blindness in the developing world. Although medications can slow progressive wet AMD, currently, no drugs to treat dry-AMD are available. We use a systems or in silico biology analysis to identify chemicals and drugs approved by the Food and Drug Administration for other indications that can be used to treat and prevent AMD. Methods We queried National Center for Biotechnology Information to identify genes associated with AMD, wet AMD, dry AMD, intermediate AMD, and geographic atrophy to date. We combined genes from various AMD subtypes to reflect distinct stages of disease. Enrichment analysis using the ToppGene platform predicted molecules that can influence AMD genes. Compounds without clinical indications or with deleterious effects were manually filtered. Results We identified several drug/chemical classes that can affect multiple genes involved in AMD. The drugs predicted from this analysis include antidiabetics, lipid-lowering agents, and antioxidants, which could theoretically be repurposed for AMD. Metformin was identified as the drug with the strongest association with wet AMD genes and is among the top candidates in all dry AMD subtypes. Curcumin, statins, and antioxidants are also among the top drugs correlating with AMD-risk genes. Conclusions We use a systematic computational process to discover potential therapeutic targets for AMD. Our systematic and unbiased approach can be used to guide targeted preclinical/clinical studies for AMD and other ocular diseases. Translational Relevance Advanced bioinformatics models identify novel chemicals and approved drug candidates that can be efficacious for different subtypes of AMD.
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Affiliation(s)
- Urooba Nadeem
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Bingqing Xie
- Department of Medicine, University of Chicago, IL, USA
| | - Edward F Xie
- Chicago Medical School at Rosalind Franklin University of Medicine and Science, Chicago, IL, USA
| | - Mark D'Souza
- Center for Research Informatics, The University of Chicago, Chicago, IL, USA
| | - David Dao
- Department of Ophthalmology and Visual Science, University of Chicago, Chicago, IL, USA
| | | | - Dimitra Skondra
- Department of Ophthalmology and Visual Science, University of Chicago, Chicago, IL, USA
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Ye Z. Identification of T cell-related biomarkers for breast cancer based on weighted gene co-expression network analysis. J Chemother 2022:1-9. [PMID: 35822502 DOI: 10.1080/1120009x.2022.2097431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Breast cancer is the most frequent malignancy worldwide, with immunotherapy and targeted therapy being key strategies to improving the prognosis. We downloaded mRNA expression dataset of breast cancer from The Cancer Genome Atlas (TCGA) database, and divided preprocessed genes into 12 modules based on gene expression profile by weighted gene co-expression network analysis (WGCNA). The StromalScore, ImmuneScore and ESTIMATEScore of samples were assessed. The Kaplan-Meier curve showed that ImmuneScore was notably correlated with breast cancer patient's prognosis. By analyzing the connectivity between module eigengenes and clinical traits, the gene module closely related to ImmuneScore was obtained. Further, through intramodular gene connectivity and protein-protein interaction network topology analysis of module genes, hub genes (HLA-E, HLA-DPB1 and HLA-DRB1) in immune-related module were screened out. Finally, bioinformatics analysis displayed that HLA-DPB1 and HLA-DRB1 were notably overexpressed and HLA-E was underexpressed in breast cancer tissues. TIMER database analysis showed that three hub gene levels were significantly correlated with infiltration levels of CD8+ T cells and CD4+ T cells. Meanwhile, Pearson correlation analysis revealed positive correlation between three hub genes and those of immune checkpoint genes (LAG3, PD-1, PD-L1). Additionally, prognosis could be effectively evaluated by HLA-DPB1 and HLA-DRB1 levels, and differentially activated signalling pathways between high- and low-expression groups of HLA-E and HLA-DPB1 were obtained by gene set enrichment analysis. To conclude, this study identified three T cell-related biomarkers for breast cancer based on TCGA-BRCA dataset, and the screened genes could provide references for breast cancer immunotherapy.
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Affiliation(s)
- Zhenkai Ye
- Department of Radiotherapy, Minzu Hospital of Guangxi Zhuang Autonomous Region, Affiliated Minzu Hospital of Guangxi Medical University, Nanning, Guangxi, China
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Fan Y, Kao C, Yang F, Wang F, Yin G, Wang Y, He Y, Ji J, Liu L. Integrated Multi-Omics Analysis Model to Identify Biomarkers Associated With Prognosis of Breast Cancer. Front Oncol 2022; 12:899900. [PMID: 35761863 PMCID: PMC9232398 DOI: 10.3389/fonc.2022.899900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 05/12/2022] [Indexed: 12/13/2022] Open
Abstract
Background With the rapid development and wide application of high-throughput sequencing technology, biomedical research has entered the era of large-scale omics data. We aim to identify genes associated with breast cancer prognosis by integrating multi-omics data. Method Gene-gene interactions were taken into account, and we applied two differential network methods JDINAC and LGCDG to identify differential genes. The patients were divided into case and control groups according to their survival time. The TCGA and METABRIC database were used as the training and validation set respectively. Result In the TCGA dataset, C11orf1, OLA1, RPL31, SPDL1 and IL33 were identified to be associated with prognosis of breast cancer. In the METABRIC database, ZNF273, ZBTB37, TRIM52, TSGA10, ZNF727, TRAF2, TSPAN17, USP28 and ZNF519 were identified as hub genes. In addition, RPL31, TMEM163 and ZNF273 were screened out in both datasets. GO enrichment analysis shows that most of these hub genes were involved in zinc ion binding. Conclusion In this study, a total of 15 hub genes associated with long-term survival of breast cancer were identified, which can promote understanding of the molecular mechanism of breast cancer and provide new insight into clinical research and treatment.
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Affiliation(s)
- Yeye Fan
- School of Mathematics, Shandong University, Jinan, China
| | - Chunyu Kao
- Zhongtai Securities Institute for Financial Studies, Shandong University, Jinan, China
| | - Fu Yang
- Zhongtai Securities Institute for Financial Studies, Shandong University, Jinan, China
| | - Fei Wang
- Department of Breast Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Institute of Translational Medicine of Breast Disease Prevention and Treatment, Shandong University, Jinan, China
| | - Gengshen Yin
- Department of Breast Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Institute of Translational Medicine of Breast Disease Prevention and Treatment, Shandong University, Jinan, China
| | - Yongjiu Wang
- Department of Breast Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Institute of Translational Medicine of Breast Disease Prevention and Treatment, Shandong University, Jinan, China
| | - Yong He
- School of Mathematics, Shandong University, Jinan, China.,Zhongtai Securities Institute for Financial Studies, Shandong University, Jinan, China
| | - Jiadong Ji
- Zhongtai Securities Institute for Financial Studies, Shandong University, Jinan, China
| | - Liyuan Liu
- School of Mathematics, Shandong University, Jinan, China.,Department of Breast Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Institute of Translational Medicine of Breast Disease Prevention and Treatment, Shandong University, Jinan, China
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Yin Z, Li Y, Zhang X, Xia M, Chen Z, Zhao L, Liang F. Moxibustion ameliorates cognitive function in older adults with mild cognitive impairment: a systematic review and meta-analysis of randomized controlled trials. Eur J Integr Med 2022. [DOI: 10.1016/j.eujim.2022.102133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Mechanism of Zhen Wu Decoction in the Treatment of Heart Failure Based on Network Pharmacology and Molecular Docking. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:4877920. [PMID: 35341142 PMCID: PMC8941561 DOI: 10.1155/2022/4877920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 02/10/2022] [Accepted: 02/14/2022] [Indexed: 11/18/2022]
Abstract
Heart failure (HF) is a serious manifestation or advanced stage of various cardiovascular diseases, and its mortality and rehospitalization rate are still on the rise in China. Based on the network pharmacology method, 59 components of Zhen Wu decoction (ZWD) and 83 target genes related to HF were obtained. Through the PPI network, four potential therapeutic targets were identified: AKT1, IL6, JUN, and MAPK8. The beneficial components of ZWD might intervene HF through the AGE-RAGE signalling pathway in the diabetes component, fluid shear stress and atherosclerosis, the TNF signalling pathway, TB, and Kaposi sarcoma related herpesvirus infection, according to a KEGG enrichment study. The protein interaction network of candidate targets was constructed by the STRING database, and the protein interaction network was clustered by MEODE software. GO and KEGG enrichment analyses were performed on the core modules obtained by clustering. Finally, AutoDock Vina software was used for molecular docking verification of key targets and active ingredients. The result was that 75 active ingredients and 109 genes were screened as potential active ingredients and potential targets of Shengjie Tongyu decoction for CHF treatment. The main active components were quercetin, luteolin, kaempferol, dehydrated icariin, isorhamnetin, formononetin, and other flavonoids. Il-6, MAPK1, MAPK8, AKT1, VEGFA, and JUN were selected as the core targets. Molecular docking showed that the key components were well connected with the target. GO enrichment analysis showed that Shengjie Tongyu decoction could play a role through multiple biological pathways including angiogenesis, regulation of endothelial cell proliferation, binding of cytokine receptors, negative regulation of apoptotic signalling pathways, regulation of nitric oxide synthase activity, and reactive oxygen metabolism. Key pathways mainly focus on the toll-like receptor signalling pathway, nod-like receptor signalling pathway, MAPK signalling pathway, mTOR signalling pathway, JAK-STAT signalling pathway, VEGF signalling pathway, and other pathways. Through molecular docking technology, it was found that a variety of effective components in ZWD, such as kaempferol. Molecular docking technology has preliminatively verified the network pharmacology and laid a foundation for the follow-up pharmacological research.
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Gao WL, Niu L, Chen WL, Zhang YQ, Huang WH. Integrative Analysis of the Expression Levels and Prognostic Values for NEK Family Members in Breast Cancer. Front Genet 2022; 13:798170. [PMID: 35368696 PMCID: PMC8967485 DOI: 10.3389/fgene.2022.798170] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/07/2022] [Indexed: 12/29/2022] Open
Abstract
Background: In the latest rankings, breast cancer ranks first in incidence and fifth in mortality among female malignancies worldwide. Early diagnosis and treatment can improve the prognosis and prolong the survival of breast cancer (BC) patients. The NIMA-related kinase (NEK), a group of serine/threonine kinase, is a large and conserved gene family that includes NEK1–NEK11. The NEK plays a pivotal role in the cell cycle and microtubule formation. However, an integrative analysis of the effect and prognosis value of NEK family members on BC patients is still lacking. Methods: In this study, the expression profiles of NEK family members in BC and its subgroups were analyzed using UALCAN, GEPIA2, and Human Protein Atlas datasets. The prognostic values of NEK family members in BC were evaluated using the Kaplan–Meier plotter. Co-expression profiles and genetic alterations of NEK family members were analyzed using the cBioPortal database. The function and pathway enrichment analysis of the NEK family were performed using the WebGestalt database. The correlation analysis of the NEK family and immune cell infiltration in BC was conducted using the TIMER 2.0 database. Results: In this study, we compared and analyzed the prognosis values of the NEKs. We found that NEK9 was highly expressed in normal breast tissues than BC, and NEK2, NEK6, and NEK11 were significantly highly expressed in BC than adjacent normal tissues. Interestingly, the expression levels of NEK2, NEK6, and NEK10 were not only remarkably correlated with the tumor stage but also with the molecular subtype. Through multilevel research, we found that high expression levels of NEK1, NEK3, NEK8, NEK9, NEK10, and NEK11 suggested a better prognosis value in BC, while high expression levels of NEK2 and NEK6 suggested a poor prognosis value in BC. Conclusion: Our studies show the prognosis values of the NEKs in BC. Thus, we suggest that NEKs may be regarded as novel biomarkers for predicting potential prognosis values and potential therapeutic targets of BC patients.
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Affiliation(s)
- Wen-Liang Gao
- Department of Breast-Thyroid-Surgery and Cancer Research Center, Xiang’an Hospital of Xiamen University, Xiamen, China
- Xiamen Research Center of Clinical Medicine in Breast and Thyroid Cancers, Xiamen, China
- Xiamen Key Laboratory of Endocrine-Related Cancer Precision Medicine, Xiamen, China
| | - Lei Niu
- Department of Breast-Thyroid-Surgery and Cancer Research Center, Xiang’an Hospital of Xiamen University, Xiamen, China
- Xiamen Research Center of Clinical Medicine in Breast and Thyroid Cancers, Xiamen, China
- Xiamen Key Laboratory of Endocrine-Related Cancer Precision Medicine, Xiamen, China
| | - Wei-Ling Chen
- Department of Breast-Thyroid-Surgery and Cancer Research Center, Xiang’an Hospital of Xiamen University, Xiamen, China
- Xiamen Research Center of Clinical Medicine in Breast and Thyroid Cancers, Xiamen, China
- Xiamen Key Laboratory of Endocrine-Related Cancer Precision Medicine, Xiamen, China
| | - Yong-Qu Zhang
- Department of Breast-Thyroid-Surgery and Cancer Research Center, Xiang’an Hospital of Xiamen University, Xiamen, China
- Xiamen Research Center of Clinical Medicine in Breast and Thyroid Cancers, Xiamen, China
- Xiamen Key Laboratory of Endocrine-Related Cancer Precision Medicine, Xiamen, China
- *Correspondence: Yong-Qu Zhang, ; Wen-He Huang,
| | - Wen-He Huang
- Department of Breast-Thyroid-Surgery and Cancer Research Center, Xiang’an Hospital of Xiamen University, Xiamen, China
- Xiamen Research Center of Clinical Medicine in Breast and Thyroid Cancers, Xiamen, China
- Xiamen Key Laboratory of Endocrine-Related Cancer Precision Medicine, Xiamen, China
- *Correspondence: Yong-Qu Zhang, ; Wen-He Huang,
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Xiang J, Meng X, Zhao Y, Wu FX, Li M. HyMM: hybrid method for disease-gene prediction by integrating multiscale module structure. Brief Bioinform 2022; 23:6547263. [PMID: 35275996 DOI: 10.1093/bib/bbac072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 01/18/2022] [Accepted: 02/13/2022] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Identifying disease-related genes is an important issue in computational biology. Module structure widely exists in biomolecule networks, and complex diseases are usually thought to be caused by perturbations of local neighborhoods in the networks, which can provide useful insights for the study of disease-related genes. However, the mining and effective utilization of the module structure is still challenging in such issues as a disease gene prediction. RESULTS We propose a hybrid disease-gene prediction method integrating multiscale module structure (HyMM), which can utilize multiscale information from local to global structure to more effectively predict disease-related genes. HyMM extracts module partitions from local to global scales by multiscale modularity optimization with exponential sampling, and estimates the disease relatedness of genes in partitions by the abundance of disease-related genes within modules. Then, a probabilistic model for integration of gene rankings is designed in order to integrate multiple predictions derived from multiscale module partitions and network propagation, and a parameter estimation strategy based on functional information is proposed to further enhance HyMM's predictive power. By a series of experiments, we reveal the importance of module partitions at different scales, and verify the stable and good performance of HyMM compared with eight other state-of-the-arts and its further performance improvement derived from the parameter estimation. CONCLUSIONS The results confirm that HyMM is an effective framework for integrating multiscale module structure to enhance the ability to predict disease-related genes, which may provide useful insights for the study of the multiscale module structure and its application in such issues as a disease-gene prediction.
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Affiliation(s)
- Ju Xiang
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, China; Department of Basic Medical Sciences & Academician Workstation, Changsha Medical University, Changsha, Hunan 410219, China
| | - Xiangmao Meng
- School of Computer Science and Engineering, Central South University, Changsha 410083, China
| | - Yichao Zhao
- School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, China
| | - Fang-Xiang Wu
- Division of Biomedical Engineering and Department of Mechanical Engineering, University of Saskatchewan, Saskatoon, SK, S7N 5A9, Canada
| | - Min Li
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, China
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Xiang J, Zhang J, Zhao Y, Wu FX, Li M. Biomedical data, computational methods and tools for evaluating disease-disease associations. Brief Bioinform 2022; 23:6522999. [PMID: 35136949 DOI: 10.1093/bib/bbac006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 12/12/2022] Open
Abstract
In recent decades, exploring potential relationships between diseases has been an active research field. With the rapid accumulation of disease-related biomedical data, a lot of computational methods and tools/platforms have been developed to reveal intrinsic relationship between diseases, which can provide useful insights to the study of complex diseases, e.g. understanding molecular mechanisms of diseases and discovering new treatment of diseases. Human complex diseases involve both external phenotypic abnormalities and complex internal molecular mechanisms in organisms. Computational methods with different types of biomedical data from phenotype to genotype can evaluate disease-disease associations at different levels, providing a comprehensive perspective for understanding diseases. In this review, available biomedical data and databases for evaluating disease-disease associations are first summarized. Then, existing computational methods for disease-disease associations are reviewed and classified into five groups in terms of the usages of biomedical data, including disease semantic-based, phenotype-based, function-based, representation learning-based and text mining-based methods. Further, we summarize software tools/platforms for computation and analysis of disease-disease associations. Finally, we give a discussion and summary on the research of disease-disease associations. This review provides a systematic overview for current disease association research, which could promote the development and applications of computational methods and tools/platforms for disease-disease associations.
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Affiliation(s)
- Ju Xiang
- School of Computer Science and Engineering, Central South University, China
| | - Jiashuai Zhang
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, China
| | - Yichao Zhao
- School of Computer Science and Engineering, Central South University, China
| | - Fang-Xiang Wu
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, China
| | - Min Li
- Division of Biomedical Engineering and Department of Mechanical Engineering at University of Saskatchewan, Saskatoon, Canada
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35
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Noor A. Improving bioinformatics software quality through incorporation of software engineering practices. PeerJ Comput Sci 2022; 8:e839. [PMID: 35111923 PMCID: PMC8771759 DOI: 10.7717/peerj-cs.839] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 12/13/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Bioinformatics software is developed for collecting, analyzing, integrating, and interpreting life science datasets that are often enormous. Bioinformatics engineers often lack the software engineering skills necessary for developing robust, maintainable, reusable software. This study presents review and discussion of the findings and efforts made to improve the quality of bioinformatics software. METHODOLOGY A systematic review was conducted of related literature that identifies core software engineering concepts for improving bioinformatics software development: requirements gathering, documentation, testing, and integration. The findings are presented with the aim of illuminating trends within the research that could lead to viable solutions to the struggles faced by bioinformatics engineers when developing scientific software. RESULTS The findings suggest that bioinformatics engineers could significantly benefit from the incorporation of software engineering principles into their development efforts. This leads to suggestion of both cultural changes within bioinformatics research communities as well as adoption of software engineering disciplines into the formal education of bioinformatics engineers. Open management of scientific bioinformatics development projects can result in improved software quality through collaboration amongst both bioinformatics engineers and software engineers. CONCLUSIONS While strides have been made both in identification and solution of issues of particular import to bioinformatics software development, there is still room for improvement in terms of shifts in both the formal education of bioinformatics engineers as well as the culture and approaches of managing scientific bioinformatics research and development efforts.
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Wang R, Hu X, Wang J, Zhou L, Hong Y, Zhang Y, Xiong F, Zhang X, Ye WC, Wang H. Proanthocyanidin A1 promotes the production of platelets to ameliorate chemotherapy-induced thrombocytopenia through activating JAK2/STAT3 pathway. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022; 95:153880. [PMID: 34906892 DOI: 10.1016/j.phymed.2021.153880] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 11/22/2021] [Accepted: 12/02/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Chemotherapy-induced thrombocytopenia (CIT) is a severe adverse drug reaction, and the main reason for CIT is the destruction of megakaryocytes (MKs, precursor cells of platelet) in bone marrow by chemotherapy. Peanut skin, the seed coat of Arachis hypogaea L., is a traditional Chinese medicine commonly used to treat thrombocytopenia. However, its active compounds and the mechanisms remain unclear. PURPOSE This study aims to clarify the active compounds of peanut skin to exhibit thrombogenic effects against CIT and their underlying mechanisms in vitro and in vivo. STUDY DESIGN The bioassay-guided isolation based on the proliferation of MKs was used to explore the possible platelet-enhancing ingredients in peanut skin. HSCCC technique coupled with preparative HPLC was used to separate the active compounds. Dami cells and carboplatin-treated mice model were used to evaluate the thrombogenic effects of PS-1. Network pharmacology, molecular docking, dynamics simulation studies, kinase activity, surface plasmon resonance (SPR), cellular thermal shift assay (CETSA), isothermal dose-response fingerprint (ITDRFCETSA) and western blot analysis were performed to investigate the mechanisms of PS-1. RESULTS Proanthocyanidin A1 (PS-1) and its stereoisomers (PS-2-4) were demonstrated to promote the proliferation of MKs (Dami cells), especially PS-1 (EC50 = 8.58 μM). Further studies demonstrated that PS-1 could induce the differentiation of Dami cells in dose/time-dependent manner. Biological target analysis showed that PS-1 directly bound to JAK2 (KD = 2.06 μM) to exert potent activating effect (EC50 = 0.66 μM). Oral administration of PS-1 (25 or 50 mg/kg) significantly improved CIT, but this effect was confirmed to be inhibited by JAK2 inhibitor AG490, indicating that PS-1 exerted its efficacy through JAK2 in vivo. CONCLUSION Proanthocyanins (PS-1-4) derived from peanut skin were first clarified as platelet-enhancing ingredients to improve CIT. The underlying mechanism of PS-1 was proved to promote the proliferation and differentiation of MKs via JAK2/STAT3 pathway both in vitro and in vivo.
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Affiliation(s)
- Rong Wang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Xiaolong Hu
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Jingjin Wang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Lina Zhou
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Yu Hong
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Yuanhao Zhang
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215028, People's Republic of China
| | - Fei Xiong
- State Key Laboratory of Bioelectronics, Jiangsu Laboratory for Biomaterials and Devices, Southeast University, Nanjing 210009, People's Republic of China
| | - Xiaoqi Zhang
- Institute of Traditional Chinese Medicine & Natural Products, Jinan University, Guangzhou 510632, People's Republic of China
| | - Wen-Cai Ye
- Institute of Traditional Chinese Medicine & Natural Products, Jinan University, Guangzhou 510632, People's Republic of China
| | - Hao Wang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China.
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System and network biology-based computational approaches for drug repositioning. COMPUTATIONAL APPROACHES FOR NOVEL THERAPEUTIC AND DIAGNOSTIC DESIGNING TO MITIGATE SARS-COV-2 INFECTION 2022. [PMCID: PMC9300680 DOI: 10.1016/b978-0-323-91172-6.00003-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recent advances in computational biology have not only fastened the drug discovery process but have also proven to be a powerful tool for the search of existing molecules of therapeutic value for drug repurposing. The system biology-based drug repurposing approaches shorten the time and reduced the cost of the whole process when compared to de novo drug discovery. In the present pandemic situation, these computational approaches have emerged as a boon to tackle the COVID-19 associated morbidities and mortalities. In this chapter, we present the overview of system biology-based network system approaches which can be exploited for the drug repurposing of disease. Besides, we have included information on relevant repurposed drugs which are currently used for the treatment of COVID-19.
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Zhang Y, Wang H, Oliveira RHM, Zhao C, Popel AS. Systems biology of angiogenesis signaling: Computational models and omics. WIREs Mech Dis 2021; 14:e1550. [PMID: 34970866 PMCID: PMC9243197 DOI: 10.1002/wsbm.1550] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 01/10/2023]
Abstract
Angiogenesis is a highly regulated multiscale process that involves a plethora of cells, their cellular signal transduction, activation, proliferation, differentiation, as well as their intercellular communication. The coordinated execution and integration of such complex signaling programs is critical for physiological angiogenesis to take place in normal growth, development, exercise, and wound healing, while its dysregulation is critically linked to many major human diseases such as cancer, cardiovascular diseases, and ocular disorders; it is also crucial in regenerative medicine. Although huge efforts have been devoted to drug development for these diseases by investigation of angiogenesis‐targeted therapies, only a few therapeutics and targets have proved effective in humans due to the innate multiscale complexity and nonlinearity in the process of angiogenic signaling. As a promising approach that can help better address this challenge, systems biology modeling allows the integration of knowledge across studies and scales and provides a powerful means to mechanistically elucidate and connect the individual molecular and cellular signaling components that function in concert to regulate angiogenesis. In this review, we summarize and discuss how systems biology modeling studies, at the pathway‐, cell‐, tissue‐, and whole body‐levels, have advanced our understanding of signaling in angiogenesis and thereby delivered new translational insights for human diseases. This article is categorized under:Cardiovascular Diseases > Computational Models Cancer > Computational Models
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Affiliation(s)
- Yu Zhang
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hanwen Wang
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Rebeca Hannah M Oliveira
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Chen Zhao
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Aleksander S Popel
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Zhang Y, Ma X, Li H, Zhuang J, Feng F, Liu L, Liu C, Sun C. Identifying the Effect of Ursolic Acid Against Triple-Negative Breast Cancer: Coupling Network Pharmacology With Experiments Verification. Front Pharmacol 2021; 12:685773. [PMID: 34858165 PMCID: PMC8631906 DOI: 10.3389/fphar.2021.685773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 10/20/2021] [Indexed: 11/13/2022] Open
Abstract
Triple negative breast cancer (TNBC) is a subtype of breast cancer with complex heterogeneity, high invasiveness, and long-term poor prognosis. With the development of molecular pathology and molecular genetics, the gene map of TNBC with distinctive biological characteristics has been outlined more clearly. Natural plant extracts such as paclitaxel, vinblastine, colchicine etc., have occupied an important position in the treatment of hormone-independent breast cancer. Ursolic acid (UA), a triterpenoid acid compound derived from apple, pear, loquat leaves, etc., has been reported to be effective in a variety of cancer treatments, but there are few reports on the treatment of TNBC. This study performed comprehensive bioinformatics analysis and in vitro experiments to identify the effect of UA on TNBC treatment and its potential molecular mechanism. Our results showed that UA could not only reduce the proliferation, migration, and invasion in MDA-MB-231 and MDA-MB-468 cell lines with a dose-dependent manner but also induce cell cycle arrest and apoptosis. Meanwhile, we collected the gene expression data GSE45827 and GSE65194 from GEO for comparison between TNBC and normal cell type and obtained 724 DEGs. Subsequently, PLK1 and CCNB1 related to TNBC were screened as the key targets via topological analysis and molecular docking, and gene set enrichment analysis identified the key pathway as the p53 signaling pathway. In addition, quantitative real-time PCR and western blot verified the key genes were PLK1 and CCNB1. In vivo and in vitro experiments showed that UA could inhibit the growth of TNBC cells, and down-regulate the protein expression levels of PLK1 and CCNB1 by mediating p53 signaling pathway. These findings provide strong evidence for UA intervention in TNBC via multi-target therapy.
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Affiliation(s)
- Yubao Zhang
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Xiaoran Ma
- First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Huayao Li
- College of Basic Medical, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jing Zhuang
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, China
| | - Fubin Feng
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, China
| | - Lijuan Liu
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, China
| | - Cun Liu
- First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Changgang Sun
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, China.,Qingdao Academy of Chinese Medical Sciences, Shandong University of Traditional Chinese Medicine, Qingdao, China
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40
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Wu J, Zhang Q, Li G. Identification of cancer-related module in protein-protein interaction network based on gene prioritization. J Bioinform Comput Biol 2021; 20:2150031. [PMID: 34860145 DOI: 10.1142/s0219720021500311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
With the rapid development of deep sequencing technologies, a large amount of high-throughput data has been available for studying the carcinogenic mechanism at the molecular level. It has been widely accepted that the development and progression of cancer are regulated by modules/pathways rather than individual genes. The investigation of identifying cancer-related active modules has received an extensive attention. In this paper, we put forward an identification method ModFinder by integrating both biological networks and gene expression profiles. More concretely, a gene scoring function is devised by using the regression model with [Formula: see text]-step random walk kernel, and the genes are ranked according to both of their active scores and degrees in the PPI network. Then a greedy algorithm NSEA is introduced to find an active module with high score and strong connectivity. Experiments were performed on both simulated data and real biological one, i.e. breast cancer and cervical cancer. Compared with the previous methods SigMod, LEAN and RegMod, ModFinder shows competitive performance. It can successfully identify a well-connected module that contains a large proportion of cancer-related genes, including some well-known oncogenes or tumor suppressors enriched in cancer-related pathways.
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Affiliation(s)
- Jingli Wu
- Guangxi Key Lab of Multi-Source Information Mining & Security, Guangxi Normal University, Guilin 541004, P. R. China.,Yimeng Executive Leadership Academy, Linyi 276000, P. R. China
| | - Qi Zhang
- College of Computer Science and Information Engineering, Guangxi Normal University, Guilin 541004, P. R. China
| | - Gaoshi Li
- Guangxi Key Lab of Multi-Source Information Mining & Security, Guangxi Normal University, Guilin 541004, P. R. China
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41
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Wu S, Chen D, Snyder MP. Network biology bridges the gaps between quantitative genetics and multi-omics to map complex diseases. Curr Opin Chem Biol 2021; 66:102101. [PMID: 34861483 DOI: 10.1016/j.cbpa.2021.102101] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/17/2021] [Accepted: 10/27/2021] [Indexed: 12/27/2022]
Abstract
With advances in high-throughput sequencing technologies, quantitative genetics approaches have provided insights into genetic basis of many complex diseases. Emerging in-depth multi-omics profiling technologies have created exciting opportunities for systematically investigating intricate interaction networks with different layers of biological molecules underlying disease etiology. Herein, we summarized two main categories of biological networks: evidence-based and statistically inferred. These different types of molecular networks complement each other at both bulk and single-cell levels. We also review three main strategies to incorporate quantitative genetics results with multi-omics data by network analysis: (a) network propagation, (b) functional module-based methods, (c) comparative/dynamic networks. These strategies not only aid in elucidating molecular mechanisms of complex diseases but can guide the search for therapeutic targets.
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Affiliation(s)
- Si Wu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
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42
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Minadakis G, Muñoz-Pomer Fuentes A, Tsouloupas G, Papatheodorou I, Spyrou GM. PathExNET: A tool for extracting pathway expression networks from gene expression statistics. Comput Struct Biotechnol J 2021; 19:4336-4344. [PMID: 34429851 PMCID: PMC8363825 DOI: 10.1016/j.csbj.2021.07.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 07/12/2021] [Accepted: 07/28/2021] [Indexed: 11/26/2022] Open
Abstract
A fundamental issue related to the understanding of the molecular mechanisms, is the way in which common pathways act across different biological experiments related to complex diseases. Using network-based approaches, this work aims to provide a numeric characterization of pathways across different biological experiments, in the prospect to create unique footprints that may characterise a specific disease under study at a pathway network level. In this line we propose PathExNET, a web service that allows the creation of pathway-to-pathway expression networks that hold the over- and under expression information obtained from differential gene expression analyses. The unique numeric characterization of pathway expression status related to a specific biological experiment (or disease), as well as the creation of diverse combination of pathway networks generated by PathExNET, is expected to provide a concrete contribution towards the individualization of disease, and further lead to a more precise personalised medicine and management of treatment. PathExNET is available at: https://bioinformatics.cing.ac.cy/PathExNET and at https://pathexnet.cing-big.hpcf.cyi.ac.cy/.
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Affiliation(s)
- George Minadakis
- Bioinformatics Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, 2371 Ayios Dometios, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, 6 Iroon Avenue, 2371 Ayios Dometios, Nicosia, Cyprus
| | | | - George Tsouloupas
- HPC Facility, The Cyprus Institute, 20 Konstantinou Kavafi Street, 2121, Aglantzia, Nicosia, Cyprus
| | - Irene Papatheodorou
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - George M. Spyrou
- Bioinformatics Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, 2371 Ayios Dometios, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, 6 Iroon Avenue, 2371 Ayios Dometios, Nicosia, Cyprus
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Tosadori G, Di Silvestre D, Spoto F, Mauri P, Laudanna C, Scardoni G. Analysing omics data sets with weighted nodes networks (WNNets). Sci Rep 2021; 11:14447. [PMID: 34262093 PMCID: PMC8280138 DOI: 10.1038/s41598-021-93699-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 06/16/2021] [Indexed: 11/30/2022] Open
Abstract
Current trends in biomedical research indicate data integration as a fundamental step towards precision medicine. In this context, network models allow representing and analysing complex biological processes. However, although effective in unveiling network properties, these models fail in considering the individual, biochemical variations occurring at molecular level. As a consequence, the analysis of these models partially loses its predictive power. To overcome these limitations, Weighted Nodes Networks (WNNets) were developed. WNNets allow to easily and effectively weigh nodes using experimental information from multiple conditions. In this study, the characteristics of WNNets were described and a proteomics data set was modelled and analysed. Results suggested that degree, an established centrality index, may offer a novel perspective about the functional role of nodes in WNNets. Indeed, degree allowed retrieving significant differences between experimental conditions, highlighting relevant proteins, and provided a novel interpretation for degree itself, opening new perspectives in experimental data modelling and analysis. Overall, WNNets may be used to model any high-throughput experimental data set requiring weighted nodes. Finally, improving the power of the analysis by using centralities such as betweenness may provide further biological insights and unveil novel, interesting characteristics of WNNets.
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Affiliation(s)
- Gabriele Tosadori
- Center for BioMedical Computing (CBMC), University of Verona, Strada le Grazie 8, 37134, Verona, Italy.
- Section of General Pathology, Department of Medicine, University of Verona, 37134, Verona, Italy.
| | - Dario Di Silvestre
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), via F.lli Cervi 93, Segrate, 20090, Milan, Italy
| | - Fausto Spoto
- Department of Computer Science, University of Verona, Strada le Grazie 15, 37134, Verona, Italy
| | - Pierluigi Mauri
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), via F.lli Cervi 93, Segrate, 20090, Milan, Italy
| | - Carlo Laudanna
- Section of General Pathology, Department of Medicine, University of Verona, 37134, Verona, Italy.
| | - Giovanni Scardoni
- Center for BioMedical Computing (CBMC), University of Verona, Strada le Grazie 8, 37134, Verona, Italy
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Xiang J, Zhang J, Zheng R, Li X, Li M. NIDM: network impulsive dynamics on multiplex biological network for disease-gene prediction. Brief Bioinform 2021; 22:6236070. [PMID: 33866352 DOI: 10.1093/bib/bbab080] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/11/2021] [Accepted: 02/21/2021] [Indexed: 12/12/2022] Open
Abstract
The prediction of genes related to diseases is important to the study of the diseases due to high cost and time consumption of biological experiments. Network propagation is a popular strategy for disease-gene prediction. However, existing methods focus on the stable solution of dynamics while ignoring the useful information hidden in the dynamical process, and it is still a challenge to make use of multiple types of physical/functional relationships between proteins/genes to effectively predict disease-related genes. Therefore, we proposed a framework of network impulsive dynamics on multiplex biological network (NIDM) to predict disease-related genes, along with four variants of NIDM models and four kinds of impulsive dynamical signatures (IDSs). NIDM is to identify disease-related genes by mining the dynamical responses of nodes to impulsive signals being exerted at specific nodes. By a series of experimental evaluations in various types of biological networks, we confirmed the advantage of multiplex network and the important roles of functional associations in disease-gene prediction, demonstrated superior performance of NIDM compared with four types of network-based algorithms and then gave the effective recommendations of NIDM models and IDS signatures. To facilitate the prioritization and analysis of (candidate) genes associated to specific diseases, we developed a user-friendly web server, which provides three kinds of filtering patterns for genes, network visualization, enrichment analysis and a wealth of external links (http://bioinformatics.csu.edu.cn/DGP/NID.jsp). NIDM is a protocol for disease-gene prediction integrating different types of biological networks, which may become a very useful computational tool for the study of disease-related genes.
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Affiliation(s)
- Ju Xiang
- School of Computer Science and Engineering, Central South University, Human, China
| | - Jiashuai Zhang
- School of Computer Science and Engineering, Central South University, Human, China
| | - Ruiqing Zheng
- School of Computer Science and Engineering, Central South University, China
| | - Xingyi Li
- School of Computer Science and Engineering, Central South University, Changsha, China
| | - Min Li
- School of Computer Science and Engineering, Central South University, Changsha, China
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45
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Wang Y, Yang H, Chen L, Jafari M, Tang J. Network-based modeling of herb combinations in traditional Chinese medicine. Brief Bioinform 2021; 22:6217717. [PMID: 33834186 PMCID: PMC8425426 DOI: 10.1093/bib/bbab106] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 12/12/2022] Open
Abstract
Traditional Chinese medicine (TCM) has been practiced for thousands of years for treating human diseases. In comparison to modern medicine, one of the advantages of TCM is the principle of herb compatibility, known as TCM formulae. A TCM formula usually consists of multiple herbs to achieve the maximum treatment effects, where their interactions are believed to elicit the therapeutic effects. Despite being a fundamental component of TCM, the rationale of combining specific herb combinations remains unclear. In this study, we proposed a network-based method to quantify the interactions in herb pairs. We constructed a protein–protein interaction network for a given herb pair by retrieving the associated ingredients and protein targets, and determined multiple network-based distances including the closest, shortest, center, kernel, and separation, both at the ingredient and at the target levels. We found that the frequently used herb pairs tend to have shorter distances compared to random herb pairs, suggesting that a therapeutic herb pair is more likely to affect neighboring proteins in the human interactome. Furthermore, we found that the center distance determined at the ingredient level improves the discrimination of top-frequent herb pairs from random herb pairs, suggesting the rationale of considering the topologically important ingredients for inferring the mechanisms of action of TCM. Taken together, we have provided a network pharmacology framework to quantify the degree of herb interactions, which shall help explore the space of herb combinations more effectively to identify the synergistic compound interactions based on network topology.
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Affiliation(s)
| | - Hongbin Yang
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Linxiao Chen
- Department of Mathematics and Statistics, University of Helsinki, Finland
| | | | - Jing Tang
- Faculty of Medicine of the University of Helsinki and Group Leader of Network Pharmacology for Precision Medicine group, Finland
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46
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Zhao M, He W, Tang J, Zou Q, Guo F. A comprehensive overview and critical evaluation of gene regulatory network inference technologies. Brief Bioinform 2021; 22:6128842. [PMID: 33539514 DOI: 10.1093/bib/bbab009] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/11/2020] [Accepted: 01/06/2021] [Indexed: 12/12/2022] Open
Abstract
Gene regulatory network (GRN) is the important mechanism of maintaining life process, controlling biochemical reaction and regulating compound level, which plays an important role in various organisms and systems. Reconstructing GRN can help us to understand the molecular mechanism of organisms and to reveal the essential rules of a large number of biological processes and reactions in organisms. Various outstanding network reconstruction algorithms use specific assumptions that affect prediction accuracy, in order to deal with the uncertainty of processing. In order to study why a certain method is more suitable for specific research problem or experimental data, we conduct research from model-based, information-based and machine learning-based method classifications. There are obviously different types of computational tools that can be generated to distinguish GRNs. Furthermore, we discuss several classical, representative and latest methods in each category to analyze core ideas, general steps, characteristics, etc. We compare the performance of state-of-the-art GRN reconstruction technologies on simulated networks and real networks under different scaling conditions. Through standardized performance metrics and common benchmarks, we quantitatively evaluate the stability of various methods and the sensitivity of the same algorithm applying to different scaling networks. The aim of this study is to explore the most appropriate method for a specific GRN, which helps biologists and medical scientists in discovering potential drug targets and identifying cancer biomarkers.
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Affiliation(s)
- Mengyuan Zhao
- School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Wenying He
- School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Jijun Tang
- University of South Carolina, Tianjin, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
| | - Fei Guo
- School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University, Tianjin, China
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Zanin M, Aitya NA, Basilio J, Baumbach J, Benis A, Behera CK, Bucholc M, Castiglione F, Chouvarda I, Comte B, Dao TT, Ding X, Pujos-Guillot E, Filipovic N, Finn DP, Glass DH, Harel N, Iesmantas T, Ivanoska I, Joshi A, Boudjeltia KZ, Kaoui B, Kaur D, Maguire LP, McClean PL, McCombe N, de Miranda JL, Moisescu MA, Pappalardo F, Polster A, Prasad G, Rozman D, Sacala I, Sanchez-Bornot JM, Schmid JA, Sharp T, Solé-Casals J, Spiwok V, Spyrou GM, Stalidzans E, Stres B, Sustersic T, Symeonidis I, Tieri P, Todd S, Van Steen K, Veneva M, Wang DH, Wang H, Wang H, Watterson S, Wong-Lin K, Yang S, Zou X, Schmidt HH. An Early Stage Researcher's Primer on Systems Medicine Terminology. NETWORK AND SYSTEMS MEDICINE 2021; 4:2-50. [PMID: 33659919 PMCID: PMC7919422 DOI: 10.1089/nsm.2020.0003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/27/2020] [Indexed: 12/19/2022] Open
Abstract
Background: Systems Medicine is a novel approach to medicine, that is, an interdisciplinary field that considers the human body as a system, composed of multiple parts and of complex relationships at multiple levels, and further integrated into an environment. Exploring Systems Medicine implies understanding and combining concepts coming from diametral different fields, including medicine, biology, statistics, modeling and simulation, and data science. Such heterogeneity leads to semantic issues, which may slow down implementation and fruitful interaction between these highly diverse fields. Methods: In this review, we collect and explain more than100 terms related to Systems Medicine. These include both modeling and data science terms and basic systems medicine terms, along with some synthetic definitions, examples of applications, and lists of relevant references. Results: This glossary aims at being a first aid kit for the Systems Medicine researcher facing an unfamiliar term, where he/she can get a first understanding of them, and, more importantly, examples and references for digging into the topic.
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Affiliation(s)
- Massimiliano Zanin
- Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, Madrid, Spain
| | - Nadim A.A. Aitya
- Intelligent Systems Research Centre, School of Computing, Engineering and Intelligent Systems, Ulster University, Ulster, United Kingdom
| | - José Basilio
- Center for Physiology and Pharmacology, Institute of Vascular Biology and Thrombosis Research, Medical University of Vienna, Vienna, Austria
| | - Jan Baumbach
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Arriel Benis
- Faculty of Technology Management, Holon Institute of Technology (HIT), Holon, Israel
| | - Chandan K. Behera
- Intelligent Systems Research Centre, School of Computing, Engineering and Intelligent Systems, Ulster University, Ulster, United Kingdom
| | - Magda Bucholc
- Intelligent Systems Research Centre, School of Computing, Engineering and Intelligent Systems, Ulster University, Ulster, United Kingdom
| | - Filippo Castiglione
- CNR National Research Council, IAC Institute for Applied Computing, Rome, Italy
| | - Ioanna Chouvarda
- Lab of Computing, Medical Informatics, and Biomedical Imaging Technologies, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Blandine Comte
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Tien-Tuan Dao
- Biomechanics and Bioengineering Laboratory (UMR CNRS 7338), Université de Technologie de Compiègne, Compiègne, France
- Labex MS2T “Control of Technological Systems-of-Systems,” CNRS and Université de Technologie de Compiègne, Compiègne, France
| | - Xuemei Ding
- Intelligent Systems Research Centre, School of Computing, Engineering and Intelligent Systems, Ulster University, Ulster, United Kingdom
| | - Estelle Pujos-Guillot
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Nenad Filipovic
- Faculty of Engineering, University of Kragujevac, Kragujevac, Serbia
- Bioengineering Research and Development Center (BioIRC), Kragujevac, Serbia
- Steinbeis Advanced Risk Technologies Institute doo Kragujevac, Kragujevac, Serbia
| | - David P. Finn
- Pharmacology and Therapeutics, School of Medicine, Galway Neuroscience Centre, National University of Ireland, Galway, Republic of Ireland
| | - David H. Glass
- School of Computing, Ulster University, Ulster, United Kingdom
| | - Nissim Harel
- Faculty of Sciences, Holon Institute of Technology (HIT), Holon, Israel
| | - Tomas Iesmantas
- Department of Mathematics and Natural Sciences, Kaunas University of Technology, Kaunas, Lithuania
| | - Ilinka Ivanoska
- Faculty of Computer Science and Engineering, Ss. Cyril and Methodius University, Skopje, Macedonia
| | - Alok Joshi
- Intelligent Systems Research Centre, School of Computing, Engineering and Intelligent Systems, Ulster University, Ulster, United Kingdom
| | - Karim Zouaoui Boudjeltia
- Laboratory of Experimental Medicine (ULB 222), Medicine Faculty, Université libre de Bruxelles, CHU de Charleroi, Charleroi, Belgium
| | - Badr Kaoui
- Biomechanics and Bioengineering Laboratory (UMR CNRS 7338), Université de Technologie de Compiègne, Compiègne, France
- Labex MS2T “Control of Technological Systems-of-Systems,” CNRS and Université de Technologie de Compiègne, Compiègne, France
| | - Daman Kaur
- Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute, Ulster University, Ulster, United Kingdom
| | - Liam P. Maguire
- Intelligent Systems Research Centre, School of Computing, Engineering and Intelligent Systems, Ulster University, Ulster, United Kingdom
| | - Paula L. McClean
- Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute, Ulster University, Ulster, United Kingdom
| | - Niamh McCombe
- Intelligent Systems Research Centre, School of Computing, Engineering and Intelligent Systems, Ulster University, Ulster, United Kingdom
| | - João Luís de Miranda
- Escola Superior de Tecnologia e Gestão, Instituto Politécnico de Portalegre, Portalegre, Portugal
- Centro de Recursos Naturais e Ambiente (CERENA), Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | | | | | - Annikka Polster
- Centre for Molecular Medicine Norway (NCMM), Forskningparken, Oslo, Norway
| | - Girijesh Prasad
- Intelligent Systems Research Centre, School of Computing, Engineering and Intelligent Systems, Ulster University, Ulster, United Kingdom
| | - Damjana Rozman
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Ioan Sacala
- Faculty of Automatic Control and Computers, University Politehnica of Bucharest, Bucharest, Romania
| | - Jose M. Sanchez-Bornot
- Intelligent Systems Research Centre, School of Computing, Engineering and Intelligent Systems, Ulster University, Ulster, United Kingdom
| | - Johannes A. Schmid
- Center for Physiology and Pharmacology, Institute of Vascular Biology and Thrombosis Research, Medical University of Vienna, Vienna, Austria
| | - Trevor Sharp
- Department of Pharmacology, University of Oxford, Oxford, United Kingdom
| | - Jordi Solé-Casals
- Data and Signal Processing Research Group, University of Vic–Central University of Catalonia, Vic, Spain
- Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
- College of Artificial Intelligence, Nankai University, Tianjin, China
| | - Vojtěch Spiwok
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic
| | - George M. Spyrou
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Egils Stalidzans
- Computational Systems Biology Group, Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia
| | - Blaž Stres
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
- Faculty of Civil and Geodetic Engineering, University of Ljubljana, Ljubljana, Slovenia
- Department of Automation, Biocybernetics and Robotics, Jozef Stefan Institute, Ljubljana, Slovenia
| | - Tijana Sustersic
- Faculty of Engineering, University of Kragujevac, Kragujevac, Serbia
- Bioengineering Research and Development Center (BioIRC), Kragujevac, Serbia
- Steinbeis Advanced Risk Technologies Institute doo Kragujevac, Kragujevac, Serbia
| | - Ioannis Symeonidis
- Center for Research and Technology Hellas, Hellenic Institute of Transport, Thessaloniki, Greece
| | - Paolo Tieri
- CNR National Research Council, IAC Institute for Applied Computing, Rome, Italy
| | - Stephen Todd
- Altnagelvin Area Hospital, Western Health and Social Care Trust, Altnagelvin, United Kingdom
| | - Kristel Van Steen
- BIO3-Systems Genetics, GIGA-R, University of Liege, Liege, Belgium
- BIO3-Systems Medicine, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | - Da-Hui Wang
- State Key Laboratory of Cognitive Neuroscience and Learning, and School of Systems Science, Beijing Normal University, Beijing, China
| | - Haiying Wang
- School of Computing, Ulster University, Ulster, United Kingdom
| | - Hui Wang
- School of Computing, Ulster University, Ulster, United Kingdom
| | - Steven Watterson
- Northern Ireland Centre for Stratified Medicine, Ulster University, Londonderry, United Kingdom
| | - KongFatt Wong-Lin
- Intelligent Systems Research Centre, School of Computing, Engineering and Intelligent Systems, Ulster University, Ulster, United Kingdom
| | - Su Yang
- Intelligent Systems Research Centre, School of Computing, Engineering and Intelligent Systems, Ulster University, Ulster, United Kingdom
| | - Xin Zou
- Shanghai Centre for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Harald H.H.W. Schmidt
- Faculty of Health, Medicine & Life Science, Maastricht University, Maastricht, The Netherlands
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Liang R, Chen W, Chen XY, Fan HN, Zhang J, Zhu JS. Dihydroartemisinin inhibits the tumorigenesis and invasion of gastric cancer by regulating STAT1/KDR/MMP9 and P53/BCL2L1/CASP3/7 pathways. Pathol Res Pract 2021; 218:153318. [PMID: 33370709 DOI: 10.1016/j.prp.2020.153318] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/28/2020] [Accepted: 12/08/2020] [Indexed: 12/20/2022]
Abstract
Dihydroartemisinin (DHA), an effective antimalarial drug, has been widely investigated as an anti-tumor agent. Although previous studies have indicated the potential therapeutic effects of DHA on multiple malignancies, its detailed molecular mechanisms in gastric cancer (GC) are still undocumented. In the present study, we applied network pharmacology and bioinformatics (gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses) to obtain the collective targets of DHA and GC and analyzed their involvement in constructing a protein-protein interaction (PPI) network. The top 10% hub targets in this network were identified, and TCGA database was utilized for the single gene analysis of their correlation with the prognosis of GC. CCK8, EdU, Transwell, and flow cytometry analyses were conducted, and subcutaneous xenograft tumor models were constructed to assess the effects of DHA on the tumorigenesis and invasion of GC. Furthermore, the targets of DHA were verified by molecular docking, quantitative real-time PCR (qPCR) and western blot analyses in GC cells. The results indicated that the common targets of DHA and GC were enriched in multiple cancer-related pathways including KDR, STAT1 and apoptosis signaling pathways, where the core genes included KDR, MMP9, STAT1, TP53, CASP3/7 and BCL2L1. The lowered expression of KDR and increased expression of TP53 and CASP7 harbored a favorable survival for patients with GC patients. CASP7 showed a positive correlation with CASP3 but a negative correlation with KDR and could be regarded as an independent protective factor for overall survival in GC. Moreover, DHA treatment induced cell apoptosis and suppressed the cell proliferation, DNA synthesis, cycle progression and invasive capabilities both in vitro and in vivo. DHA also upregulated p53, CASP3, and cleaved-CASP3 and downregulated BCL2L1, MMP9, KDR, p-KDR, STAT1 and p-STAT1 in GC cell lines. In conclusion, DHA could suppress the tumorigenesis and invasion of GC by regulating STAT1/KDR/MMP9 and p53/BCL2L1/CASP3/7 pathways. Our findings might provide a novel approach for the treatment of GC.
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Affiliation(s)
- Rui Liang
- Department of Gastroenterology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Wei Chen
- Department of Gastroenterology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Xiao-Yu Chen
- Department of Gastroenterology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Hui-Ning Fan
- Department of Gastroenterology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Jing Zhang
- Department of Gastroenterology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China.
| | - Jin-Shui Zhu
- Department of Gastroenterology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China.
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49
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Jiang L, Cui H, Zhang C, Cao X, Gu N, Zhu Y, Wang J, Yang Z, Li C. Repetitive Transcranial Magnetic Stimulation for Improving Cognitive Function in Patients With Mild Cognitive Impairment: A Systematic Review. Front Aging Neurosci 2021; 12:593000. [PMID: 33519418 PMCID: PMC7842279 DOI: 10.3389/fnagi.2020.593000] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 12/02/2020] [Indexed: 12/14/2022] Open
Abstract
Background: Mild cognitive impairment (MCI) is an early stage of Alzheimer's disease. Repetitive transcranial magnetic stimulation (rTMS) has been widely employed in MCI research. However, there is no reliable systematic evidence regarding the effects of rTMS on MCI. The aim of this review was to evaluate the efficacy and safety of rTMS in the treatment of MCI. Methods: A comprehensive literature search of nine electronic databases was performed to identify articles published in English or Chinese before June 20, 2019. The identified articles were screened, data were extracted, and the methodological quality of the included trials was assessed. The meta-analysis was performed using the RevMan 5.3 software. We used the GRADE approach to rate the quality of the evidence. Results: Nine studies comprising 369 patients were included. The meta-analysis showed that rTMS may significantly improve global cognitive function (standardized mean difference [SMD] 2.09, 95% confidence interval [CI] 0.94 to 3.24, p = 0.0004, seven studies, n = 296; low-quality evidence) and memory (SMD 0.44, 95% CI 0.16 to 0.72, p = 0.002, six studies, n = 204; moderate-quality evidence). However, there was no significant improvement in executive function and attention (p > 0.05). Subgroup analyses revealed the following: (1) rTMS targeting the left hemisphere significantly enhanced global cognitive function, while rTMS targeting the bilateral hemispheres significantly enhanced global cognitive function and memory; (2) high-frequency rTMS significantly enhanced global cognitive function and memory; and (3) a high number of treatments ≥20 times could improve global cognitive function and memory. There was no significant difference in dropout rate (p > 0.05) between the rTMS and control groups. However, patients who received rTMS had a higher rate of mild adverse effects (risk ratio 2.03, 95% CI 1.16 to 3.52, p = 0.01, seven studies, n = 317; moderate-quality evidence). Conclusions: rTMS appears to improve global cognitive function and memory in patients with MCI and may have good acceptability and mild adverse effects. Nevertheless, these results should be interpreted cautiously due to the relatively small number of trials, particularly for low-frequency rTMS.
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Affiliation(s)
- Lijuan Jiang
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huiru Cui
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Caidi Zhang
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xinyi Cao
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Nannan Gu
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yikang Zhu
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jijun Wang
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute of Psychology and Behavioral Science, Shanghai Jiao Tong University, Shanghai, China.,Center for Excellence in Brain Science and Intelligence Technology (CEBSIT), Chinese Academy of Science, Beijing, China
| | - Zhi Yang
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute of Psychology and Behavioral Science, Shanghai Jiao Tong University, Shanghai, China.,Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China.,Laboratory of Psychological Heath and Imaging, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chunbo Li
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute of Psychology and Behavioral Science, Shanghai Jiao Tong University, Shanghai, China.,Center for Excellence in Brain Science and Intelligence Technology (CEBSIT), Chinese Academy of Science, Beijing, China.,Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
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50
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Pane K, Affinito O, Zanfardino M, Castaldo R, Incoronato M, Salvatore M, Franzese M. An Integrative Computational Approach Based on Expression Similarity Signatures to Identify Protein-Protein Interaction Networks in Female-Specific Cancers. Front Genet 2021; 11:612521. [PMID: 33424936 PMCID: PMC7793872 DOI: 10.3389/fgene.2020.612521] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 10/28/2020] [Indexed: 11/13/2022] Open
Abstract
Breast, ovarian, and endometrial cancers have a major impact on mortality in women. These tumors share hormone-dependent mechanisms involved in female-specific cancers which support tumor growth in a different manner. Integrated computational approaches may allow us to better detect genomic similarities between these different female-specific cancers, helping us to deliver more sophisticated diagnosis and precise treatments. Recently, several initiatives of The Cancer Genome Atlas (TCGA) have encouraged integrated analyses of multiple cancers rather than individual tumors. These studies revealed common genetic alterations (driver genes) even in clinically distinct entities such as breast, ovarian, and endometrial cancers. In this study, we aimed to identify expression similarity signatures by extracting common genes among TCGA breast (BRCA), ovarian (OV), and uterine corpus endometrial carcinoma (UCEC) cohorts and infer co-regulatory protein-protein interaction networks that might have a relationship with the estrogen signaling pathway. Thus, we carried out an unsupervised principal component analysis (PCA)-based computational approach, using RNA sequencing data of 2,015 female cancer and 148 normal samples, in order to simultaneously capture the data heterogeneity of intertumors. Firstly, we identified tumor-associated genes from gene expression profiles. Secondly, we investigated the signaling pathways and co-regulatory protein-protein interaction networks underlying these three cancers by leveraging the Ingenuity Pathway Analysis software. In detail, we discovered 1,643 expression similarity signatures (638 downregulated and 1,005 upregulated genes, with respect to normal phenotype), denoted as tumor-associated genes. Through functional genomic analyses, we assessed that these genes were involved in the regulation of cell-cycle-dependent mechanisms, including metaphase kinetochore formation and estrogen-dependent S-phase entry. Furthermore, we generated putative co-regulatory protein-protein interaction networks, based on upstream regulators such as the ERBB2/HER2 gene. Moreover, we provided an ad-hoc bioinformatics workflow with a manageable list of intertumor expression similarity signatures for the three female-specific cancers. The expression similarity signatures identified in this study might uncover potential estrogen-dependent molecular mechanisms promoting carcinogenesis.
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