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Danishuddin, Haque MA, Malik MZ, Arya R, Singh P, Lee JS, Kim JJ, Lee KW, Jung TS. Unveiling the Mechanisms Underlying the Immunotherapeutic Potential of Gene-miRNA and Drugs in Head and Neck Cancer. Pharmaceuticals (Basel) 2024; 17:921. [PMID: 39065771 PMCID: PMC11280033 DOI: 10.3390/ph17070921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 07/02/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024] Open
Abstract
Head and neck cancer ranks as the sixth-most common malignancy worldwide, characterized by high mortality and recurrence rates. Research studies indicate that molecular diagnostics play a crucial role in the early detection and prognostic evaluation of these diseases. This study aimed to identify potential biomarkers for head and neck cancer and elucidate their interactions with miRNAs and possible therapeutic drugs. Four drivers, namely, FN1, IL1A, COL1A1, and MMP9, were identified using network biology and machine learning approaches. Gene set variation analysis (GSVA) showed that these genes were significantly involved in different biological processes and pathways, including coagulation, UV-response-down, apoptosis, NOTCH signaling, Wnt-beta catenin, and other signal pathways. The diagnostic value of these hub genes was validated using receiver operating characteristic (ROC) curves. The top interactive miRNAs, including miR-128-3p, miR-218-5p, miR-214-3p, miR-124-3p, miR-129-2-3p, and miR-1-3p, targeted the key genes. Furthermore, the interaction between the key genes and drugs was also identified. In summary, the key genes and miRNAs or drugs reported in this study might provide valuable information for potential biomarkers to increase the prognosis and diagnosis of head and neck cancer.
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Affiliation(s)
- Danishuddin
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea; (D.); (M.A.H.); (R.A.)
| | - Md Azizul Haque
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea; (D.); (M.A.H.); (R.A.)
| | - Md. Zubbair Malik
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute (DDI), Dasman 15462, Kuwait;
| | - Rakesh Arya
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea; (D.); (M.A.H.); (R.A.)
| | - Pooja Singh
- Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University (GNU), Jinju 52828, Republic of Korea;
| | - Jeong-Sang Lee
- GSCRO, Research Spin-Off Company, Innopolis Jeonbuk, Jeonju 55069, Republic of Korea;
- Department of Food and Nutrition, College of Medical Science, Jeonju University, Jeonju 55069, Republic of Korea
| | - Jong-Joo Kim
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea; (D.); (M.A.H.); (R.A.)
| | - Keun-Woo Lee
- Korea Quantum Computing (KQC), Busan 48058, Republic of Korea
- Angel i-Drug Design (AiDD), Jinju 52650, Republic of Korea
| | - Tae-Sung Jung
- Laboratory of Aquatic Animal Diseases, Research Institute of Natural Science, College of Veterinary Medicine, Gyeongsang National University (GNU), Jinju 52828, Republic of Korea
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Priya A, Dashti M, Thanaraj TA, Irshad M, Singh V, Tandon R, Mehrotra R, Singh AK, Mago P, Singh V, Malik MZ, Ray AK. Identification of potential regulatory mechanisms and therapeutic targets for lung cancer. J Biomol Struct Dyn 2024:1-18. [PMID: 38319037 DOI: 10.1080/07391102.2024.2310208] [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: 06/12/2023] [Accepted: 01/18/2024] [Indexed: 02/07/2024]
Abstract
Lung cancer poses a significant health threat globally, especially in regions like India, with 5-year survival rates remain alarmingly low. Our study aimed to uncover key markers for effective treatment and early detection. We identified specific genes related to lung cancer using the BioXpress database and delved into their roles through DAVID enrichment analysis. By employing network theory, we explored the intricate interactions within lung cancer networks, identifying ASPM and MKI67 as crucial regulator genes. Predictions of microRNA and transcription factor interactions provided additional insights. Examining gene expression patterns using GEPIA and KM Plotter revealed the clinical relevance of these key genes. In our pursuit of targeted therapies, Drug Bank pointed to methotrexate as a potential drug for the identified key regulator genes. Confirming this, molecular docking studies through Swiss Dock showed promising binding interactions. To ensure stability, we conducted molecular dynamics simulations using the AMBER 16 suite. In summary, our study pinpoints ASPM and MKI67 as vital regulators in lung cancer networks. The identification of hub genes and functional pathways enhances our understanding of molecular processes, offering potential therapeutic targets. Importantly, methotrexate emerged as a promising drug candidate, supported by robust docking and simulation studies. These findings lay a solid foundation for further experimental validations and hold promise for advancing personalized therapeutic strategies in lung cancer.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anjali Priya
- Department of Environmental Studies, University of Delhi, New Delhi, India
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | | | | | | | - Virendra Singh
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Ravi Tandon
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Rekha Mehrotra
- Department of Microbiology, Shaheed Rajguru College of Applied Sciences for Women, University of Delhi, New Delhi, India
| | - Alok Kumar Singh
- Department of Zoology, Ramjas College, University of Delhi, New Delhi, India
| | - Payal Mago
- Department of Botany, Shri Aurobindo College, University of Delhi, New Delhi, India to Campus Of Open Learning, University of Delhi, New Delhi, India
- Shaheed Rajguru College of Applied Sciences for Women, University of Delhi, New Delhi, India
| | - Vishal Singh
- Delhi School of Public Health, Institution of Eminence, University of Delhi, New Delhi, India
| | | | - Ashwini Kumar Ray
- Department of Environmental Studies, University of Delhi, New Delhi, India
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Pandaleke TA, Handono K, Widasmara D, Susianti H. The immunomodulatory activity of Orthosiphon aristatus against atopic dermatitis: Evidence-based on network pharmacology and molecular simulations. J Taibah Univ Med Sci 2024; 19:164-174. [PMID: 38047238 PMCID: PMC10692725 DOI: 10.1016/j.jtumed.2023.10.005] [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: 05/15/2023] [Revised: 08/11/2023] [Accepted: 10/26/2023] [Indexed: 12/05/2023] Open
Abstract
Objectives To explore the potential activity of Orthosiphon aristatus (OA) against atopic dermatitis (AD). Methods Phytocompounds from OA were identified through chromatography analysis, then continued to target identification and functional annotation to explore the potential target of OA. Then, network pharmacology from annotated proteins determined protein targets for OA phytocompounds. Protein with highest rank according to the betweenness and closeness algorithm then continued to molecular docking and validated through molecular dynamics analysis. Results Chromatography data analysis revealed thirty-six compounds, predominantly classified as carboxylic acid, fatty acyls, and polyphenols. Upon identifying these compounds, network biology-based target identification revealed their potential bioactivity in modulating inflammation in AD. Tumour Necrosis Factor-alpha (TNF-α) and Prostaglandin G/H synthase 2 (PTGS2) emerged as the most probable targets based on hub centrality in the protein-protein interaction network. Later, molecular docking analyses highlighted sixteen compounds with good inhibitory activity against these two proteins. Notably, molecular dynamics simulation revealed that three compounds out of the previous sixteen potential compounds were more likely to act as the TNF-α and PTGS2 inhibitor as well as their native inhibitor. Those compounds are (1R,9R)-5-Cyclohexyl-11- (propylsulfonyl)-7,11- diazatricyclo[7.3.1.02,7]trideca- 2,4-dien-6-one, also known as ZINC8297940, as the best TNF-α inhibitor along with dl-Leucineamide and Benazol P as the potential inhibitor of PTGS2. Conclusions These findings suggest that OA may exert therapeutic effects against AD by controlling inflammation through TNF-α and PTGS2 signalling pathways.
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Affiliation(s)
- Thigita A. Pandaleke
- Doctoral Program of Medical Science, Universitas Brawijaya, Malang, East Java, Indonesia
- Department of Dermatology and Venereology, Faculty of Medicine, Sam Ratulangi University, RD Kandou Hospital, Jl. Raya Tanawangko No.56, Manado 95163, North Sulawesi, Indonesia
| | - Kusworini Handono
- Department of Clinical Pathology, Faculty of Medicine, Universitas Brawijaya – Saiful Anwar Hospital, Malang, East Java, Indonesia
| | - Dhelya Widasmara
- Department of Dermatology and Venereology, Faculty of Medicine, Universitas Brawijaya – Saiful Anwar Hospital, Malang, East Java, Indonesia
| | - Hani Susianti
- Department of Clinical Pathology, Faculty of Medicine, Universitas Brawijaya – Saiful Anwar Hospital, Malang, East Java, Indonesia
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Hayat S, Ishrat R. Exploring potential genes and pathways related to lung cancer: a graph theoretical analysis. Bioinformation 2023; 19:954-963. [PMID: 37928493 PMCID: PMC10625372 DOI: 10.6026/97320630019954] [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: 09/01/2023] [Revised: 09/30/2023] [Accepted: 09/30/2023] [Indexed: 11/07/2023] Open
Abstract
Lung cancer is the primary and third most frequently detected form of cancer in both males and females. The present study tries to perform integrated analysis in male as well as female patients inclusively both smoker and non-smokers. This study aims to identify diagnostic biomarkers and therapeutic targets for lung cancer patients using human microarray profile datasets. Differentially expressed genes (DEGs) were identified using a PPI network from the String database, and major modules or clusters were extracted using MCODE. The Cytohubba plug-in was used to find hub genes from the PPI network using centralities approaches. Twenty significant hub genes (CCND1, CDK1, CCNB1, CDH1, TP53, CTNNB1, EGFR, ESR1, CDK2, CCNA2, RHOA, EGF, FN1, HSP90AA1, STAT3, JUN, NOTCH1, IL6, SRC, and CD44) were identified as promising diagnostic biomarkers and therapeutic targets for lung cancer treatment. Survival analysis and hub gene validation were also conducted. GO enrichment and pathway analysis were conducted to identify their important functions. These hub genes were also used to identify targeted drugs. The findings suggest that the identified genes have the potential to be used as diagnostic biomarkers and therapeutic targets for lung cancer treatment.
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Affiliation(s)
- Shaheen Hayat
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi-110025
| | - Romana Ishrat
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi-110025
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de Godoi RS, Garcia ALH, Borges MS, George HK, Ferraz ADBF, Corrêa DS, da Silva FR, da Silva J. Protective effect of Hovenia dulcis Thunb. leaf extracts against ethanol-induced DNA damage in SH-SY5Y cells. JOURNAL OF ETHNOPHARMACOLOGY 2023; 304:116042. [PMID: 36529249 DOI: 10.1016/j.jep.2022.116042] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/01/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Hovenia dulcis Thunb. has been used as a medicinal herb for the treatment of hepatic diseases and alcohol intoxication. AIM OF THE STUDY The genotoxic effect and the antigenotoxic potential of ethanolic extract of H. dulcis leaves and its methanolic fraction were evaluated against ethanol-induced damages in SH-SY5Y cells. MATERIALS AND METHODS The phytochemical analysis and antioxidant activity of H. dulcis extracts were also assessed. In addition, a systems biology analysis was performed to investigate the molecular pathway of action of the H. dulcis leaves compounds. RESULTS The ethanolic extract and its methanolic fraction presented genotoxicity through comet assay at 0.5 and 0.25 mg/mL. On the other hand, both extracts showed protective action against ethanol at all concentrations. Additionally, an NBT assay was performed and demonstrated an ability of the extracts to reduce superoxide anion formation when SH-SY5Y cells were challenged with ethanol. HPLC analysis indicated the presence of quercitrin, isoquercitrin, and rutin. Further, system biology assays indicated a molecular action pathway, where the compounds from the leaves of H. dulcis, in addition to performing free radical scavenging activity, activate PP2A, and may inhibit the apoptosis pathway activated by ethanol-induced oxidative stress. CONCLUSIONS This work is important to indicate potential antigenotoxic and antioxidant properties of H. dulcis leaves, and its use can be investigated against DNA damage induced by ethanol.
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Affiliation(s)
- Rafael Souza de Godoi
- Laboratory of Genetic Toxicology, Postgraduate Program in Cellular and Molecular Biology Applied to Health (PPGBioSaúde), Lutheran University of Brazil (ULBRA), Laboratory of Genetic Toxicology, Av. Farroupilha, 8001, 92425-900, Canoas, RS, Brazil
| | - Ana Letícia Hilario Garcia
- Laboratory of Genetic Toxicology, Postgraduate Program in Cellular and Molecular Biology Applied to Health (PPGBioSaúde), Lutheran University of Brazil (ULBRA), Laboratory of Genetic Toxicology, Av. Farroupilha, 8001, 92425-900, Canoas, RS, Brazil; Laboratory of Genetic Toxicology, Postgraduate Program in Health and Human Development (PPGSDH), La Salle University (UniLaSalle), Av. Victor Barreto, 2288, 92010-000, Canoas, RS, Brazil.
| | - Malu Siqueira Borges
- Laboratory of Genetic Toxicology, Postgraduate Program in Cellular and Molecular Biology Applied to Health (PPGBioSaúde), Lutheran University of Brazil (ULBRA), Laboratory of Genetic Toxicology, Av. Farroupilha, 8001, 92425-900, Canoas, RS, Brazil
| | - Hellen Kaiane George
- Product and Development Research Center, Lutheran University of Brazil (ULBRA), Av. Farroupilha, 8001, 92425-900, Canoas, RS, Brazil
| | | | - Dione Silva Corrêa
- Product and Development Research Center, Lutheran University of Brazil (ULBRA), Av. Farroupilha, 8001, 92425-900, Canoas, RS, Brazil
| | - Fernanda Rabaioli da Silva
- Laboratory of Genetic Toxicology, Postgraduate Program in Health and Human Development (PPGSDH), La Salle University (UniLaSalle), Av. Victor Barreto, 2288, 92010-000, Canoas, RS, Brazil
| | - Juliana da Silva
- Laboratory of Genetic Toxicology, Postgraduate Program in Cellular and Molecular Biology Applied to Health (PPGBioSaúde), Lutheran University of Brazil (ULBRA), Laboratory of Genetic Toxicology, Av. Farroupilha, 8001, 92425-900, Canoas, RS, Brazil; Laboratory of Genetic Toxicology, Postgraduate Program in Health and Human Development (PPGSDH), La Salle University (UniLaSalle), Av. Victor Barreto, 2288, 92010-000, Canoas, RS, Brazil.
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Robin V, Bodein A, Scott-Boyer MP, Leclercq M, Périn O, Droit A. Overview of methods for characterization and visualization of a protein-protein interaction network in a multi-omics integration context. Front Mol Biosci 2022; 9:962799. [PMID: 36158572 PMCID: PMC9494275 DOI: 10.3389/fmolb.2022.962799] [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: 06/06/2022] [Accepted: 08/16/2022] [Indexed: 11/26/2022] Open
Abstract
At the heart of the cellular machinery through the regulation of cellular functions, protein-protein interactions (PPIs) have a significant role. PPIs can be analyzed with network approaches. Construction of a PPI network requires prediction of the interactions. All PPIs form a network. Different biases such as lack of data, recurrence of information, and false interactions make the network unstable. Integrated strategies allow solving these different challenges. These approaches have shown encouraging results for the understanding of molecular mechanisms, drug action mechanisms, and identification of target genes. In order to give more importance to an interaction, it is evaluated by different confidence scores. These scores allow the filtration of the network and thus facilitate the representation of the network, essential steps to the identification and understanding of molecular mechanisms. In this review, we will discuss the main computational methods for predicting PPI, including ones confirming an interaction as well as the integration of PPIs into a network, and we will discuss visualization of these complex data.
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Affiliation(s)
- Vivian Robin
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Antoine Bodein
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Marie-Pier Scott-Boyer
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Mickaël Leclercq
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Olivier Périn
- Digital Sciences Department, L'Oréal Advanced Research, Aulnay-sous-bois, France
| | - Arnaud Droit
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
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Ahmed MM, Shafat Z, Tazyeen S, Ali R, Almashjary MN, Al-Raddadi R, Harakeh S, Alam A, Haque S, Ishrat R. Identification of pathogenic genes associated with CKD: An integrated bioinformatics approach. Front Genet 2022; 13:891055. [PMID: 36035163 PMCID: PMC9403320 DOI: 10.3389/fgene.2022.891055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/28/2022] [Indexed: 11/23/2022] Open
Abstract
Chronic kidney disease (CKD) is defined as a persistent abnormality in the structure and function of kidneys and leads to high morbidity and mortality in individuals across the world. Globally, approximately 8%–16% of the population is affected by CKD. Proper screening, staging, diagnosis, and the appropriate management of CKD by primary care clinicians are essential in preventing the adverse outcomes associated with CKD worldwide. In light of this, the identification of biomarkers for the appropriate management of CKD is urgently required. Growing evidence has suggested the role of mRNAs and microRNAs in CKD, however, the gene expression profile of CKD is presently uncertain. The present study aimed to identify diagnostic biomarkers and therapeutic targets for patients with CKD. The human microarray profile datasets, consisting of normal samples and treated samples were analyzed thoroughly to unveil the differentially expressed genes (DEGs). After selection, the interrelationship among DEGs was carried out to identify the overlapping DEGs, which were visualized using the Cytoscape program. Furthermore, the PPI network was constructed from the String database using the selected DEGs. Then, from the PPI network, significant modules and sub-networks were extracted by applying the different centralities methods (closeness, betweenness, stress, etc.) using MCODE, Cytohubba, and Centiserver. After sub-network analysis we identified six overlapped hub genes (RPS5, RPL37A, RPLP0, CXCL8, HLA-A, and ANXA1). Additionally, the enrichment analysis was undertaken on hub genes to determine their significant functions. Furthermore, these six genes were used to find their associated miRNAs and targeted drugs. Finally, two genes CXCL8 and HLA-A were common for Ribavirin drug (the gene-drug interaction), after docking studies HLA-A was selected for further investigation. To conclude our findings, we can say that the identified hub genes and their related miRNAs can serve as potential diagnostic biomarkers and therapeutic targets for CKD treatment strategies.
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Affiliation(s)
- Mohd Murshad Ahmed
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Zoya Shafat
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Safia Tazyeen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Rafat Ali
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
- Department of Biosciences, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India
| | - Majed N. Almashjary
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Rajaa Al-Raddadi
- Community Medicine Department, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Steve Harakeh
- King Fahd Medical Research Center, and Yousef Abdullatif Jameel Chair of Prophetic Medicine Application, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Aftab Alam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Romana Ishrat
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
- *Correspondence: Romana Ishrat,
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Chen H, Hu X, Hu Y, Zhou J, Chen M. CoVM2: Molecular Biological Data Integration of SARS-CoV-2 Proteins in a Macro-to-Micro Method. Biomolecules 2022; 12:biom12081067. [PMID: 36008961 PMCID: PMC9405999 DOI: 10.3390/biom12081067] [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: 06/08/2022] [Revised: 07/27/2022] [Accepted: 07/29/2022] [Indexed: 02/01/2023] Open
Abstract
The COVID-19 pandemic has been a major public health event since 2020. Multiple variant strains of SARS-CoV-2, the causative agent of COVID-19, were detected based on the mutation sites in their sequences. These sequence mutations may lead to changes in the protein structures and affect the binding states of SARS-CoV-2 and human proteins. Experimental research on SARS-CoV-2 has accumulated a large amount of structural data and protein-protein interactions (PPIs), but the studies on the SARS-CoV-2–human PPI networks lack integration of physical associations with possible protein docking information. In addition, the docking structures of variant viral proteins with human receptor proteins are still insufficient. This study constructed SARS-CoV-2–human protein–protein interaction network with data integration methods. Crystal structures were collected to map the interaction pairs. The pairs of direct interactions and physical associations were selected and analyzed for variant docking calculations. The study examined the structures of spike (S) glycoprotein of variants Delta B.1.617.2, Omicron BA.1, and Omicron BA.2. The calculated docking structures of S proteins and potential human receptors were obtained. The study integrated binary protein interactions with 3D docking structures to fulfill an extended view of SARS-CoV-2 proteins from a macro- to micro-scale.
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Affiliation(s)
- Hongjun Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (H.C.); (X.H.); (Y.H.)
| | - Xiaotian Hu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (H.C.); (X.H.); (Y.H.)
| | - Yanshi Hu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (H.C.); (X.H.); (Y.H.)
| | - Jiawen Zhou
- Chu Kochen Honors College, Zhejiang University, Hangzhou 310058, China;
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (H.C.); (X.H.); (Y.H.)
- Institute of Hematology, Zhejiang University School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou 310058, China
- Correspondence: ; Tel.: +86-(0)571-8820-6612
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Identification of the Key miRNAs and Genes Associated with the Regulation of Non-Small Cell Lung Cancer: A Network-Based Approach. Genes (Basel) 2022; 13:genes13071174. [PMID: 35885958 PMCID: PMC9317345 DOI: 10.3390/genes13071174] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/18/2022] [Accepted: 06/20/2022] [Indexed: 11/26/2022] Open
Abstract
Lung cancer is the major cause of cancer-associated deaths across the world in both men and women. Lung cancer consists of two major clinicopathological categories, i.e., small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC). Lack of diagnosis of NSCLC at an early stage in addition to poor prognosis results in ineffective treatment, thus, biomarkers for appropriate diagnosis and exact prognosis of NSCLC need urgent attention. The proposed study aimed to reveal essential microRNAs (miRNAs) involved in the carcinogenesis of NSCLC that probably could act as potential biomarkers. The NSCLC-associated expression datasets revealed 12 differentially expressed miRNAs (DEMs). MiRNA-mRNA network identified key miRNAs and their associated genes, for which functional enrichment analysis was applied. Further, survival and validation analysis for key genes was performed and consequently transcription factors (TFs) were predicted. We obtained twelve miRNAs as common DEMs after assessment of all datasets. Further, four key miRNAs and nine key genes were extracted from significant modules based on the centrality approach. The key genes and miRNAs reported in our study might provide some information for potential biomarkers profitable to increased prognosis and diagnosis of lung cancer.
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The impact of the suppression of highly connected protein interactions on the corona virus infection. Sci Rep 2022; 12:9188. [PMID: 35654986 PMCID: PMC9160517 DOI: 10.1038/s41598-022-13373-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 05/09/2022] [Indexed: 11/28/2022] Open
Abstract
Several highly effective Covid-19 vaccines are in emergency use, although more-infectious coronavirus strains, could delay the end of the pandemic even further. Because of this, it is highly desirable to develop fast antiviral drug treatments to accelerate the lasting immunity against the virus. From a theoretical perspective, computational approaches are useful tools for antiviral drug development based on the data analysis of gene expression, chemical structure, molecular pathway, and protein interaction mapping. This work studies the structural stability of virus–host interactome networks based on the graphical representation of virus–host protein interactions as vertices or nodes connected by commonly shared proteins. These graphical network visualization methods are analogous to those use in the design of artificial neural networks in neuromorphic computing. In standard protein-node-based network representation, virus–host interaction merges with virus–protein and host–protein networks, introducing redundant links associated with the internal virus and host networks. On the contrary, our approach provides a direct geometrical representation of viral infection structure and allows the effective and fast detection of the structural robustness of the virus–host network through proteins removal. This method was validated by applying it to H1N1 and HIV viruses, in which we were able to pinpoint the changes in the Interactome Network produced by known vaccines. The application of this method to the SARS-CoV-2 virus–host protein interactome implies that nonstructural proteins nsp4, nsp12, nsp16, the nuclear pore membrane glycoprotein NUP210, and ubiquitin specific peptidase USP54 play a crucial role in the viral infection, and their removal may provide an efficient therapy. This method may be extended to any new mutations or other viruses for which the Interactome Network is experimentally determined. Since time is of the essence, because of the impact of more-infectious strains on controlling the spread of the virus, this method may be a useful tool for novel antiviral therapies.
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Sajad M, Ahmed MM, Thakur SC. An integrated bioinformatics strategy to elucidate the function of hub genes linked to Alzheimer's disease. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Khan MS, Yousafi Q, Bibi S, Azhar M, Ihsan A. Bioinformatics-Based Approaches to Study Virus-Host Interactions During SARS-CoV-2 Infection. Methods Mol Biol 2022; 2452:197-212. [PMID: 35554909 DOI: 10.1007/978-1-0716-2111-0_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
As the knowledge of biomolecules is increasing from the last decades, it is helping the researchers to understand the unsolved issues regarding virology. Recent technologies in high-throughput sequencing are providing the swift generation of SARS-CoV-2 genomic data with the basic inside of viral infection. Owing to various virus-host protein interactions, high-throughput technologies are unable to provide complete details of viral pathogenesis. Identifying the virus-host protein interactions using bioinformatics approaches can assist in understanding the mechanism of SARS-CoV-2 infection and pathogenesis. In this chapter, recent integrative bioinformatics approaches are discussed to help the virologists and computational biologists in the identification of structurally similar proteins of human and SARS-CoV-2 virus, and to predict the potential of virus-host interactions. Considering experimental and time limitations for effective viral drug development, computational aided drug design (CADD) can reduce the gap between drug prediction and development. More research with respect to evolutionary solutions could be helpful to make a new pipeline for virus-host protein-protein interactions and provide more understanding to disclose the cases of host switch, and also expand the virulence of the pathogen and host range in developing viral infections.
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Affiliation(s)
- Muhammad Saad Khan
- Department of Biosciences, COMSATS University Islamabad, Sahiwal, Pakistan
| | - Qudsia Yousafi
- Department of Biosciences, COMSATS University Islamabad, Sahiwal, Pakistan
| | - Shabana Bibi
- Yunnan Herbal Laboratory, School of Ecology and Environmental Sciences, Yunnan University, Kunming, Yunnan, China
| | - Muhammad Azhar
- Department of Biosciences, COMSATS University Islamabad, Sahiwal, Pakistan
| | - Awais Ihsan
- Department of Biosciences, COMSATS University Islamabad, Sahiwal, Pakistan.
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13
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Wang YJ, Downey MA, Choi S, Shoup TM, Elmaleh DR. Cromolyn platform suppresses fibrosis and inflammation, promotes microglial phagocytosis and neurite outgrowth. Sci Rep 2021; 11:22161. [PMID: 34772945 PMCID: PMC8589953 DOI: 10.1038/s41598-021-00465-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/07/2021] [Indexed: 12/18/2022] Open
Abstract
Neurodegenerative diseases are characterized by chronic neuroinflammation and may perpetuate ongoing fibrotic reactions within the central nervous system. Unfortunately, there is no therapeutic available that treats neurodegenerative inflammation and its sequelae. Here we utilize cromolyn, a mast cell inhibitor with anti-inflammatory capabilities, and its fluorinated analogue F-cromolyn to study fibrosis-related protein regulation and secretion downstream of neuroinflammation and their ability to promote microglial phagocytosis and neurite outgrowth. In this report, RNA-seq analysis shows that administration of the pro-inflammatory cytokine TNF-α to HMC3 human microglia results in a robust upregulation of fibrosis-associated genes. Subsequent treatment with cromolyn and F-cromolyn resulted in reduced secretion of collagen XVIII, fibronectin, and tenascin-c. Additionally, we show that cromolyn and F-cromolyn reduce pro-inflammatory proteins PLP1, PELP1, HSP90, IL-2, GRO-α, Eotaxin, and VEGF-Α, while promoting secretion of anti-inflammatory IL-4 in HMC3 microglia. Furthermore, cromolyn and F-cromolyn augment neurite outgrowth in PC12 neuronal cells in concert with nerve growth factor. Treatment also differentially altered secretion of neurogenesis-related proteins TTL, PROX1, Rab35, and CSDE1 in HMC3 microglia. Finally, iPSC-derived human microglia more readily phagocytose Aβ42 with cromolyn and F-cromolyn relative to controls. We propose the cromolyn platform targets multiple proteins upstream of PI3K/Akt/mTOR, NF-κB, and GSK-3β signaling pathways to affect cytokine, chemokine, and fibrosis-related protein expression.
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Affiliation(s)
| | | | - Sungwoon Choi
- Department of New Drug Discovery, Chungnam National University, Daejeon, South Korea
| | - Timothy M Shoup
- Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02129-2060, USA
| | - David R Elmaleh
- AZTherapies, Inc., Boston, MA, USA.
- Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02129-2060, USA.
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14
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Onisiforou A, Spyrou GM. Identification of viral-mediated pathogenic mechanisms in neurodegenerative diseases using network-based approaches. Brief Bioinform 2021; 22:bbab141. [PMID: 34237135 PMCID: PMC8574625 DOI: 10.1093/bib/bbab141] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/01/2021] [Accepted: 03/23/2021] [Indexed: 12/18/2022] Open
Abstract
During the course of a viral infection, virus-host protein-protein interactions (PPIs) play a critical role in allowing viruses to replicate and survive within the host. These interspecies molecular interactions can lead to viral-mediated perturbations of the human interactome causing the generation of various complex diseases. Evidences suggest that viral-mediated perturbations are a possible pathogenic etiology in several neurodegenerative diseases (NDs). These diseases are characterized by chronic progressive degeneration of neurons, and current therapeutic approaches provide only mild symptomatic relief; therefore, there is unmet need for the discovery of novel therapeutic interventions. In this paper, we initially review databases and tools that can be utilized to investigate viral-mediated perturbations in complex NDs using network-based analysis by examining the interaction between the ND-related PPI disease networks and the virus-host PPI network. Afterwards, we present our theoretical-driven integrative network-based bioinformatics approach that accounts for pathogen-genes-disease-related PPIs with the aim to identify viral-mediated pathogenic mechanisms focusing in multiple sclerosis (MS) disease. We identified seven high centrality nodes that can act as disease communicator nodes and exert systemic effects in the MS-enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways network. In addition, we identified 12 KEGG pathways, 5 Reactome pathways and 52 Gene Ontology Immune System Processes by which 80 viral proteins from eight viral species might exert viral-mediated pathogenic mechanisms in MS. Finally, our analysis highlighted the Th17 differentiation pathway, a disease communicator node and part of the 12 underlined KEGG pathways, as a key viral-mediated pathogenic mechanism and a possible therapeutic target for MS disease.
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Affiliation(s)
- Anna Onisiforou
- Department of Bioinformatics, Cyprus Institute of Neurology & Genetics, and the Cyprus School of Molecular Medicine, Cyprus
| | - George M Spyrou
- Department of Bioinformatics, Cyprus Institute of Neurology & Genetics, and professor at the Cyprus School of Molecular Medicine, Cyprus
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15
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de Godoi RS, Almerão MP, da Silva FR. In silico evaluation of the antidiabetic activity of natural compounds from Hovenia dulcis Thunberg. J Herb Med 2021. [DOI: 10.1016/j.hermed.2020.100349] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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16
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Pincot DDA, Ledda M, Feldmann MJ, Hardigan MA, Poorten TJ, Runcie DE, Heffelfinger C, Dellaporta SL, Cole GS, Knapp SJ. Social network analysis of the genealogy of strawberry: retracing the wild roots of heirloom and modern cultivars. G3-GENES GENOMES GENETICS 2021; 11:6117203. [PMID: 33772307 PMCID: PMC8022721 DOI: 10.1093/g3journal/jkab015] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/12/2020] [Indexed: 01/22/2023]
Abstract
The widely recounted story of the origin of cultivated strawberry (Fragaria × ananassa) oversimplifies the complex interspecific hybrid ancestry of the highly admixed populations from which heirloom and modern cultivars have emerged. To develop deeper insights into the three-century-long domestication history of strawberry, we reconstructed the genealogy as deeply as possible—pedigree records were assembled for 8,851 individuals, including 2,656 cultivars developed since 1775. The parents of individuals with unverified or missing pedigree records were accurately identified by applying an exclusion analysis to array-genotyped single-nucleotide polymorphisms. We identified 187 wild octoploid and 1,171 F. × ananassa founders in the genealogy, from the earliest hybrids to modern cultivars. The pedigree networks for cultivated strawberry are exceedingly complex labyrinths of ancestral interconnections formed by diverse hybrid ancestry, directional selection, migration, admixture, bottlenecks, overlapping generations, and recurrent hybridization with common ancestors that have unequally contributed allelic diversity to heirloom and modern cultivars. Fifteen to 333 ancestors were predicted to have transmitted 90% of the alleles found in country-, region-, and continent-specific populations. Using parent–offspring edges in the global pedigree network, we found that selection cycle lengths over the past 200 years of breeding have been extraordinarily long (16.0-16.9 years/generation), but decreased to a present-day range of 6.0-10.0 years/generation. Our analyses uncovered conspicuous differences in the ancestry and structure of North American and European populations, and shed light on forces that have shaped phenotypic diversity in F. × ananassa.
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Affiliation(s)
- Dominique D A Pincot
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Mirko Ledda
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Mitchell J Feldmann
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Michael A Hardigan
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Thomas J Poorten
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Daniel E Runcie
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Christopher Heffelfinger
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Stephen L Dellaporta
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Glenn S Cole
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Steven J Knapp
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
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Younis H, Anwar MW, Khan MUG, Sikandar A, Bajwa UI. A New Sequential Forward Feature Selection (SFFS) Algorithm for Mining Best Topological and Biological Features to Predict Protein Complexes from Protein-Protein Interaction Networks (PPINs). Interdiscip Sci 2021; 13:371-388. [PMID: 33959851 DOI: 10.1007/s12539-021-00433-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 04/09/2021] [Accepted: 04/15/2021] [Indexed: 10/21/2022]
Abstract
Protein-protein interaction plays an important role in the understanding of biological processes in the body. A network of dynamic protein complexes within a cell that regulates most biological processes is known as a protein-protein interaction network (PPIN). Complex prediction from PPINs is a challenging task. Most of the previous computation approaches mine cliques, stars, linear and hybrid structures as complexes from PPINs by considering topological features and fewer of them focus on important biological information contained within protein amino acid sequence. In this study, we have computed a wide variety of topological features and integrate them with biological features computed from protein amino acid sequence such as bag of words, physicochemical and spectral domain features. We propose a new Sequential Forward Feature Selection (SFFS) algorithm, i.e., random forest-based Boruta feature selection for selecting the best features from computed large feature set. Decision tree, linear discriminant analysis and gradient boosting classifiers are used as learners. We have conducted experiments by considering two reference protein complex datasets of yeast, i.e., CYC2008 and MIPS. Human and mouse complex information is taken from CORUM 3.0 dataset. Protein interaction information is extracted from the database of interacting proteins (DIP). Our proposed SFFS, i.e., random forest-based Brouta feature selection in combination with decision trees, linear discriminant analysis and Gradient Boosting Classifiers outperforms other state of art algorithms by achieving precision, recall and F-measure rates, i.e. 94.58%, 94.92% and 94.45% for MIPS, 96.31%, 93.55% and 96.02% for CYC2008, 98.84%, 98.00%, 98.87 % for CORUM humans and 96.60%, 96.70%, 96.32% for CORUM mouse dataset complexes, respectively.
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Affiliation(s)
- Haseeb Younis
- School of Professional Advancement, University of Management and Technology, Lahore, Pakistan.,Department of Computer Science, COMSATS University Islamabad, Lahore, Pakistan
| | | | - Muhammad Usman Ghani Khan
- Department of Computer Science and Engineering, University of Engineering and Technology, Lahore, Pakistan
| | - Aisha Sikandar
- Govt. Girls Post Graduate College No.1 Abbottabad, Abbottabad, Pakistan
| | - Usama Ijaz Bajwa
- Department of Computer Science, COMSATS University Islamabad, Lahore, Pakistan
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18
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Transcriptional Profiling of Whisker Follicles and of the Striatum in Methamphetamine Self-Administered Rats. Int J Mol Sci 2020; 21:ijms21228856. [PMID: 33238484 PMCID: PMC7700365 DOI: 10.3390/ijms21228856] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/20/2020] [Accepted: 11/20/2020] [Indexed: 02/07/2023] Open
Abstract
Methamphetamine (MA) use disorder is a chronic neuropsychiatric disease characterized by recurrent binge episodes, intervals of abstinence, and relapses to MA use. Therefore, identification of the key genes and pathways involved is important for improving the diagnosis and treatment of this disorder. In this study, high-throughput RNA sequencing was performed to find the key genes and examine the comparability of gene expression between whisker follicles and the striatum of rats following MA self-administration. A total of 253 and 87 differentially expressed genes (DEGs) were identified in whisker follicles and the striatum, respectively. Multivariate and network analyses were performed on these DEGs to find hub genes and key pathways within the constructed network. A total of 129 and 49 genes were finally selected from the DEG sets of whisker follicles and of the striatum. Statistically significant DEGs were found to belong to the classes of genes involved in nicotine addiction, cocaine addiction, and amphetamine addiction in the striatum as well as in Parkinson’s, Huntington’s, and Alzheimer’s diseases in whisker follicles. Of note, several genes and pathways including retrograde endocannabinoid signaling and the synaptic vesicle cycle pathway were common between the two tissues. Therefore, this study provides the first data on gene expression levels in whisker follicles and in the striatum in relation to MA reward and thereby may accelerate the research on the whisker follicle as an alternative source of biomarkers for the diagnosis of MA use disorder.
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19
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Chen CC, Jeong H, Qian X, Yoon BJ. TOPAS: network-based structural alignment of RNA sequences. Bioinformatics 2020; 35:2941-2948. [PMID: 30629122 DOI: 10.1093/bioinformatics/btz001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 12/07/2018] [Accepted: 01/04/2019] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION For many RNA families, the secondary structure is known to be better conserved among the member RNAs compared to the primary sequence. For this reason, it is important to consider the underlying folding structures when aligning RNA sequences, especially for those with relatively low sequence identity. Given a set of RNAs with unknown structures, simultaneous RNA alignment and folding algorithms aim to accurately align the RNAs by jointly predicting their consensus secondary structure and the optimal sequence alignment. Despite the improved accuracy of the resulting alignment, the computational complexity of simultaneous alignment and folding for a pair of RNAs is O(N6), which is too costly to be used for large-scale analysis. RESULTS In order to address this shortcoming, in this work, we propose a novel network-based scheme for pairwise structural alignment of RNAs. The proposed algorithm, TOPAS, builds on the concept of topological networks that provide structural maps of the RNAs to be aligned. For each RNA sequence, TOPAS first constructs a topological network based on the predicted folding structure, which consists of sequential edges and structural edges weighted by the base-pairing probabilities. The obtained networks can then be efficiently aligned by using probabilistic network alignment techniques, thereby yielding the structural alignment of the RNAs. The computational complexity of our proposed method is significantly lower than that of the Sankoff-style dynamic programming approach, while yielding favorable alignment results. Furthermore, another important advantage of the proposed algorithm is its capability of handling RNAs with pseudoknots while predicting the RNA structural alignment. We demonstrate that TOPAS generally outperforms previous RNA structural alignment methods on RNA benchmarks in terms of both speed and accuracy. AVAILABILITY AND IMPLEMENTATION Source code of TOPAS and the benchmark data used in this paper are available at https://github.com/bjyoontamu/TOPAS.
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Affiliation(s)
- Chun-Chi Chen
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA.,TEES-AgriLife Center for Bioinformatics & Genomic Systems Engineering, Texas A&M University, College Station, TX, USA
| | - Hyundoo Jeong
- Department of Electronic Engineering, Chosun University, Gwangju, Republic of Korea
| | - Xiaoning Qian
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA.,TEES-AgriLife Center for Bioinformatics & Genomic Systems Engineering, Texas A&M University, College Station, TX, USA
| | - Byung-Jun Yoon
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA.,TEES-AgriLife Center for Bioinformatics & Genomic Systems Engineering, Texas A&M University, College Station, TX, USA
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20
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Wei CX, Burrow MF, Botelho MG, Lam H, Leung WK. In Vitro Salivary Protein Adsorption Profile on Titanium and Ceramic Surfaces and the Corresponding Putative Immunological Implications. Int J Mol Sci 2020; 21:E3083. [PMID: 32349305 PMCID: PMC7247707 DOI: 10.3390/ijms21093083] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/17/2020] [Accepted: 04/24/2020] [Indexed: 12/23/2022] Open
Abstract
Immune responses triggered by implant abutment surfaces contributed by surface-adsorbed proteins are critical in clinical implant integration. How material surface-adsorbed proteins relate to host immune responses remain unclear. This study aimed to profile and address the immunological roles of surface-adsorbed salivary proteins on conventional implant abutment materials. Standardized polished bocks (5 × 5 × 1 mm3) were prepared from titanium and feldspathic ceramic. Salivary acquired pellicle formed in vitro was examined by liquid chromatography-tandem mass spectrometry and gene ontology (GO) analysis to identify and characterize the adsorbed proteins. Out of 759 proteins identified from pooled saliva samples, 396 were found to be attached to the two materials tested-369 on titanium and 298 on ceramic, with 281 common to both. GO annotation of immune processes was undertaken to form a protein-protein interaction network, and 14 hub proteins (≥6 interaction partners) (coding genes: B2M, C3, CLU, DEFA1, HSP90AA1, HSP90AB1, LTF, PIGR, PSMA2, RAC1, RAP1A, S100A8, S100A9, and SLP1) were identified as the key proteins connecting multiple (6-9) immune processes. The results offered putative immunological prospects of implant abutment material surface-adsorbed salivary proteins, which could potentially underpin the dynamic nature of implant-mucosal/implant-microbial interactions.
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Affiliation(s)
- Chen-Xuan Wei
- Faculty of Dentistry, The University of Hong Kong, Hong Kong, China; (C.-X.W.); (M.F.B.); (M.G.B.)
| | - Michael Francis Burrow
- Faculty of Dentistry, The University of Hong Kong, Hong Kong, China; (C.-X.W.); (M.F.B.); (M.G.B.)
| | - Michael George Botelho
- Faculty of Dentistry, The University of Hong Kong, Hong Kong, China; (C.-X.W.); (M.F.B.); (M.G.B.)
| | - Henry Lam
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong, China;
| | - Wai Keung Leung
- Faculty of Dentistry, The University of Hong Kong, Hong Kong, China; (C.-X.W.); (M.F.B.); (M.G.B.)
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21
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Byun S, Han S, Zheng Y, Planelles V, Lee Y. The landscape of alternative splicing in HIV-1 infected CD4 T-cells. BMC Med Genomics 2020; 13:38. [PMID: 32241262 PMCID: PMC7118826 DOI: 10.1186/s12920-020-0680-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Background Elucidating molecular mechanisms that are altered during HIV-1 infection may provide a better understanding of the HIV-1 life cycle and how it interacts with infected T-cells. One such mechanism is alternative splicing (AS), which has been studied for HIV-1 itself, but no systematic analysis has yet been performed on infected T-cells. We hypothesized that AS patterns in infected T-cells may illuminate the molecular mechanisms underlying HIV-1 infection and identify candidate molecular markers for specifically targeting infected T-cells. Methods We downloaded previously published raw RNA-seq data obtained from HIV-1 infected and non-infected T-cells. We estimated percent spliced in (PSI) levels for each AS exon, then identified differential AS events in the infected cells (FDR < 0.05, PSI difference > 0.1). We performed functional gene set enrichment analysis on the genes with differentially expressed AS exons to identify their functional roles. In addition, we used RT-PCR to validate differential alternative splicing events in cyclin T1 (CCNT1) as a case study. Results We identified 427 candidate genes with differentially expressed AS exons in infected T-cells, including 20 genes related to cell surface, 35 to kinases, and 121 to immune-related genes. In addition, protein-protein interaction analysis identified six essential subnetworks related to the viral life cycle, including Transcriptional regulation by TP53, Class I MHC mediated antigen, G2/M transition, and late phase of HIV life cycle. CCNT1 exon 7 was more frequently skipped in infected T-cells, leading to loss of the key Cyclin_N motif and affecting HIV-1 transcriptional elongation. Conclusions Our findings may provide new insight into systemic host AS regulation under HIV-1 infection and may provide useful initial candidates for the discovery of new markers for specifically targeting infected T-cells.
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Affiliation(s)
- Seyoun Byun
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Seonggyun Han
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Yue Zheng
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Vicente Planelles
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Younghee Lee
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, USA. .,Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA.
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22
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Li H, Zhou DS, Chang H, Wang L, Liu W, Dai SX, Zhang C, Cai J, Liu W, Li X, Fan W, Tang W, Tang W, Liu F, He Y, Bai Y, Hu Z, Xiao X, Gao L, Li M. Interactome Analyses implicated CAMK2A in the genetic predisposition and pharmacological mechanism of Bipolar Disorder. J Psychiatr Res 2019; 115:165-175. [PMID: 31150948 DOI: 10.1016/j.jpsychires.2019.05.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/21/2019] [Accepted: 05/24/2019] [Indexed: 12/17/2022]
Abstract
Bipolar disorder (BPD) is a severe mental illness characterized by fluctuations in mood states, behaviors and energy levels. Growing evidence suggests that genes associated with specific illnesses tend to interact together and encode a tight protein-protein interaction (PPI) network, providing valuable information for understanding their pathogenesis. To gain insights into the genetic and physiological foundation of BPD, we conduct the physical PPI analysis of 184 BPD risk genes distilled from genome-wide association studies and exome sequencing studies. We have identified several hub genes (CAMK2A, HSP90AA1 and PLCG1) among those risk genes, and observed significant enrichment of the BPD risk genes in certain pathways such as calcium signaling, oxytocin signaling and circadian entrainment. Furthermore, while none of the 184 genetic risk genes are "well established" BPD drug targets, our PPI analysis showed that αCaMKII (encoded by CAMK2A) had direct physical PPIs with targets (HRH1, SCN5A and CACNA1E) of clinically used anti-manic BPD drugs, such as carbamazepine. We thus speculated that αCaMKII might be involved in the cellular pharmacological actions of those drugs. Using cultured rat primary cortical neurons, we found that carbamazepine treatment induced phosphorylation of αCaMKII in dose-dependent manners. Intriguingly, previous study showed that CAMK2A heterozygous knockout (CAMK2A+/-) mice exhibited infradian oscillation of locomotor activities that can be rescued by carbamazepine. Our data, in combination with previous studies, provide convergent evidence for the involvement of CAMK2A in the risk of BPD.
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Affiliation(s)
- Huijuan Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Dong-Sheng Zhou
- Department of Psychiatry, Ningbo Kangning Hospital, Ningbo, Zhejiang, China
| | - Hong Chang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Lu Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Weipeng Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Shao-Xing Dai
- Yunnan Key Laboratory of Primate Biomedicine Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Chen Zhang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun Cai
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weiqing Liu
- Department of Psychiatry, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Xingxing Li
- Department of Psychiatry, Ningbo Kangning Hospital, Ningbo, Zhejiang, China
| | - Weixing Fan
- Jinhua Second Hospital, Jinhua, Zhejiang, China
| | - Wei Tang
- Wenzhou Kangning Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Wenxin Tang
- Hangzhou Seventh People's Hospital, Hangzhou, Zhejiang, China
| | - Fang Liu
- Department of Psychiatry, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Yuanfang He
- Department of Psychiatry, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Yan Bai
- Department of Psychiatry, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Zhonghua Hu
- Institute of Molecular Precision Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China; Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Xiao Xiao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Lei Gao
- Department of Bioinformatics, School of Life Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Tai'an, Shandong, China.
| | - Ming Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China; (m)CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
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23
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Yue B, Li H, Liu M, Wu J, Li M, Lei C, Huang B, Chen H. Characterization of lncRNA-miRNA-mRNA Network to Reveal Potential Functional ceRNAs in Bovine Skeletal Muscle. Front Genet 2019; 10:91. [PMID: 30842787 PMCID: PMC6391848 DOI: 10.3389/fgene.2019.00091] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/29/2019] [Indexed: 01/14/2023] Open
Abstract
There is growing evidence that non-coding RNAs are emerging as critical regulators of skeletal muscle development. In order to reveal their functional roles and regulatory mechanisms, we constructed a lncRNA–miRNA–mRNA network according to the ceRNA (competitive endogenous RNA) theory, using our high-throughput sequencing data. Subsequently, the network analysis, GO (Gene Ontology) analysis, and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis were performed for functional annotation and exploration of lncRNA ceRNAs. The results uncovered a scale-free characteristics network which exhibited high functional specificity for bovine skeletal muscle development: co-expression lncRNAs were significantly enriched in muscle development related biological processes and the Wnt signaling pathway. Furthermore, GSEA (Gene Set Enrichment Analysis) indicated that the risk score has a tendency to associate with myogenesis, and differentially expressed RNAs were validated by qPCR, further confirming the credibility of our network. In summary, this study provides insights into lncRNA-mediated ceRNA function and mechanisms in bovine skeletal muscle development and will expand our understanding of lncRNA biology in mammals.
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Affiliation(s)
- Binglin Yue
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Hui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Mei Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Jiyao Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Mingxun Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
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Precision medicine review: rare driver mutations and their biophysical classification. Biophys Rev 2019; 11:5-19. [PMID: 30610579 PMCID: PMC6381362 DOI: 10.1007/s12551-018-0496-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 12/18/2018] [Indexed: 02/07/2023] Open
Abstract
How can biophysical principles help precision medicine identify rare driver mutations? A major tenet of pragmatic approaches to precision oncology and pharmacology is that driver mutations are very frequent. However, frequency is a statistical attribute, not a mechanistic one. Rare mutations can also act through the same mechanism, and as we discuss below, “latent driver” mutations may also follow the same route, with “helper” mutations. Here, we review how biophysics provides mechanistic guidelines that extend precision medicine. We outline principles and strategies, especially focusing on mutations that drive cancer. Biophysics has contributed profoundly to deciphering biological processes. However, driven by data science, precision medicine has skirted some of its major tenets. Data science embodies genomics, tissue- and cell-specific expression levels, making it capable of defining genome- and systems-wide molecular disease signatures. It classifies cancer driver genes/mutations and affected pathways, and its associated protein structural data guide drug discovery. Biophysics complements data science. It considers structures and their heterogeneous ensembles, explains how mutational variants can signal through distinct pathways, and how allo-network drugs can be harnessed. Biophysics clarifies how one mutation—frequent or rare—can affect multiple phenotypic traits by populating conformations that favor interactions with other network modules. It also suggests how to identify such mutations and their signaling consequences. Biophysics offers principles and strategies that can help precision medicine push the boundaries to transform our insight into biological processes and the practice of personalized medicine. By contrast, “phenotypic drug discovery,” which capitalizes on physiological cellular conditions and first-in-class drug discovery, may not capture the proper molecular variant. This is because variants of the same protein can express more than one phenotype, and a phenotype can be encoded by several variants.
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Leitner DM, Yamato T. MAPPING ENERGY TRANSPORT NETWORKS IN PROTEINS. REVIEWS IN COMPUTATIONAL CHEMISTRY 2018. [DOI: 10.1002/9781119518068.ch2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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26
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Tian Y, Ma Y, Wu S, Zhang T, Li Z, Wang G, Zhang J. Understand the acquired resistance of RTK inhibitors by computational receptor tyrosine kinases network. Comput Biol Chem 2018; 76:275-282. [DOI: 10.1016/j.compbiolchem.2018.07.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 06/27/2018] [Accepted: 07/27/2018] [Indexed: 10/28/2022]
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Sobrinho Santos EM, Almeida AC, Santos HO, Cangussu ASR, Almeida DA, Costa KS. Leader gene of Corynebacterium pseudotuberculosis may be useful in vaccines against caseous lymphadenitis of goats: a bioinformatics approach. J Vet Med Sci 2018; 80:1317-1324. [PMID: 29937460 PMCID: PMC6115270 DOI: 10.1292/jvms.16-0581] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
We conducted an in silico analysis to search for important genes in the
pathogenesis of Caseous Lymphadenitis (CL), with prospects for use in formulating
effective vaccines against this disease. For this, we performed a survey of proteins
expressed by Corynebacterium pseudotuberculosis, using protein sequences
collected from the NCBI GenPept database and the keywords “caseous lymphadenitis” and
“Corynebacterium pseudotuberculosis” and “goats”. A network was
developed using the STRING 10 database, with a confidence score of 0.900. For every gene
interaction identified, we summed the interaction score of each gene, generating a
combined association score to obtain a single score named weighted number of links (WNL).
Genes with the highest WNL were named “leader genes”. Ontological analysis was extracted
from the STRING database through Kyoto Encyclopedia of Genes and Genomes (KEGG) database.
A search in the GenPept database revealed 2,124 proteins. By using and plotting with
STRING 10, we then developed an in silico network model comprised of 1,243 genes/proteins
interconnecting through 3,330 interactions. The highest WNL values were identified in the
rplB gene, which was named the leader gene. Our ontological analysis
shows that this protein acts effectively mainly on Metabolic pathways and Biosynthesis of
secondary metabolites. In conclusion, the in silico analyses showed that
rplB has good potential for vaccine development. However, functional
assays are needed to make sure that this protein can potentially induce both humoral and
cellular immune responses against C. pseudotuberculosis in goats.
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Affiliation(s)
- Eliane Macedo Sobrinho Santos
- Department of Dentistry, Universidade Estadual de Montes Claros, Minas Gerais, 39400-000, Brazil.,Instituto Federal do Norte de Minas Gerais, Campus Araçuaí, Minas Gerais, 39600-000, Brazil
| | | | | | | | | | - Kattyanne Souza Costa
- Research and Development Laboratory of Vallée S.A., Montes Claros, Minas Gerais, 39400-000, Brazil
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Zhang Q, Wang S, Pan Y, Su D, Lu Q, Zuo Y, Yang L. Characterization of proteins in different subcellular localizations for Escherichia coli K12. Genomics 2018; 111:1134-1141. [PMID: 30026105 DOI: 10.1016/j.ygeno.2018.07.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 07/07/2018] [Accepted: 07/11/2018] [Indexed: 10/28/2022]
Abstract
Knowing the comprehensive knowledge about the protein subcellular localization is an important step to understand the function of the proteins. Recent advances in system biology have allowed us to develop more accurate methods for characterizing the proteins at subcellular localization level. In this study, the analysis method was developed to characterize the topological properties and biological properties of the cytoplasmic proteins, inner membrane proteins, outer membrane proteins and periplasmic proteins in Escherichia coli (E. coli). Statistical significant differences were found in all topological properties and biological properties among proteins in different subcellular localizations. In addition, investigation was carried out to analyze the differences in 20 amino acid compositions for four protein categories. We also found that there were significant differences in all of the 20 amino acid compositions. These findings may be helpful for understanding the comprehensive relationship between protein subcellular localization and biological function.
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Affiliation(s)
- Qi Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Shiyuan Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yi Pan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Dongqing Su
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Qianzi Lu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yongchun Zuo
- The State key Laboratory of Reproductive Regulation, Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China.
| | - Lei Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
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Liu H, Guo X, Han J, Luo R, Chen HF. Order-disorder transition of intrinsically disordered kinase inducible transactivation domain of CREB. J Chem Phys 2018; 148:225101. [PMID: 29907037 DOI: 10.1063/1.5027869] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Transcription factor cyclic Adenosine monophosphate response-element binding protein plays a critical role in the cyclic AMP response pathway via its intrinsically disordered kinase inducible transactivation domain (KID). KID is one of the most studied intrinsically disordered proteins (IDPs), although most previous studies focus on characterizing its disordered state structures. An interesting question that remains to be answered is how the order-disorder transition occurs at experimental conditions. Thanks to the newly developed IDP-specific force field ff14IDPSFF, the quality of conformer sampling for IDPs has been dramatically improved. In this study, molecular dynamics (MD) simulations were used to study the order-to-disorder transition kinetics of KID based on the good agreement with the experiment on its disordered-state properties. Specifically, we tested four force fields, ff99SBildn, ff99IDPs, ff14IDPSFF, and ff14IDPs in the simulations of KID and found that ff14IDPSFF can generate more diversified disordered conformers and also reproduce more accurate experimental secondary chemical shifts. Kinetics analysis of MD simulations demonstrates that the order-disorder transition of KID obeys the first-order kinetics, and the transition nucleus is I127/L128/L141. The possible transition pathways from the nucleus to the last folded residues were identified as I127-R125-L138-L141-S143-A145 and L128-R125-L138-L141-S143-A145 based on a residue-level dynamical network analysis. These computational studies not only provide testable prediction/hypothesis on the order-disorder transition of KID but also confirm that the ff14IDPSFF force field can be used to explore the correlation between the structure and function of IDPs.
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Affiliation(s)
- Hao Liu
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Xiang Guo
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Jingcheng Han
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Ray Luo
- Departments of Molecular Biology and Biochemistry, Chemical Engineering and Materials Science, Biomedical Engineering, University of California, Irvine, California 92697-3900, USA
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
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30
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Amiri Dashatan N, Rezaie Tavirani M, Zali H, Koushki M, Ahmadi N. Prediction of Leishmania major Key Proteins Via Topological Analysis of Protein-Protein Interaction Network. Galen Med J 2018; 7:e1129. [PMID: 34466438 PMCID: PMC8344062 DOI: 10.22086/gmj.v0i0.1129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 02/22/2018] [Accepted: 03/18/2018] [Indexed: 11/30/2022] Open
Abstract
Background: Although leishmaniasis is regarded as a public health problem, no effective vaccine or decisive treatment has been introduced for this disease. Therefore, representing novel therapeutic proteins is essential. Protein-protein Interaction network analysis is a suitable tool to discover novel drug targets for leishmania major. To this aim, gene and protein expression data is used for instructing protein network and the key proteins are highlighted. Materials and Methods: In this computational and bioinformatics study, the protein/gene expression data related to leishmania major were studied, and 252 candidate proteins were extracted. Then, the protein networks of these proteins were explored and visualized by using String database and Cytoscape software. Finally, clustering and gene ontology were performed by MCODE and PANTHER databases, respectively. Results: Based on gene ontology analysis, most of the leishmania major proteins were located in cell compartments and membrane. Catalytic activity and binding were regarded as the relevant molecular functions and metabolic and cellular processes were the significant biological process. In this network analysis, UB-EP52, EF-2, chaperonin, Hsp70.4, Hsp60, tubulin alpha and beta chain, and ENOL and LACK were introduced as hub-bottleneck proteins. Based on clustering analysis, Lmjf.32.3270, ENOL and Lmjf.13.0290 were determined as seed proteins in each cluster. Conclusion: The results indicated that hub proteins play a significant role in pathogenesis and life cycle of leishmania major. Further studies of hubs will provide a better understanding of leishmaniasis mechanisms. Finally, these key hub proteins could be a suitable and helpful potential for drug targets and treating leishmaniasis by considering their validation.
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Affiliation(s)
- Nasrin Amiri Dashatan
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Hakimeh Zali
- Advanced Technologies in Medicine. Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehdi Koushki
- Department of Clinical Biochemistry, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Nayebali Ahmadi
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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31
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George G, Singh S, Lokappa SB, Varkey J. Gene co-expression network analysis for identifying genetic markers in Parkinson's disease - a three-way comparative approach. Genomics 2018; 111:819-830. [PMID: 29852216 DOI: 10.1016/j.ygeno.2018.05.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 04/16/2018] [Accepted: 05/06/2018] [Indexed: 12/30/2022]
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder involving progressive deterioration of dopaminergic neurons. Although few genetic markers for familial PD are known, the etiology of sporadic PD remains poorly understood. Microarray data was analysed for induced pluripotent stem cells (iPSCs) derived from PD patients and mature neuronal cells (mDA) differentiated from these iPSCs. Combining expression and semantic similarity, a highly-correlated PD interactome was constructed that included interactions of established Parkinson's disease marker genes. A novel three-way comparative approach was employed, delineating topologically and functionally important genes. These genes showed involvement in pathways like Parkin-ubiquitin proteosomal system (UPS), immune associated biological processes and apoptosis. Of interest are three genes, eEF1A1, CASK, and PSMD6 that are linked to PARK2 activity in the cell and thereby form attractive candidate genes for understanding PD. Network biology approach delineated in this study can be applied to other neurodegenerative disorders for identification of important genetic regulators.
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Affiliation(s)
- Gincy George
- Department of Bioinformatics, Karunya University, Karunya Nagar, Tamil Nadu 641114, India
| | - Sachidanand Singh
- Department of Bioinformatics, Karunya University, Karunya Nagar, Tamil Nadu 641114, India; Institute of Bio-Sciences and Technology, Shri Ramswaroop Memorial University, Deva Road, Uttar Pradesh 225003, India
| | - Sowmya Bekshe Lokappa
- Department of Bioinformatics, Karunya University, Karunya Nagar, Tamil Nadu 641114, India; Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA 90033, USA.
| | - Jobin Varkey
- Department of Bioinformatics, Karunya University, Karunya Nagar, Tamil Nadu 641114, India; Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA 90033, USA.
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32
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Büttner P, Ueberham L, Shoemaker MB, Roden DM, Dinov B, Hindricks G, Bollmann A, Husser D. Identification of Central Regulators of Calcium Signaling and ECM-Receptor Interaction Genetically Associated With the Progression and Recurrence of Atrial Fibrillation. Front Genet 2018; 9:162. [PMID: 29868113 PMCID: PMC5964985 DOI: 10.3389/fgene.2018.00162] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 04/20/2018] [Indexed: 01/04/2023] Open
Abstract
Atrial fibrillation (AF) is a multifactorial disease with a strong genetic background. It is assumed that common and rare genetic variants contribute to the progression and recurrence of AF. The pathophysiological impact of those variants, especially when they are synonymous or non-coding, is often elusive and translation into functional experiments is difficult. In this study, we propose a method to go straight from genetic variants to defined gene targets. We focused on 55 genes from calcium signaling and 26 genes from extra cellular matrix ECM–receptor interaction that we found to be associated with the progression and recurrence of AF. These genes were mapped on protein–protein interaction data from three different databases. Based on the concept that central regulators are highly connected with their neighbors, we identified central hub proteins according to random walk analysis derived scores representing interaction grade. Our approach resulted in the identification of EGFR, RYR2, and PRKCA (calcium signaling) and FN1 and LAMA1 (ECM–receptor interaction) which represent promising targets for further functional characterization or pharmaceutical intervention.
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Affiliation(s)
- Petra Büttner
- Department of Electrophysiology, Heart Center Leipzig, Leipzig University, Leipzig, Germany
| | - Laura Ueberham
- Department of Electrophysiology, Heart Center Leipzig, Leipzig University, Leipzig, Germany
| | - M B Shoemaker
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Dan M Roden
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Borislav Dinov
- Department of Electrophysiology, Heart Center Leipzig, Leipzig University, Leipzig, Germany
| | - Gerhard Hindricks
- Department of Electrophysiology, Heart Center Leipzig, Leipzig University, Leipzig, Germany
| | - Andreas Bollmann
- Department of Electrophysiology, Heart Center Leipzig, Leipzig University, Leipzig, Germany
| | - Daniela Husser
- Department of Electrophysiology, Heart Center Leipzig, Leipzig University, Leipzig, Germany
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MTGO: PPI Network Analysis Via Topological and Functional Module Identification. Sci Rep 2018; 8:5499. [PMID: 29615773 PMCID: PMC5882952 DOI: 10.1038/s41598-018-23672-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 02/28/2018] [Indexed: 11/08/2022] Open
Abstract
Protein-protein interaction (PPI) networks are viable tools to understand cell functions, disease machinery, and drug design/repositioning. Interpreting a PPI, however, it is a particularly challenging task because of network complexity. Several algorithms have been proposed for an automatic PPI interpretation, at first by solely considering the network topology, and later by integrating Gene Ontology (GO) terms as node similarity attributes. Here we present MTGO - Module detection via Topological information and GO knowledge, a novel functional module identification approach. MTGO let emerge the bimolecular machinery underpinning PPI networks by leveraging on both biological knowledge and topological properties. In particular, it directly exploits GO terms during the module assembling process, and labels each module with its best fit GO term, easing its functional interpretation. MTGO shows largely better results than other state of the art algorithms (including recent GO-based ones) when searching for small or sparse functional modules, while providing comparable or better results all other cases. MTGO correctly identifies molecular complexes and literature-consistent processes in an experimentally derived PPI network of Myocardial infarction. A software version of MTGO is available freely for non-commercial purposes at https://gitlab.com/d1vella/MTGO .
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34
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Li S, Musungu B, Lightfoot D, Ji P. The Interactomic Analysis Reveals Pathogenic Protein Networks in Phomopsis longicolla Underlying Seed Decay of Soybean. Front Genet 2018; 9:104. [PMID: 29666630 PMCID: PMC5891612 DOI: 10.3389/fgene.2018.00104] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 03/15/2018] [Indexed: 12/31/2022] Open
Abstract
Phomopsis longicolla T. W. Hobbs (syn. Diaporthe longicolla) is the primary cause of Phomopsis seed decay (PSD) in soybean, Glycine max (L.) Merrill. This disease results in poor seed quality and is one of the most economically important seed diseases in soybean. The objectives of this study were to infer protein-protein interactions (PPI) and to identify conserved global networks and pathogenicity subnetworks in P. longicolla including orthologous pathways for cell signaling and pathogenesis. The interlog method used in the study identified 215,255 unique PPIs among 3,868 proteins. There were 1,414 pathogenicity related genes in P. longicolla identified using the pathogen host interaction (PHI) database. Additionally, 149 plant cell wall degrading enzymes (PCWDE) were detected. The network captured five different classes of carbohydrate degrading enzymes, including the auxiliary activities, carbohydrate esterases, glycoside hydrolases, glycosyl transferases, and carbohydrate binding molecules. From the PPI analysis, novel interacting partners were determined for each of the PCWDE classes. The most predominant class of PCWDE was a group of 60 glycoside hydrolases proteins. The glycoside hydrolase subnetwork was found to be interacting with 1,442 proteins within the network and was among the largest clusters. The orthologous proteins FUS3, HOG, CYP1, SGE1, and the g5566t.1 gene identified in this study could play an important role in pathogenicity. Therefore, the P. longicolla protein interactome (PiPhom) generated in this study can lead to a better understanding of PPIs in soybean pathogens. Furthermore, the PPI may aid in targeting of genes and proteins for further studies of the pathogenicity mechanisms.
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Affiliation(s)
- Shuxian Li
- Crop Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service, Stoneville, MS, United States
| | - Bryan Musungu
- Department of Plant Biology, Southern Illinois University, Carbondale, IL, United States
| | - David Lightfoot
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL, United States
| | - Pingsheng Ji
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
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Zhou M, Diao Z, Yue X, Chen Y, Zhao H, Cheng L, Sun J. Construction and analysis of dysregulated lncRNA-associated ceRNA network identified novel lncRNA biomarkers for early diagnosis of human pancreatic cancer. Oncotarget 2018; 7:56383-56394. [PMID: 27487139 PMCID: PMC5302921 DOI: 10.18632/oncotarget.10891] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 07/19/2016] [Indexed: 12/14/2022] Open
Abstract
It is increasing evidence that ceRNA activity of long non-coding RNAs (lncRNAs) played critical roles in both normal physiology and tumorigenesis. However, functional roles and regulatory mechanisms of lncRNAs as ceRNAs in pancreatic ductal adenocarcinoma (PDAC), and their potential implications for early diagnosis remain unclear. In this study, we performed a genome-wide analysis to investigate potential lncRNA-mediated ceRNA interplay based on "ceRNA hypothesis". A dysregulated lncRNA-associated ceRNA network (DLCN) was constructed by utilizing sample-matched miRNA, lncRNA and mRNA expression profiles in PDAC and normal samples in combination with miRNA regulatory network. The results of network analysis uncovered seven novel lncRNAs as functional ceRNAs whose aberrant expression will result in the extensive variation in tumorigenic or tumor-suppressive gene expression through DLCN at the post-transcriptional level contributing to PDAC. Therefore, we developed a 7-lncRNA signature (termed LncRisk-7) based on the expression data of seven lncRNAs and SVM algorithm as a novel diagnostic tool to improve early diagnosis of PDAC. The LncRisk-7 achieved high performance in distinguishing PDAC patients from nonmalignant pancreas samples in the discovery cohort and was further confirmed in another two independent validation cohorts. Functional analysis demonstrated that seven lncRNA biomarkers act as ceRNAs involving the regulation of cell death, cell adhesion and cell cycle. This study will help to improve our understanding of the lncRNA-mediated ceRNA regulatory mechanisms in the pathogenesis of PDAC and provide novel lncRNAs as candidate diagnostic biomarkers or potential therapeutic targets.
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Affiliation(s)
- Meng Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, PR China
| | - Zhiyong Diao
- Department of Plastic Surgery, the First Affiliated Hospital of Harbin Medical University, Harbin, 150001, PR China
| | - Xiaolong Yue
- Medical Oncology Department, Affiliated Tumor Hospital, Harbin Medical University, Harbin, 150001, PR China
| | - Yang Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, PR China
| | - Hengqiang Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, PR China
| | - Liang Cheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, PR China
| | - Jie Sun
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, PR China
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Felgueiras J, Silva JV, Fardilha M. Adding biological meaning to human protein-protein interactions identified by yeast two-hybrid screenings: A guide through bioinformatics tools. J Proteomics 2018; 171:127-140. [DOI: 10.1016/j.jprot.2017.05.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 04/26/2017] [Accepted: 05/13/2017] [Indexed: 02/02/2023]
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37
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Khan FM, Sadeghi M, Gupta SK, Wolkenhauer O. A Network-Based Integrative Workflow to Unravel Mechanisms Underlying Disease Progression. Methods Mol Biol 2018; 1702:247-276. [PMID: 29119509 DOI: 10.1007/978-1-4939-7456-6_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Unraveling mechanisms underlying diseases has motivated the development of systems biology approaches. The key challenges for the development of mathematical models and computational tool are (1) the size of molecular networks, (2) the nonlinear nature of spatio-temporal interactions, and (3) feedback loops in the structure of interaction networks. We here propose an integrative workflow that combines structural analyses of networks, high-throughput data, and mechanistic modeling. As an illustration of the workflow, we use prostate cancer as a case study with the aim of identifying key functional components associated with primary to metastasis transitions. Analysis carried out by the workflow revealed that HOXD10, BCL2, and PGR are the most important factors affected in primary prostate samples, whereas, in the metastatic state, STAT3, JUN, and JUNB are playing a central role. The identified key elements of each network are validated using patient survival analysis. The workflow presented here allows experimentalists to use heterogeneous data sources for the identification of diagnostic and prognostic signatures.
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Affiliation(s)
- Faiz M Khan
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051, Rostock, Germany
| | - Mehdi Sadeghi
- Research Institute for Fundamental Sciences (RIFS), University of Tabriz, Tabriz, Iran
| | - Shailendra K Gupta
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051, Rostock, Germany.,Chhattisgarh Swami Vivekanand Technical University, Bhilai, Chhattisgarh, India
| | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051, Rostock, Germany. .,Chhattisgarh Swami Vivekanand Technical University, Bhilai, Chhattisgarh, India. .,Stellenbosch Institute of Advanced Study (STIAS), Wallenberg Research Centre, Stellenbosch University, Stellenbosch, South Africa.
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Gnanasekaran R. Computational study to understand the energy transfer pathways within amicyanin. J Mol Graph Model 2017; 78:88-95. [PMID: 29054098 DOI: 10.1016/j.jmgm.2017.09.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 09/28/2017] [Accepted: 09/30/2017] [Indexed: 11/27/2022]
Abstract
Vibrational energy diffusivities between the residues present in Amicyanin copper protein are calculated and presented in form of communication map. From those results energy flow pathways from the copper metal ion to the inter protein residue Glu31 are identified. Our finding suggests many different pathways are possible and copper metal ion in oxidized and reduced state switches the pathways. Our finding also suggests the cooperative nature of surrounding residues and water molecules towards selecting the pathways. The major transport channels in the oxidised state are, Cu2+---> MET28---> LYS29---> TYR30---> GLU31 and Cu2+---> MET98---> TYR30--- > GLU31. And in the reduced state Cu+---> CYS9---> TYR30---> GLU31 and Cu+---> MET28---> LYS2---> TYR30---> GLU31. We studied further the interaction energies between the copper ion and neighbouring residues using B3LYP/QZVP method. Both the methods complement each other in predicting the energy flow pathways and the cooperative nature of residues.
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Abstract
Hundreds of different species colonize multicellular organisms making them "metaorganisms". A growing body of data supports the role of microbiota in health and in disease. Grasping the principles of host-microbiota interactions (HMIs) at the molecular level is important since it may provide insights into the mechanisms of infections. The crosstalk between the host and the microbiota may help resolve puzzling questions such as how a microorganism can contribute to both health and disease. Integrated superorganism networks that consider host and microbiota as a whole-may uncover their code, clarifying perhaps the most fundamental question: how they modulate immune surveillance. Within this framework, structural HMI networks can uniquely identify potential microbial effectors that target distinct host nodes or interfere with endogenous host interactions, as well as how mutations on either host or microbial proteins affect the interaction. Furthermore, structural HMIs can help identify master host cell regulator nodes and modules whose tweaking by the microbes promote aberrant activity. Collectively, these data can delineate pathogenic mechanisms and thereby help maximize beneficial therapeutics. To date, challenges in experimental techniques limit large-scale characterization of HMIs. Here we highlight an area in its infancy which we believe will increasingly engage the computational community: predicting interactions across kingdoms, and mapping these on the host cellular networks to figure out how commensal and pathogenic microbiota modulate the host signaling and broadly cross-species consequences.
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Affiliation(s)
- Emine Guven-Maiorov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, United States of America
| | - Chung-Jung Tsai
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, United States of America
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, United States of America
- Sackler Inst. of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
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40
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Wang X, Jin Y. Predicted networks of protein-protein interactions in Stegodyphus mimosarum by cross-species comparisons. BMC Genomics 2017; 18:716. [PMID: 28893204 PMCID: PMC5594591 DOI: 10.1186/s12864-017-4085-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 08/23/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Stegodyphus mimosarum is a candidate model organism belonging to the class Arachnida in the phylum Arthropoda. Studies on the biology of S. mimosarum over the past several decades have consisted of behavioral research and comparison of gene sequences based on the assembled genome sequence. Given the lack of systematic protein analyses and the rich source of information in the genome, we predicted the relationships of proteins in S. mimosarum by bioinformatics comparison with genome-wide proteins from select model organisms using gene mapping. RESULTS The protein-protein interactions (PPIs) of 11 organisms were integrated from four databases (BioGrid, InAct, MINT, and DIP). Here, we present comprehensive prediction and analysis of 3810 proteins in S. mimosarum with regard to interactions between proteins using PPI data of organisms. Interestingly, a portion of the protein interactions conserved among Saccharomyces cerevisiae, Homo sapiens, Arabidopsis thaliana, and Drosophila melanogaster were found to be associated with RNA splicing. In addition, overlap of predicted PPIs in reference organisms, Gene Ontology, and topology models in S. mimosarum are also reported. CONCLUSIONS Addition of Stegodyphus, a spider representative of interactomic research, provides the possibility of obtaining deeper insights into the evolution of PPI networks among different animal species. This work largely supports the utility of the "stratus clouds" model for predicted PPIs, providing a roadmap for integrative systems biology in S. mimosarum.
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Affiliation(s)
- Xiu Wang
- Institute of Ecology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, ZJ310058, People's Republic of China.,Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, ZJ310058, People's Republic of China
| | - Yongfeng Jin
- Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, ZJ310058, People's Republic of China.
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Brito AF, Pinney JW. Protein-Protein Interactions in Virus-Host Systems. Front Microbiol 2017; 8:1557. [PMID: 28861068 PMCID: PMC5562681 DOI: 10.3389/fmicb.2017.01557] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 08/02/2017] [Indexed: 01/10/2023] Open
Abstract
To study virus–host protein interactions, knowledge about viral and host protein architectures and repertoires, their particular evolutionary mechanisms, and information on relevant sources of biological data is essential. The purpose of this review article is to provide a thorough overview about these aspects. Protein domains are basic units defining protein interactions, and the uniqueness of viral domain repertoires, their mode of evolution, and their roles during viral infection make viruses interesting models of study. Mutations at protein interfaces can reduce or increase their binding affinities by changing protein electrostatics and structural properties. During the course of a viral infection, both pathogen and cellular proteins are constantly competing for binding partners. Endogenous interfaces mediating intraspecific interactions—viral–viral or host–host interactions—are constantly targeted and inhibited by exogenous interfaces mediating viral–host interactions. From a biomedical perspective, blocking such interactions is the main mechanism underlying antiviral therapies. Some proteins are able to bind multiple partners, and their modes of interaction define how fast these “hub proteins” evolve. “Party hubs” have multiple interfaces; they establish simultaneous/stable (domain–domain) interactions, and tend to evolve slowly. On the other hand, “date hubs” have few interfaces; they establish transient/weak (domain–motif) interactions by means of short linear peptides (15 or fewer residues), and can evolve faster. Viral infections are mediated by several protein–protein interactions (PPIs), which can be represented as networks (protein interaction networks, PINs), with proteins being depicted as nodes, and their interactions as edges. It has been suggested that viral proteins tend to establish interactions with more central and highly connected host proteins. In an evolutionary arms race, viral and host proteins are constantly changing their interface residues, either to evade or to optimize their binding capabilities. Apart from gaining and losing interactions via rewiring mechanisms, virus–host PINs also evolve via gene duplication (paralogy); conservation (orthology); horizontal gene transfer (HGT) (xenology); and molecular mimicry (convergence). The last sections of this review focus on PPI experimental approaches and their limitations, and provide an overview of sources of biomolecular data for studying virus–host protein interactions.
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Affiliation(s)
- Anderson F Brito
- Department of Life Sciences, Centre for Integrative Systems Biology and Bioinformatics, Imperial College LondonLondon, United Kingdom
| | - John W Pinney
- Department of Life Sciences, Centre for Integrative Systems Biology and Bioinformatics, Imperial College LondonLondon, United Kingdom
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Unraveling a tumor type-specific regulatory core underlying E2F1-mediated epithelial-mesenchymal transition to predict receptor protein signatures. Nat Commun 2017; 8:198. [PMID: 28775339 PMCID: PMC5543083 DOI: 10.1038/s41467-017-00268-2] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 06/15/2017] [Indexed: 12/18/2022] Open
Abstract
Cancer is a disease of subverted regulatory pathways. In this paper, we reconstruct the regulatory network around E2F, a family of transcription factors whose deregulation has been associated to cancer progression, chemoresistance, invasiveness, and metastasis. We integrate gene expression profiles of cancer cell lines from two E2F1-driven highly aggressive bladder and breast tumors, and use network analysis methods to identify the tumor type-specific core of the network. By combining logic-based network modeling, in vitro experimentation, and gene expression profiles from patient cohorts displaying tumor aggressiveness, we identify and experimentally validate distinctive, tumor type-specific signatures of receptor proteins associated to epithelial-mesenchymal transition in bladder and breast cancer. Our integrative network-based methodology, exemplified in the case of E2F1-induced aggressive tumors, has the potential to support the design of cohort- as well as tumor type-specific treatments and ultimately, to fight metastasis and therapy resistance.Deregulation of E2F family transcription factors is associated with cancer progression and metastasis. Here, the authors construct a map of the regulatory network around the E2F family, and using gene expression profiles, identify tumour type-specific regulatory cores and receptor expression signatures associated with epithelial-mesenchymal transition in bladder and breast cancer.
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Drug Target Protein-Protein Interaction Networks: A Systematic Perspective. BIOMED RESEARCH INTERNATIONAL 2017; 2017:1289259. [PMID: 28691014 PMCID: PMC5485489 DOI: 10.1155/2017/1289259] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 03/09/2017] [Accepted: 05/10/2017] [Indexed: 01/17/2023]
Abstract
The identification and validation of drug targets are crucial in biomedical research and many studies have been conducted on analyzing drug target features for getting a better understanding on principles of their mechanisms. But most of them are based on either strong biological hypotheses or the chemical and physical properties of those targets separately. In this paper, we investigated three main ways to understand the functional biomolecules based on the topological features of drug targets. There are no significant differences between targets and common proteins in the protein-protein interactions network, indicating the drug targets are neither hub proteins which are dominant nor the bridge proteins. According to some special topological structures of the drug targets, there are significant differences between known targets and other proteins. Furthermore, the drug targets mainly belong to three typical communities based on their modularity. These topological features are helpful to understand how the drug targets work in the PPI network. Particularly, it is an alternative way to predict potential targets or extract nontargets to test a new drug target efficiently and economically. By this way, a drug target's homologue set containing 102 potential target proteins is predicted in the paper.
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Malhotra AG, Jha M, Singh S, Pandey KM. Construction of a Comprehensive Protein-Protein Interaction Map for Vitiligo Disease to Identify Key Regulatory Elements: A Systemic Approach. Interdiscip Sci 2017; 10:500-514. [PMID: 28290051 DOI: 10.1007/s12539-017-0213-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 12/09/2016] [Accepted: 12/29/2016] [Indexed: 12/14/2022]
Abstract
Vitiligo is an idiopathic disorder characterized by depigmented patches on the skin due to progressive loss of melanocytes. Several genetic, immunological, and pathophysiological investigations have established vitiligo as a polygenetic disorder with multifactorial etiology. However, no definite model explaining the interplay between these causative factors has been established hitherto. Therefore, we studied the disorder at the system level to identify the key proteins involved by exploring their molecular connectivity in terms of topological parameters. The existing research data helped us in collating 215 proteins involved in vitiligo onset or progression. Interaction study of these proteins leads to a comprehensive vitiligo map with 4845 protein nodes linked with 107,416 edges. Based on centrality measures, a backbone network with 500 nodes has been derived. This has presented a clear overview of the proteins and processes involved and the crosstalk between them. Clustering backbone proteins revealed densely connected regions inferring major molecular interaction modules essential for vitiligo. Finally, a list of top order proteins that play a key role in the disease pathomechanism has been formulated. This includes SUMO2, ESR1, COPS5, MYC, SMAD3, and Cullin proteins. While this list is in fair agreement with the available literature, it also introduces new candidate proteins that can be further explored. A subnetwork of 64 vitiligo core proteins was built by analyzing the backbone and seed protein networks. Our finding suggests that the topology, along with functional clustering, provides a deep insight into the behavior of proteins. This in turn aids in the illustration of disease condition and discovery of significant proteins involved in vitiligo.
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Affiliation(s)
- Anvita Gupta Malhotra
- Department of Biological Science and Engineering, Maulana Azad National Institute of Technology (MANIT), Bhopal, 462003, India
| | - Mohit Jha
- Department of Biological Science and Engineering, Maulana Azad National Institute of Technology (MANIT), Bhopal, 462003, India
| | - Sudha Singh
- Department of Biological Science and Engineering, Maulana Azad National Institute of Technology (MANIT), Bhopal, 462003, India
| | - Khushhali M Pandey
- Department of Biological Science and Engineering, Maulana Azad National Institute of Technology (MANIT), Bhopal, 462003, India.
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Kapetis D, Sassone J, Yang Y, Galbardi B, Xenakis MN, Westra RL, Szklarczyk R, Lindsey P, Faber CG, Gerrits M, Merkies ISJ, Dib-Hajj SD, Mantegazza M, Waxman SG, Lauria G. Network topology of NaV1.7 mutations in sodium channel-related painful disorders. BMC SYSTEMS BIOLOGY 2017; 11:28. [PMID: 28235406 PMCID: PMC5324268 DOI: 10.1186/s12918-016-0382-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 12/20/2016] [Indexed: 11/30/2022]
Abstract
BACKGROUND Gain-of-function mutations in SCN9A gene that encodes the voltage-gated sodium channel NaV1.7 have been associated with a wide spectrum of painful syndromes in humans including inherited erythromelalgia, paroxysmal extreme pain disorder and small fibre neuropathy. These mutations change the biophysical properties of NaV1.7 channels leading to hyperexcitability of dorsal root ganglion nociceptors and pain symptoms. There is a need for better understanding of how gain-of-function mutations alter the atomic structure of Nav1.7. RESULTS We used homology modeling to build an atomic model of NaV1.7 and a network-based theoretical approach, which can predict interatomic interactions and connectivity arrangements, to investigate how pain-related NaV1.7 mutations may alter specific interatomic bonds and cause connectivity rearrangement, compared to benign variants and polymorphisms. For each amino acid substitution, we calculated the topological parameters betweenness centrality (B ct ), degree (D), clustering coefficient (CC ct ), closeness (C ct ), and eccentricity (E ct ), and calculated their variation (Δ value = mutant value -WT value ). Pathogenic NaV1.7 mutations showed significantly higher variation of |ΔB ct | compared to benign variants and polymorphisms. Using the cut-off value ±0.26 calculated by receiver operating curve analysis, we found that ΔB ct correctly differentiated pathogenic NaV1.7 mutations from variants not causing biophysical abnormalities (nABN) and homologous SNPs (hSNPs) with 76% sensitivity and 83% specificity. CONCLUSIONS Our in-silico analyses predict that pain-related pathogenic NaV1.7 mutations may affect the network topological properties of the protein and suggest |ΔB ct | value as a potential in-silico marker.
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Affiliation(s)
- Dimos Kapetis
- Bioinformatics Unit, IRCCS Foundation “Carlo Besta” Neurological Institute, Milan, Italy
- Neuroalgology Unit, IRCCS Foundation “Carlo Besta” Neurological Institute, Milan, Italy
| | - Jenny Sassone
- Neuroalgology Unit, IRCCS Foundation “Carlo Besta” Neurological Institute, Milan, Italy
- Present address: San Raffaele Scientific Institute and Vita-Salute University, Milan, Italy
| | - Yang Yang
- Department of Neurology, Yale University School of Medicine, New Haven, USA
- Center for Neuroscience and Regeneration Research, Yale University School of Medicine, New Haven, USA
| | - Barbara Galbardi
- Bioinformatics Unit, IRCCS Foundation “Carlo Besta” Neurological Institute, Milan, Italy
| | - Markos N. Xenakis
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
- Department of Knowledge Engineering, Maastricht University, Maastricht, The Netherlands
| | - Ronald L. Westra
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
- Department of Knowledge Engineering, Maastricht University, Maastricht, The Netherlands
| | - Radek Szklarczyk
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Patrick Lindsey
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Catharina G. Faber
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
- Department of Neurology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Monique Gerrits
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Ingemar S. J. Merkies
- Department of Neurology, Maastricht University Medical Center, Maastricht, The Netherlands
- Department of Neurology, Spaarne Hospital, Hoofddorp, The Netherlands
| | - Sulayman D. Dib-Hajj
- Department of Neurology, Yale University School of Medicine, New Haven, USA
- Center for Neuroscience and Regeneration Research, Yale University School of Medicine, New Haven, USA
| | - Massimo Mantegazza
- Laboratory of Excellence Ion Channel Science and Therapeutics, Institute of Molecular and Cellular Pharmacology, CNRS UMR7275 & University of Nice-Sophia Antipolis, Valbonne, France
| | - Stephen G. Waxman
- Department of Neurology, Yale University School of Medicine, New Haven, USA
- Center for Neuroscience and Regeneration Research, Yale University School of Medicine, New Haven, USA
| | - Giuseppe Lauria
- Neuroalgology Unit, IRCCS Foundation “Carlo Besta” Neurological Institute, Milan, Italy
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Lin TC, Lin CS, Tsai TN, Cheng SM, Lin WS, Cheng CC, Wu CH, Hsu CH. Stimulatory Influences of Far Infrared Therapy on the Transcriptome and Genetic Networks of Endothelial Progenitor Cells Receiving High Glucose Treatment. ACTA CARDIOLOGICA SINICA 2016; 31:414-28. [PMID: 27122901 DOI: 10.6515/acs20141201c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
BACKGROUND Endothelial progenitor cells (EPCs) play a fundamental role in vascular repair and angiogenesis- related diseases. It is well-known that the process of angiogenesis is faulty in patients with diabetes. Long-term exposure of peripheral blood EPCs to high glucose (HG-EPCs) has been shown to impair cell proliferation and other functional competencies. Far infrared (FIR) therapy can promote ischemia-induced angiogenesis in diabetic mice and restore high glucose-suppressed endothelial progenitor cell functions both in vitro and in vivo. However, the detail mechanisms and global transcriptome alternations are still unclear. METHODS In this study, we investigated the influences of FIR upon HG-EPC gene expressions. EPCs were obtained from the peripheral blood and treated with high glucose. These cells were then subjected to FIR irradiation and functional assays. RESULTS Those genes responsible for fibroblast growth factors, Mitogen-activated protein kinases (MAPK), Janus kinase/signal transducer and activator of transcription and prostaglandin signaling pathways were significantly induced in HG-EPCs after FIR treatment. On the other hand, mouse double minute 2 homolog, genes involved in glycogen metabolic process, and genes involved in cardiac fibrosis were down-regulated. We also observed complex genetic networks functioning in FIR-treated HG-EPCs, in which several genes, such as GATA binding protein 3, hairy and enhancer of split-1, Sprouty Homolog 2, MAPK and Sirtuin 1, acted as hubs to maintain the stability and connectivity of the whole genetic network. CONCLUSIONS Deciphering FIR-affected genes will not only provide us with new knowledge regarding angiogenesis, but also help to develop new biomarkers for evaluating the effects of FIR therapy. Our findings may also be adapted to develop new methods to increase EPC activities for treating diabetes-related ischemia and metabolic syndrome-associated cardiovascular disorders. KEY WORDS Endothelial progenitor cell; Far infrared; Microarray; Systems biology.
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Affiliation(s)
- Tzu-Chiao Lin
- Division of Cardiology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Chin-Sheng Lin
- Division of Cardiology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Tsung-Neng Tsai
- Division of Cardiology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Shu-Meng Cheng
- Division of Cardiology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Wei-Shiang Lin
- Division of Cardiology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Cheng-Chung Cheng
- Division of Cardiology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Chun-Hsien Wu
- Division of Cardiology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Chih-Hsueng Hsu
- Division of Cardiology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
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Abstract
We examine energy dynamics in the unliganded and liganded states of the homodimeric hemoglobin from Scapharca inaequivalvis (HbI), which exhibits cooperativity mediated by the cluster of water molecules at the interface upon ligand binding and dissociation. We construct and analyze a dynamic network in which nodes representing the residues, hemes, and water cluster are connected by edges that represent energy transport times, as well as a nonbonded network (NBN) indicating regions that respond rapidly to local strain within the protein via nonbonded interactions. One of the two largest NBNs includes the Lys30-Asp89 salt bridge critical for stabilizing the dimer. The other includes the hemes and surrounding residues, as well as, in the unliganded state, the cluster of water molecules between the globules. Energy transport in the protein appears to be controlled by the Lys30-Asp89 salt bridge critical for stabilizing the dimer, as well as the interface water cluster in the unliganded state. Possible connections between energy transport dynamics in response to local strain identified here and allosteric transitions in HbI are discussed.
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Affiliation(s)
- David M Leitner
- Department of Chemistry and Chemical Physics Program, University of Nevada , Reno, Nevada 89557, United States
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48
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Paul Y, Hasija Y. Gene Prioritization by Integrated Analysis of Protein Structural and Network Topological Properties for the Protein-Protein Interaction Network of Neurological Disorders. SCIENTIFICA 2016; 2016:9589404. [PMID: 27034906 PMCID: PMC4808548 DOI: 10.1155/2016/9589404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 02/11/2016] [Accepted: 02/18/2016] [Indexed: 06/05/2023]
Abstract
Neurological disorders are known to show similar phenotypic manifestations like anxiety, depression, and cognitive impairment. There is a need to identify shared genetic markers and molecular pathways in these diseases, which lead to such comorbid conditions. Our study aims to prioritize novel genetic markers that might increase the susceptibility of patients affected with one neurological disorder to other diseases with similar manifestations. Identification of pathways involving common candidate markers will help in the development of improved diagnosis and treatments strategies for patients affected with neurological disorders. This systems biology study for the first time integratively uses 3D-structural protein interface descriptors and network topological properties that characterize proteins in a neurological protein interaction network, to aid the identification of genes that are previously not known to be shared between these diseases. Results of protein prioritization by machine learning have identified known as well as new genetic markers which might have direct or indirect involvement in several neurological disorders. Important gene hubs have also been identified that provide an evidence for shared molecular pathways in the neurological disease network.
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Affiliation(s)
- Yashna Paul
- Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Main Bawana Road, New Delhi, Delhi 110042, India
| | - Yasha Hasija
- Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Main Bawana Road, New Delhi, Delhi 110042, India
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49
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Schütze T, Ulrich AKC, Apelt L, Will CL, Bartlick N, Seeger M, Weber G, Lührmann R, Stelzl U, Wahl MC. Multiple protein-protein interactions converging on the Prp38 protein during activation of the human spliceosome. RNA (NEW YORK, N.Y.) 2016; 22:265-77. [PMID: 26673105 PMCID: PMC4712676 DOI: 10.1261/rna.054296.115] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 11/17/2015] [Indexed: 05/22/2023]
Abstract
Spliceosomal Prp38 proteins contain a conserved amino-terminal domain, but only higher eukaryotic orthologs also harbor a carboxy-terminal RS domain, a hallmark of splicing regulatory SR proteins. We show by crystal structure analysis that the amino-terminal domain of human Prp38 is organized around three pairs of antiparallel α-helices and lacks similarities to RNA-binding domains found in canonical SR proteins. Instead, yeast two-hybrid analyses suggest that the amino-terminal domain is a versatile protein-protein interaction hub that possibly binds 12 other spliceosomal proteins, most of which are recruited at the same stage as Prp38. By quantitative, alanine surface-scanning two-hybrid screens and biochemical analyses we delineated four distinct interfaces on the Prp38 amino-terminal domain. In vitro interaction assays using recombinant proteins showed that Prp38 can bind at least two proteins simultaneously via two different interfaces. Addition of excess Prp38 amino-terminal domain to in vitro splicing assays, but not of an interaction-deficient mutant, stalled splicing at a precatalytic stage. Our results show that human Prp38 is an unusual SR protein, whose amino-terminal domain is a multi-interface protein-protein interaction platform that might organize the relative positioning of other proteins during splicing.
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Affiliation(s)
- Tonio Schütze
- Freie Universität Berlin, Laboratory of Structural Biochemistry, D-14195 Berlin, Germany
| | - Alexander K C Ulrich
- Freie Universität Berlin, Laboratory of Structural Biochemistry, D-14195 Berlin, Germany
| | - Luise Apelt
- Max-Planck Institute for Molecular Genetics, Otto-Warburg Laboratory, D-14195 Berlin, Germany
| | - Cindy L Will
- Max Planck Institute for Biophysical Chemistry, Department of Cellular Biochemistry, D-37077 Göttingen, Germany
| | - Natascha Bartlick
- Freie Universität Berlin, Laboratory of Structural Biochemistry, D-14195 Berlin, Germany
| | - Martin Seeger
- Freie Universität Berlin, Laboratory of Structural Biochemistry, D-14195 Berlin, Germany
| | - Gert Weber
- Freie Universität Berlin, Laboratory of Structural Biochemistry, D-14195 Berlin, Germany
| | - Reinhard Lührmann
- Max Planck Institute for Biophysical Chemistry, Department of Cellular Biochemistry, D-37077 Göttingen, Germany
| | - Ulrich Stelzl
- Max-Planck Institute for Molecular Genetics, Otto-Warburg Laboratory, D-14195 Berlin, Germany University of Graz, Institute of Pharmaceutical Sciences (IPW), Pharmaceutical Chemistry, A-8010 Graz, Austria
| | - Markus C Wahl
- Freie Universität Berlin, Laboratory of Structural Biochemistry, D-14195 Berlin, Germany
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50
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Zeidán-Chuliá F, Gürsoy M, Neves de Oliveira BH, Özdemir V, Könönen E, Gürsoy UK. A Systems Biology Approach to Reveal Putative Host-Derived Biomarkers of Periodontitis by Network Topology Characterization of MMP-REDOX/NO and Apoptosis Integrated Pathways. Front Cell Infect Microbiol 2016; 5:102. [PMID: 26793622 PMCID: PMC4707239 DOI: 10.3389/fcimb.2015.00102] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 12/15/2015] [Indexed: 01/27/2023] Open
Abstract
Periodontitis, a formidable global health burden, is a common chronic disease that destroys tooth-supporting tissues. Biomarkers of the early phase of this progressive disease are of utmost importance for global health. In this context, saliva represents a non-invasive biosample. By using systems biology tools, we aimed to (1) identify an integrated interactome between matrix metalloproteinase (MMP)-REDOX/nitric oxide (NO) and apoptosis upstream pathways of periodontal inflammation, and (2) characterize the attendant topological network properties to uncover putative biomarkers to be tested in saliva from patients with periodontitis. Hence, we first generated a protein-protein network model of interactions ("BIOMARK" interactome) by using the STRING 10 database, a search tool for the retrieval of interacting genes/proteins, with "Experiments" and "Databases" as input options and a confidence score of 0.400. Second, we determined the centrality values (closeness, stress, degree or connectivity, and betweenness) for the "BIOMARK" members by using the Cytoscape software. We found Ubiquitin C (UBC), Jun proto-oncogene (JUN), and matrix metalloproteinase-14 (MMP14) as the most central hub- and non-hub-bottlenecks among the 211 genes/proteins of the whole interactome. We conclude that UBC, JUN, and MMP14 are likely an optimal candidate group of host-derived biomarkers, in combination with oral pathogenic bacteria-derived proteins, for detecting periodontitis at its early phase by using salivary samples from patients. These findings therefore have broader relevance for systems medicine in global health as well.
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Affiliation(s)
- Fares Zeidán-Chuliá
- Programa de Pós-Graduação em Ciências Biológicas: Bioquímica, Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do SulPorto Alegre, Brazil; Department of Periodontology, Institute of Dentistry, University of TurkuTurku, Finland
| | - Mervi Gürsoy
- Department of Periodontology, Institute of Dentistry, University of Turku Turku, Finland
| | - Ben-Hur Neves de Oliveira
- Programa de Pós-Graduação em Ciências Biológicas: Bioquímica, Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul Porto Alegre, Brazil
| | - Vural Özdemir
- Faculty of Communications and Office of the President, International Technology and Innovation Policy, Gaziantep UniversityGaziantep, Turkey; Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham (Amrita University)Kollam, India
| | - Eija Könönen
- Department of Periodontology, Institute of Dentistry, University of TurkuTurku, Finland; Oral Health Care, Welfare DivisionTurku, Finland
| | - Ulvi K Gürsoy
- Department of Periodontology, Institute of Dentistry, University of Turku Turku, Finland
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