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Lin Y, Xu J, Gu Q. FerroLigandDB: A Ferroptosis Ligand Database of Structure-Activity Relations. J Chem Inf Model 2024. [PMID: 38885636 DOI: 10.1021/acs.jcim.4c00525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Ferroptosis is an iron-dependent programmed cell death characterized by lipid peroxidation that is linked to the pathophysiological processes in many diseases, such as neurodegenerative diseases, cancers, ischemia-reperfusion injuries, and organ damages. Many proteins are associated with ferroptosis signal transduction pathways. Novel chemical compounds are demanded to explore and regulate these pathways. Therefore, a ferroptosis ligand database, which holds relations among chemical structures, targets, bioactivities, and diseases, is needed for discovering and designing new ferroptosis regulators. This work reports FerroLigandDB, a manually curated database for small-molecular ferroptosis regulators. The database comprises 466 ferroptosis inducer entries (with 380 unique molecular structures) and 539 ferroptosis inhibitor entries (with 468 unique molecular structures) (note: one compound can be recorded as multiple entries due to the different assays). Each ferroptosis ligand entry is detailed with compound IDs, structure attributes, bioactivity values, test objects, target information, associated diseases, and references. The fields in the FerroLigandDB database implicitly contain relationships among chemical structures, bioactivities, targets, and diseases. Thus, FerroLigandDB is a comprehensive resource for scientists to design and discover novel ferroptosis regulators. The user interface of FerroLigandDB is implemented with query features and data visualization facilities. With compound identifiers, the compounds are linked to the records of other chemoinformatics databases (such as PubChem and SciFinder). The FerroLigandDB database is freely accessible at http://ferr.gulab.org.cn/.
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Affiliation(s)
- Yating Lin
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
| | - Jun Xu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
| | - Qiong Gu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
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2
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Kim S, Yu B, Li Q, Bolton EE. PubChem synonym filtering process using crowdsourcing. J Cheminform 2024; 16:69. [PMID: 38880887 PMCID: PMC11181558 DOI: 10.1186/s13321-024-00868-3] [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: 03/01/2024] [Accepted: 06/09/2024] [Indexed: 06/18/2024] Open
Abstract
PubChem ( https://pubchem.ncbi.nlm.nih.gov ) is a public chemical information resource containing more than 100 million unique chemical structures. One of the most requested tasks in PubChem and other chemical databases is to search chemicals by name (also commonly called a "chemical synonym"). PubChem performs this task by looking up chemical synonym-structure associations provided by individual depositors to PubChem. In addition, these synonyms are used for many purposes, including creating links between chemicals and PubMed articles (using Medical Subject Headings (MeSH) terms). However, these depositor-provided name-structure associations are subject to substantial discrepancies within and between depositors, making it difficult to unambiguously map a chemical name to a specific chemical structure. The present paper describes PubChem's crowdsourcing-based synonym filtering strategy, which resolves inter- and intra-depositor discrepancies in synonym-structure associations as well as in the chemical-MeSH associations. The PubChem synonym filtering process was developed based on the analysis of four crowd-voting strategies, which differ in the consistency threshold value employed (60% vs 70%) and how to resolve intra-depositor discrepancies (a single vote vs. multiple votes per depositor) prior to inter-depositor crowd-voting. The agreement of voting was determined at six levels of chemical equivalency, which considers varying isotopic composition, stereochemistry, and connectivity of chemical structures and their primary components. While all four strategies showed comparable results, Strategy I (one vote per depositor with a 60% consistency threshold) resulted in the most synonyms assigned to a single chemical structure as well as the most synonym-structure associations disambiguated at the six chemical equivalency contexts. Based on the results of this study, Strategy I was implemented in PubChem's filtering process that cleans up synonym-structure associations as well as chemical-MeSH associations. This consistency-based filtering process is designed to look for a consensus in name-structure associations but cannot attest to their correctness. As a result, it can fail to recognize correct name-structure associations (or incorrect ones), for example, when a synonym is provided by only one depositor or when many contributors are incorrect. However, this filtering process is an important starting point for quality control in name-structure associations in large chemical databases like PubChem.
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Affiliation(s)
- Sunghwan Kim
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Bo Yu
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Qingliang Li
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Evan E Bolton
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
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Siddika MA, Ahmed KA, Alam MS, Bushra J, Begum RA. Complete mitogenome and intra-family comparative mitogenomics showed distinct position of Pama Croaker Otolithoides pama. Sci Rep 2024; 14:13820. [PMID: 38879694 PMCID: PMC11180200 DOI: 10.1038/s41598-024-64791-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 06/13/2024] [Indexed: 06/19/2024] Open
Abstract
The Pama Croaker, Otolithoides pama, is an economically important fish species in Bangladesh. Intra-family similarities in morphology and typical barcode sequences of cox1 create ambiguities in its identification. Therefore, morphology and the complete mitochondrial genome of O. pama, and comparative mitogenomics within the family Sciaenidae have been studied. Extracted genomic DNA was subjected to Illumina-based short read sequencing for De-Novo mitogenome assembly. The complete mitogenome of O. pama (Accession: OQ784575.1) was 16,513 bp, with strong AC biasness and strand asymmetry. Relative synonymous codon usage (RSCU) among 13 protein-coding genes (PCGs) of O. pama was also analyzed. The studied mitogenomes including O. pama exhibited consistent sizes and gene orders, except for the genus Johnius which possessed notably longer mitogenomes with unique gene rearrangements. Different genetic distance metrics across 30 species of Sciaenidae family demonstrated 12S rRNA and the control region (CR) as the most conserved and variable regions, respectively, while most of the PCGs undergone a purifying selection. Different phylogenetic trees were congruent with one another, where O. pama was distinctly placed. This study would contribute to distinguishing closely related fish species of Sciaenidae family and can be instrumental in conserving the genetic diversity of O. pama.
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Affiliation(s)
- Most Ayesha Siddika
- Genetics and Molecular Biology Laboratory, Department of Zoology, University of Dhaka, Dhaka, 1000, Bangladesh
| | | | - Mohammad Shamimul Alam
- Genetics and Molecular Biology Laboratory, Department of Zoology, University of Dhaka, Dhaka, 1000, Bangladesh.
| | - Jannatul Bushra
- Genetics and Molecular Biology Laboratory, Department of Zoology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Rowshan Ara Begum
- Genetics and Molecular Biology Laboratory, Department of Zoology, University of Dhaka, Dhaka, 1000, Bangladesh
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4
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Li J, Huang Z, Wang P, Li R, Gao L, Lai KP. Therapeutic targets of formononetin for treating prostate cancer at the single-cell level. Aging (Albany NY) 2024; 16:205935. [PMID: 38874510 DOI: 10.18632/aging.205935] [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: 11/15/2023] [Accepted: 04/22/2024] [Indexed: 06/15/2024]
Abstract
Prostate cancer is one of the serious health problems of older male, about 13% of male was affected by prostate cancer. Prostate cancer is highly heterogeneity disease with complex molecular and genetic alterations. So, targeting the gene candidates in prostate cancer in single-cell level can be a promising approach for treating prostate cancer. In the present study, we analyzed the single cell sequencing data obtained from 2 previous reports to determine the differential gene expression of prostate cancer in single-cell level. By using the network pharmacology analysis, we identified the therapeutic targets of formononetin in immune cells and tissue cells of prostate cancer. We then applied molecular docking to determine the possible direct binding of formononetin to its target proteins. Our result identified a cluster of differential gene expression in prostate cancer which can serve as novel biomarkers such as immunoglobulin kappa C for prostate cancer prognosis. The result of network pharmacology delineated the roles of formononetin's targets such CD74 and THBS1 in immune cells' function of prostate cancer. Also, formononetin targeted insulin receptor and zinc-alpha-2-glycoprotein which play important roles in metabolisms of tissue cells of prostate cancer. The result of molecular docking suggested the direct binding of formononetin to its target proteins including INSR, TNF, and CXCR4. Finally, we validated our findings by using formononetin-treated human prostate cancer cell DU145. For the first time, our result suggested the use of formononetin for treating prostate cancer through targeting different cell types in a single-cell level.
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Affiliation(s)
- Jiawei Li
- Department of Urology Surgery, The Second Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, PR China
| | | | - Ping Wang
- Key Laboratory of Environmental Pollution and Integrative Omics, Guilin Medical University, Education Department of Guangxi Zhuang Autonomous Region, Guilin Medical University, Guilin, PR China
| | - Rong Li
- Key Laboratory of Environmental Pollution and Integrative Omics, Guilin Medical University, Education Department of Guangxi Zhuang Autonomous Region, Guilin Medical University, Guilin, PR China
| | - Li Gao
- Department of Urology Surgery, The Second Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, PR China
| | - Keng Po Lai
- Key Laboratory of Environmental Pollution and Integrative Omics, Guilin Medical University, Education Department of Guangxi Zhuang Autonomous Region, Guilin Medical University, Guilin, PR China
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Zhu R, Kang Y, Li Q, Peng K, Shi X, Yin Z, Xuan Y. Alpha-tocopherol inhibits ferroptosis and promotes neural function recovery in rats with spinal cord injury via downregulating Alox15. Biomed Pharmacother 2024; 175:116734. [PMID: 38754264 DOI: 10.1016/j.biopha.2024.116734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 04/27/2024] [Accepted: 05/07/2024] [Indexed: 05/18/2024] Open
Abstract
Spinal cord injury (SCI) is a type of central nervous system (CNS) injury in which ferroptosis is becoming a promising target for treatment. Alpha-tocopherol (Vitamin E, Vit E) is a compound with anti-ferroptosis activity. The mechanism of alpha-tocopherol in regulating ferroptosis after SCI has not been deeply studied. In this study, rats with SCI were treated by Alpha-tocopherol based on bioinformatic analysis and molecular docking prediction. Behavioral tests and histological findings showed that Alpha-tocopherol promoted neural function recovery and tissue repairment in rats with SCI. Subsequently, regulatory effects of Alpha-tocopherol on Alox15 and ferroptosis were detected and then localized by immunofluorescence. In vitro, alpha-tocopherol improved the ROS accumulation, iron overload, lipid peroxidation and mitochondrial dysfunction. The effects of Alpha-tocopherol on the expression of Alox15, Ptgs2 and 4Hne were validated in vitro. Finally, the inhibitory effects of Alpha-tocopherol on Alox15 and ferroptosis were weakened by the mutation of 87th residue of Alox15. In summary, alpha-tocopherol could alleviate SCI-induced ferroptosis by downregulating Alox15 to promote neural function recovery in rats with SCI. Findings in this study could help further our understanding on SCI-induced ferroptosis and provide a novel insight for treating SCI.
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Affiliation(s)
- Rui Zhu
- Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, Anhui Medical University, 218 Jixi Road, Hefei 230022, China; Department of Orthopedics, Hefei Orthopedics Hospital, 58 Chaohu Northern Road, Hefei 238001, China
| | - Yu Kang
- Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, Anhui Medical University, 218 Jixi Road, Hefei 230022, China
| | - Qiangwei Li
- School of Basic Medical Sciences, Anhui Medical University, 81 Meishan Road, Hefei 230032, China
| | - Kai Peng
- Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, Anhui Medical University, 218 Jixi Road, Hefei 230022, China; The Key Laboratory of Microbiology and Parasitology of Anhui Province, Anhui Medical University, 81 Meishan Road, Hefei 230032, China
| | - Xuanming Shi
- School of Basic Medical Sciences, Anhui Medical University, 81 Meishan Road, Hefei 230032, China.
| | - Zongsheng Yin
- Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, Anhui Medical University, 218 Jixi Road, Hefei 230022, China.
| | - Yong Xuan
- Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, Anhui Medical University, 218 Jixi Road, Hefei 230022, China; Department of Orthopedics, The Second People's Hospital of Hefei, 246 Heping Road, Hefei 230011, China.
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Jiang C, Zhang S, Jiang L, Chen Z, Chen H, Huang J, Tang J, Luo X, Yang G, Liu J, Chi H. Precision unveiled: Synergistic genomic landscapes in breast cancer-Integrating single-cell analysis and decoding drug toxicity for elite prognostication and tailored therapeutics. ENVIRONMENTAL TOXICOLOGY 2024; 39:3448-3472. [PMID: 38450906 DOI: 10.1002/tox.24205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/19/2024] [Accepted: 02/25/2024] [Indexed: 03/08/2024]
Abstract
BACKGROUND Globally, breast cancer, with diverse subtypes and prognoses, necessitates tailored therapies for enhanced survival rates. A key focus is glutamine metabolism, governed by select genes. This study explored genes associated with T cells and linked them to glutamine metabolism to construct a prognostic staging index for breast cancer patients for more precise medical treatment. METHODS Two frameworks, T-cell related genes (TRG) and glutamine metabolism (GM), stratified breast cancer patients. TRG analysis identified key genes via hdWGCNA and machine learning. T-cell communication and spatial transcriptomics emphasized TRG's clinical value. GM was defined using Cox analyses and the Lasso algorithm. Scores categorized patients as TRG_high+GM_high (HH), TRG_high+GM_low (HL), TRG_low+GM_high (LH), or TRG_low+GM_low (LL). Similarities between HL and LH birthed a "Mixed" class and the TRG_GM classifier. This classifier illuminated gene variations, immune profiles, mutations, and drug responses. RESULTS Utilizing a composite of two distinct criteria, we devised a typification index termed TRG_GM classifier, which exhibited robust prognostic potential for breast cancer patients. Our analysis elucidated distinct immunological attributes across the classifiers. Moreover, by scrutinizing the genetic variations across groups, we illuminated their unique genetic profiles. Insights into drug sensitivity further underscored avenues for tailored therapeutic interventions. CONCLUSION Utilizing TRG and GM, a robust TRG_GM classifier was developed, integrating clinical indicators to create an accurate predictive diagnostic map. Analysis of enrichment disparities, immune responses, and mutation patterns across different subtypes yields crucial subtype-specific characteristics essential for prognostic assessment, clinical decision-making, and personalized therapies. Further exploration is warranted into multiple fusions between metrics to uncover prognostic presentations across various dimensions.
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Affiliation(s)
- Chenglu Jiang
- Department of Clinical Medicine, Southwest Medical University, Luzhou, China
| | - Shengke Zhang
- Department of Clinical Medicine, Southwest Medical University, Luzhou, China
| | - Lai Jiang
- Department of Clinical Medicine, Southwest Medical University, Luzhou, China
| | - Zipei Chen
- Department of Clinical Medicine, Southwest Medical University, Luzhou, China
| | - Haiqing Chen
- Department of Clinical Medicine, Southwest Medical University, Luzhou, China
| | - Jinbang Huang
- Department of Clinical Medicine, Southwest Medical University, Luzhou, China
| | - Jingyi Tang
- Department of Clinical Medicine, Southwest Medical University, Luzhou, China
| | - Xiufang Luo
- Geriatric department, Dazhou Central Hospital, Dazhou, China
| | - Guanhu Yang
- Department of Specialty Medicine, Ohio University, Athens, Ohio, USA
| | - Jie Liu
- Department of General Surgery, Dazhou Central Hospital, Dazhou, China
| | - Hao Chi
- Department of Clinical Medicine, Southwest Medical University, Luzhou, China
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Luo Y, Deng L. DPMGCDA: Deciphering circRNA-Drug Sensitivity Associations with Dual Perspective Learning and Path-Masked Graph Autoencoder. J Chem Inf Model 2024; 64:4359-4372. [PMID: 38745420 DOI: 10.1021/acs.jcim.4c00573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Accumulating evidence has indicated that the expression of circular RNAs (circRNAs) can affect the cellular sensitivity to drugs and significantly influence drug efficacy. However, traditional experimental approaches for validating these associations are resource-intensive and time-consuming. To address this challenge, we propose a computational framework termed DPMGCDA leveraging dual perspective learning and path-masked graph autoencoder to predict circRNA-drug sensitivity associations. Initially, we construct circRNA-circRNA fusion similarity networks and drug-drug fusion similarity networks using similarity network fusion, ensuring a comprehensive integration of information. Based on the above, we built the circRNA homogeneous graph, the drug homogeneous graph, and the circRNA-drug heterogeneous graph. Next, we form the initial node features in the circRNA-drug heterogeneous graph from the homogeneous graph-level perspective and the combined feature-level perspective and complete the prediction of potential associations using the path-masked graph autoencoder in both perspectives. The predictions under both perspectives are finally combined to obtain the final prediction score. Transductive setting experiments and inductive setting experiments all demonstrate that our method, DPMGCDA, outperforms state-of-the-art approaches. Additionally, we verify the necessity of employing dual perspective learning through ablation tests and analyze the effective encoding capability of the path-masked graph autoencoder for features through embedding visualization. Moreover, case studies on four drugs corroborate DPMGCDA's ability to identify potential circRNAs associated with new drugs.
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Affiliation(s)
- Yue Luo
- School of Computer Science and Engineering, Central South University, Changsha 410083, China
| | - Lei Deng
- School of Computer Science and Engineering, Central South University, Changsha 410083, China
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Du Y. Binding Curve Viewer: Visualizing the Equilibrium and Kinetics of Protein-Ligand Binding and Competitive Binding. J Chem Inf Model 2024; 64:4180-4192. [PMID: 38720179 PMCID: PMC11134506 DOI: 10.1021/acs.jcim.4c00130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/21/2024] [Accepted: 04/25/2024] [Indexed: 05/28/2024]
Abstract
Understanding the thermodynamics and kinetics of the protein-ligand interaction is essential for biologists and pharmacologists. To visualize the equilibrium and kinetics of the binding reaction with 1:1 stoichiometry and no cooperativity, we obtained the exact relationship of the concentration of the protein-ligand complex and the time in the second-order binding process and numerically simulated the process of competitive binding. First, two common concerns in measuring protein-ligand interactions were focused on how to avoid the titration regime and how to establish the appropriate incubation time. Then, we gave examples of how the commonly used experimental conditions of [L]0 ≫ [P]0 and [I]0 ≫ [P]0 affected the estimation of the kinetic and thermodynamic properties. Theoretical inhibition curves were calculated, and the apparent IC50 and IC50 were estimated accordingly under predefined conditions. Using the estimated apparent IC50, we compared the apparent Ki and Ki calculated by using the Cheng-Prusoff equation, Lin-Riggs equation, and Wang's group equation. We also applied our tools to simulate high-throughput screening and compare the results of real experiments. The visualization tool for simulating the saturation experiment, kinetic experiments of binding and competitive binding, and inhibition curve, "Binding Curve Viewer," is available at www.eplatton.net/binding-curve-viewer.
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Affiliation(s)
- Yu Du
- Department
of Clinical Laboratory, The Second Affiliated
Hospital of Jiaxing University, Huancheng North Road 1518, Jiaxing, Zhejiang 314000, China
- The
Key Laboratory, The Second Affiliated Hospital
of Jiaxing University, Huancheng North Road 1518, Jiaxing, Zhejiang 314000, China
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Liu T, Wu H, Sun L, Wei J. Role of Inflammation in the Development of COVID-19 to Parkinson's Disease. J Inflamm Res 2024; 17:3259-3282. [PMID: 38800597 PMCID: PMC11127656 DOI: 10.2147/jir.s460161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/16/2024] [Indexed: 05/29/2024] Open
Abstract
Background The coronavirus disease 2019 (COVID-19) can lead to neurological symptoms such as headaches, confusion, seizures, hearing loss, and loss of smell. The link between COVID-19 and Parkinson's disease (PD) is being investigated, but more research is needed for a definitive connection. Methods Datasets GSE22491 and GSE164805 were selected to screen differentially expressed gene (DEG), and immune infiltration and gene set enrichment analysis (GSEA) of the DEG were performed. WGCNA analyzed the DEG and selected the intersection genes. Potential biological functions and signaling pathways were determined, and diagnostic genes were further screened using gene expression and receiver operating characteristic (ROC) curves. Screening and molecular docking of ibuprofen as a therapeutic target. The effectiveness of ibuprofen was verified by constructing a PD model in vitro, and constructing "COVID19-PD" signaling pathway, and exploring the role of angiotensin-converting enzyme 2 (ACE2) in PD. Results A total of 13 DEG were screened from the GSE36980 and GSE5281 datasets. Kyoto encyclopedia of genes and genomes (KEGG) analysis showed that the DEG were mainly associated with the hypoxia-inducible factor (HIF-1), epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor resistance, etc. After analysis, it is found that ibuprofen alleviates PD symptoms by inhibiting the expression of nuclear factor kappa-B (NF-κB), interleukin-1β (IL-1β), IL-6, and tumor necrosis factor-α (TNF-α). Based on signal pathway construction, the importance of ACE2 in COVID-19-induced PD has been identified. ACE2 is found to have widespread distribution in the brain. In the 1-methyl-4-phenyl-1,2,3,6-te-trahydropyridine (MPTP)-induced ACE2-null PD mice model, more severe motor and non-motor symptoms, increased NF-κB p65 and α-synuclein (α-syn) expression with significant aggregation, decreased tyrosine hydroxylase (TH), severe neuronal loss, and neurodegenerative disorders. Conclusion Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection increases the risk of PD through an inflammatory environment and downregulation of ACE2, providing evidence for the molecular mechanism and targeted therapy associated with COVID-19 and PD.
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Affiliation(s)
- Tingting Liu
- Institute for Brain Sciences Research, School of Life Sciences, Henan University, Institute of Neurourology and Urodynamics, Huaihe Hospital of Henan University, Kaifeng, 475004, People’s Republic of China
| | - Haojie Wu
- Institute for Brain Sciences Research, School of Life Sciences, Henan University, Institute of Neurourology and Urodynamics, Huaihe Hospital of Henan University, Kaifeng, 475004, People’s Republic of China
| | - Lin Sun
- College of Chemistry and Molecular Sciences, Henan University, Kaifeng, 475004, People’s Republic of China
| | - Jianshe Wei
- Institute for Brain Sciences Research, School of Life Sciences, Henan University, Institute of Neurourology and Urodynamics, Huaihe Hospital of Henan University, Kaifeng, 475004, People’s Republic of China
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Wang J, Sun H, Mou L, Lu Y, Wu Z, Pu Z, Yang MM. Unveiling the molecular complexity of proliferative diabetic retinopathy through scRNA-seq, AlphaFold 2, and machine learning. Front Endocrinol (Lausanne) 2024; 15:1382896. [PMID: 38800474 PMCID: PMC11116564 DOI: 10.3389/fendo.2024.1382896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 04/25/2024] [Indexed: 05/29/2024] Open
Abstract
Background Proliferative diabetic retinopathy (PDR), a major cause of blindness, is characterized by complex pathogenesis. This study integrates single-cell RNA sequencing (scRNA-seq), Non-negative Matrix Factorization (NMF), machine learning, and AlphaFold 2 methods to explore the molecular level of PDR. Methods We analyzed scRNA-seq data from PDR patients and healthy controls to identify distinct cellular subtypes and gene expression patterns. NMF was used to define specific transcriptional programs in PDR. The oxidative stress-related genes (ORGs) identified within Meta-Program 1 were utilized to construct a predictive model using twelve machine learning algorithms. Furthermore, we employed AlphaFold 2 for the prediction of protein structures, complementing this with molecular docking to validate the structural foundation of potential therapeutic targets. We also analyzed protein-protein interaction (PPI) networks and the interplay among key ORGs. Results Our scRNA-seq analysis revealed five major cell types and 14 subcell types in PDR patients, with significant differences in gene expression compared to those in controls. We identified three key meta-programs underscoring the role of microglia in the pathogenesis of PDR. Three critical ORGs (ALKBH1, PSIP1, and ATP13A2) were identified, with the best-performing predictive model demonstrating high accuracy (AUC of 0.989 in the training cohort and 0.833 in the validation cohort). Moreover, AlphaFold 2 predictions combined with molecular docking revealed that resveratrol has a strong affinity for ALKBH1, indicating its potential as a targeted therapeutic agent. PPI network analysis, revealed a complex network of interactions among the hub ORGs and other genes, suggesting a collective role in PDR pathogenesis. Conclusion This study provides insights into the cellular and molecular aspects of PDR, identifying potential biomarkers and therapeutic targets using advanced technological approaches.
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Affiliation(s)
- Jun Wang
- Department of Endocrinology, Shenzhen People’s Hospital (The Second Clinical Medical College of Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Hongyan Sun
- Department of Ophthalmology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Lisha Mou
- Imaging Department, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, China
- MetaLife Center, Shenzhen Institute of Translational Medicine, Guangdong, Shenzhen, China
| | - Ying Lu
- Imaging Department, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, China
- MetaLife Center, Shenzhen Institute of Translational Medicine, Guangdong, Shenzhen, China
| | - Zijing Wu
- Imaging Department, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, China
- MetaLife Center, Shenzhen Institute of Translational Medicine, Guangdong, Shenzhen, China
| | - Zuhui Pu
- Imaging Department, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, China
- MetaLife Center, Shenzhen Institute of Translational Medicine, Guangdong, Shenzhen, China
| | - Ming-ming Yang
- Department of Ophthalmology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
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Ullah S, Rahman W, Ullah F, Ullah A, Ahmad G, Ijaz M, Ullah H, Sharafmal DM. The HABD: Home of All Biological Databases Empowering Biological Research With Cutting-Edge Database Systems. Curr Protoc 2024; 4:e1063. [PMID: 38808697 DOI: 10.1002/cpz1.1063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
The emergence of computer technologies and computing power has led to the development of several database systems that provide standardized access to vast quantities of data, making it possible to collect, search, index, evaluate, and extract useful knowledge across various fields. The Home of All Biological Databases (HABD) has been established as a continually expanding platform that aims to store, organize, and distribute biological data in a searchable manner, removing all dead and non-accessible data. The platform meticulously categorizes data into various categories, such as COVID-19 Pandemic Database (CO-19PDB), Database relevant to Human Research (DBHR), Cancer Research Database (CRDB), Latest Database of Protein Research (LDBPR), Fungi Databases Collection (FDBC), and many other databases that are categorized based on biological phenomena. It currently provides a total of 22 databases, including 6 published, 5 submitted, and the remaining in various stages of development. These databases encompass a range of areas, including phytochemical-specific and plastic biodegradation databases. HABD is equipped with search engine optimization (SEO) analyzer and Neil Patel tools, which ensure excellent SEO and high-speed value. With timely updates, HABD aims to facilitate the processing and visualization of data for scientists, providing a one-stop-shop for all biological databases. Computer platforms, such as PhP, html, CSS, Java script and Biopython, are used to build all the databases. © 2024 Wiley Periodicals LLC.
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Affiliation(s)
- Shahid Ullah
- S-Khan Lab, Mardan, Khyber Pakhtunkhwa, Pakistan
| | | | - Farhan Ullah
- S-Khan Lab, Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Anees Ullah
- S-Khan Lab, Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Gulzar Ahmad
- S-Khan Lab, Mardan, Khyber Pakhtunkhwa, Pakistan
| | | | - Hameed Ullah
- S-Khan Lab, Mardan, Khyber Pakhtunkhwa, Pakistan
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Shi F, Zhang G, Li J, Shu L, Yu C, Ren D, Zhang Y, Zheng P. Integrated analysis of single cell-RNA sequencing and Mendelian randomization identifies lactate dehydrogenase B as a target of melatonin in ischemic stroke. CNS Neurosci Ther 2024; 30:e14741. [PMID: 38702940 PMCID: PMC11069049 DOI: 10.1111/cns.14741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/09/2024] [Accepted: 04/12/2024] [Indexed: 05/06/2024] Open
Abstract
AIMS Despite the success of single-cell RNA sequencing in identifying cellular heterogeneity in ischemic stroke, clarifying the mechanisms underlying these associations of differently expressed genes remains challenging. Several studies that integrate gene expression and gene expression quantitative trait loci (eQTLs) with genome wide-association study (GWAS) data to determine their causal role have been proposed. METHODS Here, we combined Mendelian randomization (MR) framework and single cell (sc) RNA sequencing to study how differently expressed genes (DEGs) mediating the effect of gene expression on ischemic stroke. The hub gene was further validated in the in vitro model. RESULTS We identified 2339 DEGs in 10 cell clusters. Among these DEGs, 58 genes were associated with the risk of ischemic stroke. After external validation with eQTL dataset, lactate dehydrogenase B (LDHB) is identified to be positively associated with ischemic stroke. The expression of LDHB has also been validated in sc RNA-seq with dominant expression in microglia and astrocytes, and melatonin is able to reduce the LDHB expression and activity in vitro ischemic models. CONCLUSION Our study identifies LDHB as a novel biomarker for ischemic stroke via combining the sc RNA-seq and MR analysis.
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Affiliation(s)
- Fei Shi
- Department of Neurovascular Intervention and Neurosurgery, Shanghai General HospitalShanghai Jiaotong University, School of MedicineShanghaiChina
| | - Guiyun Zhang
- Department of Neurovascular Intervention and Neurosurgery, Shanghai General HospitalShanghai Jiaotong University, School of MedicineShanghaiChina
| | - Jinshi Li
- Department of NeurologyShanghai Pudong New area People's HospitalShanghaiChina
| | - Liang Shu
- Department of NeurologyShanghai Ninth People's HospitalShanghaiChina
| | - Cong Yu
- Department of NeurosurgeryShanghai Pudong New area People's HospitalShanghaiChina
| | - Dabin Ren
- Department of NeurosurgeryShanghai Pudong New area People's HospitalShanghaiChina
| | - Yisong Zhang
- Department of NeurosurgeryShanghai Pudong New area People's HospitalShanghaiChina
| | - Ping Zheng
- Department of NeurosurgeryShanghai Pudong New area People's HospitalShanghaiChina
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Chen N, Xie QM, Song SM, Guo SN, Fang Y, Fei GH, Wu HM. Dexamethasone protects against asthma via regulating Hif-1α-glycolysis-lactate axis and protein lactylation. Int Immunopharmacol 2024; 131:111791. [PMID: 38460304 DOI: 10.1016/j.intimp.2024.111791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 02/18/2024] [Accepted: 02/29/2024] [Indexed: 03/11/2024]
Abstract
PURPOSE Asthma can not be eradicated till now and its control primarily relies on the application of corticosteroids. Recently, glycolytic reprogramming has been reportedly contributed to asthma, this study aimed to reveal whether the effect of corticosteroids on asthma control is related to their regulation of glycolysis and glycolysis-dependent protein lactylation. METHODS Ovalbumin (OVA) aeroallergen was used to challenge mice and stimulate human macrophage cell line THP-1 following dexamethasone (DEX) treatment. Airway hyperresponsiveness, airway inflammation, the expressions of key glycolytic enzymes and pyroptosis markers, the level of lactic acid, real-time glycolysis and oxidative phosphorylation (OXPHOS), and protein lactylation were analyzed. RESULTS DEX significantly attenuated OVA-induced eosinophilic airway inflammation, including airway hyperresponsiveness, leukocyte infiltration, goblet cell hyperplasia, Th2 cytokines production and pyroptosis markers expression. Meanwhile, OVA-induced Hif-1α-glycolysis axis was substantially downregulated by DEX, which resulted in low level of lactic acid. Besides, key glycolytic enzymes in the lungs of asthmatic mice were notably co-localized with F4/80-positive macrophages, indicating metabolic shift to glycolysis in lung macrophages during asthma. This was confirmed in OVA-stimulated THP-1 cells that DEX treatment resulted in reductions in pyroptosis, glycolysis and lactic acid level. Finally, protein lactylation was found significantly increased in the lungs of asthmatic mice and OVA-stimulated THP-1 cells, which were both inhibited by DEX. CONCLUSION Our present study revealed that the effect of DEX on asthma control was associated with its suppressing of Hif-1α-glycolysis-lactateaxis and subsequent protein lactylation, which may open new avenues for the therapy of eosinophilic asthma.
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Affiliation(s)
- Ning Chen
- Anhui Geriatric Institute, Department of Geriatric Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Jixi Road 218, Hefei, Anhui 230022, PR China; Key Laboratory of Respiratory Disease Research and Medical Transformation of Anhui Province, Jixi Road 218, Hefei, Anhui 230022, PR China; Key Laboratory of Geriatric Molecular Medicine of Anhui Province, Jixi Road No. 218, Hefei, Anhui 230022, PR China
| | - Qiu-Meng Xie
- Anhui Geriatric Institute, Department of Geriatric Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Jixi Road 218, Hefei, Anhui 230022, PR China; Key Laboratory of Respiratory Disease Research and Medical Transformation of Anhui Province, Jixi Road 218, Hefei, Anhui 230022, PR China; Key Laboratory of Geriatric Molecular Medicine of Anhui Province, Jixi Road No. 218, Hefei, Anhui 230022, PR China
| | - Si-Ming Song
- Anhui Geriatric Institute, Department of Geriatric Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Jixi Road 218, Hefei, Anhui 230022, PR China; Key Laboratory of Respiratory Disease Research and Medical Transformation of Anhui Province, Jixi Road 218, Hefei, Anhui 230022, PR China; Key Laboratory of Geriatric Molecular Medicine of Anhui Province, Jixi Road No. 218, Hefei, Anhui 230022, PR China
| | - Si-Nuo Guo
- Anhui Geriatric Institute, Department of Geriatric Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Jixi Road 218, Hefei, Anhui 230022, PR China; Key Laboratory of Respiratory Disease Research and Medical Transformation of Anhui Province, Jixi Road 218, Hefei, Anhui 230022, PR China; Key Laboratory of Geriatric Molecular Medicine of Anhui Province, Jixi Road No. 218, Hefei, Anhui 230022, PR China
| | - Yu Fang
- Anhui Geriatric Institute, Department of Geriatric Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Jixi Road 218, Hefei, Anhui 230022, PR China; Key Laboratory of Respiratory Disease Research and Medical Transformation of Anhui Province, Jixi Road 218, Hefei, Anhui 230022, PR China; Key Laboratory of Geriatric Molecular Medicine of Anhui Province, Jixi Road No. 218, Hefei, Anhui 230022, PR China
| | - Guang-He Fei
- Key Laboratory of Respiratory Disease Research and Medical Transformation of Anhui Province, Jixi Road 218, Hefei, Anhui 230022, PR China; Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Jixi Road 218, Hefei, Anhui 230022, PR China.
| | - Hui-Mei Wu
- Anhui Geriatric Institute, Department of Geriatric Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Jixi Road 218, Hefei, Anhui 230022, PR China; Key Laboratory of Respiratory Disease Research and Medical Transformation of Anhui Province, Jixi Road 218, Hefei, Anhui 230022, PR China; Key Laboratory of Geriatric Molecular Medicine of Anhui Province, Jixi Road No. 218, Hefei, Anhui 230022, PR China.
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Tao Y, Zhao R, Yang B, Han J, Li Y. Dissecting the shared genetic landscape of anxiety, depression, and schizophrenia. J Transl Med 2024; 22:373. [PMID: 38637810 PMCID: PMC11025255 DOI: 10.1186/s12967-024-05153-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/01/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND Numerous studies highlight the genetic underpinnings of mental disorders comorbidity, particularly in anxiety, depression, and schizophrenia. However, their shared genetic loci are not well understood. Our study employs Mendelian randomization (MR) and colocalization analyses, alongside multi-omics data, to uncover potential genetic targets for these conditions, thereby informing therapeutic and drug development strategies. METHODS We utilized the Consortium for Linkage Disequilibrium Score Regression (LDSC) and Mendelian Randomization (MR) analysis to investigate genetic correlations among anxiety, depression, and schizophrenia. Utilizing GTEx V8 eQTL and deCODE Genetics pQTL data, we performed a three-step summary-data-based Mendelian randomization (SMR) and protein-protein interaction analysis. This helped assess causal and comorbid loci for these disorders and determine if identified loci share coincidental variations with psychiatric diseases. Additionally, phenome-wide association studies, drug prediction, and molecular docking validated potential drug targets. RESULTS We found genetic correlations between anxiety, depression, and schizophrenia, and under a meta-analysis of MR from multiple databases, the causal relationships among these disorders are supported. Based on this, three-step SMR and colocalization analyses identified ITIH3 and CCS as being related to the risk of developing depression, while CTSS and DNPH1 are related to the onset of schizophrenia. BTN3A1, PSMB4, and TIMP4 were identified as comorbidity loci for both disorders. Molecules that could not be determined through colocalization analysis were also presented. Drug prediction and molecular docking showed that some drugs and proteins have good binding affinity and available structural data. CONCLUSIONS Our study indicates genetic correlations and shared risk loci between anxiety, depression, and schizophrenia. These findings offer insights into the underlying mechanisms of their comorbidities and aid in drug development.
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Affiliation(s)
- Yiming Tao
- Department of Intensive Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hankou, Wuhan, 430030, China
- Department of Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250101, Shandong, China
| | - Rui Zhao
- Department of Laboratory Medicine, The First Afliated Hospital of Chongqing Medical University, Chongqing, 400042, China
| | - Bin Yang
- Department of Intensive Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hankou, Wuhan, 430030, China
| | - Jie Han
- Department of Emergency, School of Medicine, Qingdao Municipal Hospital, Qingdao University, Qingdao, 266071, China.
| | - Yongsheng Li
- Department of Intensive Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hankou, Wuhan, 430030, China.
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Luo Q, Wang J, Ge W, Li Z, Mao Y, Wang C, Zhang L. Exploration of the potential causative genes for inflammatory bowel disease: Transcriptome-wide association analysis, Mendelian randomization analysis and Bayesian colocalisation. Heliyon 2024; 10:e28944. [PMID: 38617957 PMCID: PMC11015108 DOI: 10.1016/j.heliyon.2024.e28944] [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: 01/30/2024] [Revised: 03/27/2024] [Accepted: 03/27/2024] [Indexed: 04/16/2024] Open
Abstract
Background Inflammatory bowel disease (IBD) poses a complex challenge due to its intricate underlying mechanisms, and curative treatments remain elusive. Consequently, there is an urgent need to identify genes causally associated with IBD. Methods We extracted blood eQTL data from the GTExv8.ALL.Whole_Blood database, genome-wide association studies (GWAS) summary statistics of IBD from the IEU GWAS database, and performed a three-fold analysis protocol, including transcriptome-wide association analysis, Mendelian randomisation analysis, Bayesian colocalisation, and subsequent potential therapeutic agents identification. Results We identified four pathogenic genes, namely CARD9, RTEL1, STMN3 and ARFRP1, that promote the development of IBD, encompassing both ulcerative colitis (UC) and Crohn's disease (CD). Notably, ARFRP1 exhibited the ability to suppress IBD (encompassing UC and CD) development. Regarding drug prediction, cyclophosphamide emerged as a promising novel therapeutic option for IBD, encompassing UC and CD. Conclusion We identified several potential genes related to IBD (UC and CD), including CARD9, RTEL1, STMN3 and ARFRP1, warranting further investigation in functional studies to elucidate underlying disease mechanisms. Additionally, clinical studies exploring the potential of cyclophosphamide as a treatment avenue for IBD are warranted.
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Affiliation(s)
- Qinghua Luo
- Clinical Medical College, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Jiawen Wang
- Department of Proctology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Wei Ge
- Department of Proctology, Affiliated Hospital of Jiangxi University of Chinese Medicine, Nanchang, China
| | - Zihao Li
- Office of the President, Jiangmen Wuyi Hospital of Traditional Chinese Medicine, Jiangmen, China
| | - Yuanting Mao
- Clinical Medical College, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Chen Wang
- Department of Proctology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Leichang Zhang
- Formula-Pattern Research Center, Jiangxi University of Chinese Medicine, Jiangxi, China
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Han X, Gao Y, Zhou B, Hameed HMA, Fang C, Ju Y, He J, Fang X, Liu Z, Yu W, Xiong X, Zhong N, Zhang T. Indole Propionic Acid Disturbs the Normal Function of Tryptophanyl-tRNA Synthetase in Mycobacterium tuberculosis. ACS Infect Dis 2024; 10:1201-1211. [PMID: 38457660 DOI: 10.1021/acsinfecdis.3c00585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2024]
Abstract
Tuberculosis (TB) is the leading infectious disease caused by Mycobacterium tuberculosis and the second-most contagious killer after COVID-19. The emergence of drug-resistant TB has caused a great need to identify and develop new anti-TB drugs with novel targets. Indole propionic acid (IPA), a structural analog of tryptophan (Trp), is active against M. tuberculosis in vitro and in vivo. It has been verified that IPA exerts its antimicrobial effect by mimicking Trp as an allosteric inhibitor of TrpE, which is the first enzyme in the Trp synthesis pathway of M. tuberculosis. However, other Trp structural analogs, such as indolmycin, also target tryptophanyl-tRNA synthetase (TrpRS), which has two functions in bacteria: synthesis of tryptophanyl-AMP by catalyzing ATP + Trp and producing Trp-tRNATrp by transferring Trp to tRNATrp. So, we speculate that IPA may also target TrpRS. In this study, we found that IPA can dock into the Trp binding pocket of M. tuberculosis TrpRS (TrpRSMtb), which was further confirmed by isothermal titration calorimetry (ITC) assay. The biochemical analysis proved that TrpRS can catalyze the reaction between IPA and ATP to generate pyrophosphate (PPi) without Trp as a substrate. Overexpression of wild-type trpS in M. tuberculosis increased the MIC of IPA to 32-fold, and knock-down trpS in Mycolicibacterium smegmatis made it more sensitive to IPA. The supplementation of Trp in the medium abrogated the inhibition of M. tuberculosis by IPA. We demonstrated that IPA can interfere with the function of TrpRS by mimicking Trp, thereby impeding protein synthesis and exerting its anti-TB effect.
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Affiliation(s)
- Xingli Han
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- China-New Zealand Joint Laboratory of Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou 510530, China
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Yamin Gao
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- China-New Zealand Joint Laboratory of Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou 510530, China
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Biao Zhou
- Guangzhou Laboratory, Guangzhou Medical University, Guangzhou 511436, China
- Guangzhou International Bio Island, Guangzhou 510320, China
| | - H M Adnan Hameed
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- China-New Zealand Joint Laboratory of Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou 510530, China
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Cuiting Fang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- China-New Zealand Joint Laboratory of Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou 510530, China
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Yanan Ju
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- China-New Zealand Joint Laboratory of Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou 510530, China
| | - Jing He
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- China-New Zealand Joint Laboratory of Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou 510530, China
| | - Xiange Fang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- China-New Zealand Joint Laboratory of Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou 510530, China
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Zhiyong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- China-New Zealand Joint Laboratory of Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou 510530, China
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
- Guangzhou Laboratory, Guangzhou Medical University, Guangzhou 511436, China
| | - Wei Yu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- China-New Zealand Joint Laboratory of Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou 510530, China
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
- Guangzhou Laboratory, Guangzhou Medical University, Guangzhou 511436, China
| | - Xiaoli Xiong
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- China-New Zealand Joint Laboratory of Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou 510530, China
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Nanshan Zhong
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou 510530, China
- Guangzhou Laboratory, Guangzhou Medical University, Guangzhou 511436, China
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, The National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- China-New Zealand Joint Laboratory of Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou 510530, China
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
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He MJ, Ran DL, Zhang ZY, Fu DS, He Q, Zhang HY, Mao Y, Zhao PY, Yin GW, Zhang JA. Exploring the roles and potential therapeutic strategies of inflammation and metabolism in the pathogenesis of vitiligo: a mendelian randomization and bioinformatics-based investigation. Front Genet 2024; 15:1385339. [PMID: 38660673 PMCID: PMC11039897 DOI: 10.3389/fgene.2024.1385339] [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: 02/14/2024] [Accepted: 03/26/2024] [Indexed: 04/26/2024] Open
Abstract
Introduction Vitiligo, a common autoimmune acquired pigmentary skin disorder, poses challenges due to its unclear pathogenesis. Evidence suggests inflammation and metabolism's pivotal roles in its onset and progression. This study aims to elucidate the causal relationships between vitiligo and inflammatory proteins, immune cells, and metabolites, exploring bidirectional associations and potential drug targets. Methods Mendelian Randomization (MR) analysis encompassed 4,907 plasma proteins, 91 inflammatory proteins, 731 immune cell features, and 1400 metabolites. Bioinformatics analysis included Protein-Protein Interaction (PPI) network construction, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Subnetwork discovery and hub protein identification utilized the Molecular Complex Detection (MCODE) plugin. Colocalization analysis and drug target exploration, including molecular docking validation, were performed. Results MR analysis identified 49 proteins, 39 immune cell features, and 59 metabolites causally related to vitiligo. Bioinformatics analysis revealed significant involvement in PPI, GO enrichment, and KEGG pathways. Subnetwork analysis identified six central proteins, with Interferon Regulatory Factor 3 (IRF3) exhibiting strong colocalization evidence. Molecular docking validated Piceatannol's binding to IRF3, indicating a stable interaction. Conclusion This study comprehensively elucidates inflammation, immune response, and metabolism's intricate involvement in vitiligo pathogenesis. Identified proteins and pathways offer potential therapeutic targets, with IRF3 emerging as a promising candidate. These findings deepen our understanding of vitiligo's etiology, informing future research and drug development endeavors.
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Affiliation(s)
- Ming-jie He
- Department of Dermatology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - De-long Ran
- Department of Dermatology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Zhan-yi Zhang
- Department of Plastic and Reconstructive Surgery, The First Hospital of Jilin University, Changchun, Jilin, China
| | - De-shuang Fu
- Department of Dermatology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Qing He
- Department of Dermatology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Han-Yin Zhang
- Department of Dermatology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yu Mao
- Department of Dermatology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Peng-Yuan Zhao
- Department of Dermatology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Guang-wen Yin
- Department of Dermatology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Jiang-an Zhang
- Department of Dermatology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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Zhang X, Gao H, Wang H, Chen Z, Zhang Z, Chen X, Li Y, Qi Y, Wang R. PLANET: A Multi-objective Graph Neural Network Model for Protein-Ligand Binding Affinity Prediction. J Chem Inf Model 2024; 64:2205-2220. [PMID: 37319418 DOI: 10.1021/acs.jcim.3c00253] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Predicting protein-ligand binding affinity is a central issue in drug design. Various deep learning models have been published in recent years, where many of them rely on 3D protein-ligand complex structures as input and tend to focus on the single task of reproducing binding affinity. In this study, we have developed a graph neural network model called PLANET (Protein-Ligand Affinity prediction NETwork). This model takes the graph-represented 3D structure of the binding pocket on the target protein and the 2D chemical structure of the ligand molecule as input. It was trained through a multi-objective process with three related tasks, including deriving the protein-ligand binding affinity, protein-ligand contact map, and ligand distance matrix. Besides the protein-ligand complexes with known binding affinity data retrieved from the PDBbind database, a large number of non-binder decoys were also added to the training data for deriving the final model of PLANET. When tested on the CASF-2016 benchmark, PLANET exhibited a scoring power comparable to the best result yielded by other deep learning models as well as a reasonable ranking power and docking power. In virtual screening trials conducted on the DUD-E benchmark, PLANET's performance was notably better than several deep learning and machine learning models. As on the LIT-PCBA benchmark, PLANET achieved comparable accuracy as the conventional docking program Glide, but it only spent less than 1% of Glide's computation time to finish the same job because PLANET did not need exhaustive conformational sampling. Considering the decent accuracy and efficiency of PLANET in binding affinity prediction, it may become a useful tool for conducting large-scale virtual screening.
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Affiliation(s)
- Xiangying Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, People's Republic of China
| | - Haotian Gao
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, People's Republic of China
| | - Haojie Wang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, People's Republic of China
| | - Zhihang Chen
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, People's Republic of China
| | - Zhe Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, People's Republic of China
| | - Xinchong Chen
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, People's Republic of China
| | - Yan Li
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, People's Republic of China
| | - Yifei Qi
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, People's Republic of China
| | - Renxiao Wang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, People's Republic of China
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Balaji PD, Selvam S, Sohn H, Madhavan T. MLASM: Machine learning based prediction of anticancer small molecules. Mol Divers 2024:10.1007/s11030-024-10823-x. [PMID: 38554168 DOI: 10.1007/s11030-024-10823-x] [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: 01/03/2024] [Accepted: 02/10/2024] [Indexed: 04/01/2024]
Abstract
Cancer, being the second leading cause of death globally. So, the development of effective anticancer treatments is crucial in the field of medicine. Anticancer peptides (ACPs) have shown promising therapeutic potential in cancer treatment compared to traditional methods. However, the process of identifying ACPs through experimental means is often time-intensive and expensive. To overcome this issue, we employed a machine learning-based approach for the first time to develop an anticancer model using small molecules. Anticancer small molecules (ACSMs) are compounds that have been developed to target and inhibit cancer cells. In this study, we used 10,000 compounds to develop the machine learning models using five algorithms such as, Random Forest (RF), Light gradient boosting machine (LightGBM), K-nearest neighbors (KNN), Decision tree (DT) and Extreme Gradient Boosting (XGB). The developed models were evaluated using the test set and top three models were identified (RF, LightGBM and XGB). Furthermore, to validate the predictive performance of our models, we have performed external validation using an FDA approved anticancer compounds/drugs. Following this analysis, we found that our LightGBM model correctly predicted 9 compounds as active. However, RF and XGB exhibited some limitations by predicting 8 and 7 compounds as active out of 10, respectively. These results demonstrate that, when compared to RF and XGB, the LightGBM model showcase robust prediction capabilities, achieving a superior accuracy of 79% with an AUC of 0.88. These findings provide promising insights into the potential of our approach for predicting anticancer small molecules, highlighting the role of machine learning in advancing cancer treatment research.
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Affiliation(s)
- Priya Dharshini Balaji
- Computational Biology Laboratory, Department of Genetic Engineering, School of Bio-Engineering, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu, Tamil Nadu, 603203, India
| | - Subathra Selvam
- Computational Biology Laboratory, Department of Genetic Engineering, School of Bio-Engineering, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu, Tamil Nadu, 603203, India
| | - Honglae Sohn
- Department of Chemistry, Department of Carbon Materials, Chosun University, Gwangju, South Korea
| | - Thirumurthy Madhavan
- Computational Biology Laboratory, Department of Genetic Engineering, School of Bio-Engineering, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu, Tamil Nadu, 603203, India.
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20
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Ding L, Jiang H, Li Q, Li Q, Zhang TT, Shang L, Xie B, Zhu Y, Ding K, Shi X, Zhu T, Zhu Y. Ropivacaine as a novel AKT1 specific inhibitor regulates the stemness of breast cancer. J Exp Clin Cancer Res 2024; 43:90. [PMID: 38523299 PMCID: PMC10962119 DOI: 10.1186/s13046-024-03016-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 03/18/2024] [Indexed: 03/26/2024] Open
Abstract
BACKGROUND Ropivacaine, a local anesthetic, exhibits anti-tumor effects in various cancer types. However, its specific functions and the molecular mechanisms involved in breast cancer cell stemness remain elusive. METHODS The effects of ropivacaine on breast cancer stemness were investigated by in vitro and in vivo assays (i.e., FACs, MTT assay, mammosphere formation assay, transwell assays, western blot, and xenograft model). RNA-seq, bioinformatics analysis, Western blot, Luciferase reporter assay, and CHIP assay were used to explore the mechanistic roles of ropivacaine subsequently. RESULTS Our study showed that ropivacaine remarkably suppressed stem cells-like properties of breast cancer cells both in vitro and in vivo. RNA-seq analysis identified GGT1 as the downstream target gene responding to ropivacaine. High GGT1 levels are positively associated with a poor prognosis in breast cancer. Ropivacaine inhibited GGT1 expression by interacting with the catalytic domain of AKT1 directly to impair its kinase activity with resultant inactivation of NF-κB. Interestingly, NF-κB can bind to the promoter region of GGT1. KEGG and GSEA analysis indicated silence of GGT1 inhibited activation of NF-κB signaling pathway. Depletion of GGT1 diminished stem phenotypes of breast cancer cells, indicating the formation of NF-κB /AKT1/GGT1/NF-κB positive feedback loop in the regulation of ropivacaine-repressed stemness in breast cancer cells. CONCLUSION Our finding revealed that local anesthetic ropivacaine attenuated breast cancer stemness through AKT1/GGT1/NF-κB signaling pathway, suggesting the potential clinical value of ropivacaine in breast cancer treatment.
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Affiliation(s)
- Lin Ding
- Department of Pathophysiology, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, China
| | - Hui Jiang
- Department of Anesthesiology, the First Affiliated Hospital of Anhui Medical University, Hefei, 230032, China
| | - Qiangwei Li
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, China
| | - Qiushuang Li
- Department of Pathophysiology, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, China
| | - Tian-Tian Zhang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, China
| | - Limeng Shang
- Department of Pathophysiology, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, China
| | - Bin Xie
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, China
| | - Yaling Zhu
- Department of Pathophysiology, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, China
| | - Keshuo Ding
- Department of Pathology, School of Basic Medicine, Anhui Medical University, Hefei, China
| | - Xuanming Shi
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, China.
| | - Tao Zhu
- Department of Oncology, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China.
- Key Laboratory of Immune Response and Immunotherapy, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China.
- Shenzhen Bay Laboratory, Shenzhen, 518055, China.
| | - Yong Zhu
- Department of Pathophysiology, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, China.
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21
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Cai Y, Xiao H, Zhou Q, Lin J, Liang X, Xu W, Cao Y, Zhang X, Wang H. Comprehensive Analyses of PANoptosome with Potential Implications in Cancer Prognosis and Immunotherapy. Biochem Genet 2024:10.1007/s10528-024-10687-8. [PMID: 38436818 DOI: 10.1007/s10528-024-10687-8] [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: 07/22/2023] [Accepted: 01/04/2024] [Indexed: 03/05/2024]
Abstract
Cell death resistance significantly contributes to poor therapeutic outcomes in various cancers. PANoptosis, a unique inflammatory programmed cell death (PCD) pathway activated by specific triggers and regulated by the PANoptosome, possesses key features of apoptosis, pyroptosis, and necroptosis, but these cannot be accounted for by any of the three PCD pathways alone. While existing studies on PANoptosis have predominantly centered on infectious and inflammatory diseases, its role in cancer malignancy has been understudied. In this comprehensive investigation, we conducted pan-cancer analyses of PANoptosome component genes across 33 cancer types. We characterized the genetic, epigenetic, and transcriptomic landscapes, and introduced a PANoptosome-related potential index (PANo-RPI) for evaluating the intrinsic PANoptosome assembly potential in cancers. Our findings unveil PANo-RPI as a prognostic factor in numerous cancers, including KIRC, LGG, and PAAD. Crucially, we established a significant correlation between PANo-RPI and tumor immune responses, as well as the infiltration of diverse lymphoid and myeloid cell subsets across nearly all cancer types. Moreover, a high PANo-RPI was consistently associated with improved immunotherapy response and efficacy, as evidenced by re-analysis of multiple immunotherapy cohorts. In conclusion, our study suggests that targeting PANoptosome components and modulating PANoptosis may hold tremendous therapeutic potential in the context of cancer.
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Affiliation(s)
- Yonghua Cai
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China
| | - Heng Xiao
- Southern Medical School, No. 1023, South Shatai Road, Baiyun District, Guangzhou, 510515, Guangdong, China
| | - Qixiong Zhou
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China
| | - Jie Lin
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China
| | - Xianqiu Liang
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China
| | - Wei Xu
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China
| | - Yongfu Cao
- Department of Neurosurgery, Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.
| | - Xian Zhang
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China.
| | - Hai Wang
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China.
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22
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Dao L, Liu H, Xiu R, Yao T, Tong R, Xu L. Gramine improves sepsis-induced myocardial dysfunction by binding to NF-κB p105 and inhibiting its ubiquitination. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 125:155325. [PMID: 38295663 DOI: 10.1016/j.phymed.2023.155325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 12/16/2023] [Accepted: 12/27/2023] [Indexed: 02/13/2024]
Abstract
BACKGROUND Sepsis and its associated heart failure are among the leading causes of death. Gramine, a natural indole alkaloid, can be extracted from a wide variety of raw plants, and it exhibits therapeutic potential in pathological cardiac hypertrophy. However, the effect of gramine on inflammatory cardiomyopathy, particularly sepsis-induced myocardial injury, remains an unexplored area. PURPOSE To determine the role of gramine in sepsis-induced myocardial dysfunction and explore its underlying mechanism. STUDY DESIGN AND METHODS In mice, sepsis was established by intraperitoneally injecting lipopolysaccharide (LPS, 10 mg/kg). Subsequently, the effects of gramine administration (50 or 100 mg/kg) on LPS-triggered cardiac dysfunction in mice were investigated. For in vitro studies, isolated primary cardiomyocytes were used to assess the effect of gramine (25 or 50 µM) on LPS-induced apoptosis and inflammation. Additionally, molecular docking, co-immunoprecipitation and ubiquitination analyzes were conducted to explore the underlying mechanisms. RESULTS Gramine visibly ameliorated sepsis-induced cardiac dysfunction, inflammatory response, and mortality in vivo. Moreover, it significantly alleviated LPS-induced apoptotic and inflammatory responses in vitro. Furthermore, target prediction for gramine using the SuperPred website indicated that the nuclear factor NF-κB p105 subunit was one of the molecules ranked in priority order with a high model accuracy and a high probability score. Molecular docking studies demonstrated that gramine effectively docked to the death domain of NF-κB p105. Mechanistic studies revealed that gramine suppressed the processing of NF-κB p105 to p50 by inhibiting NF-κB p105 ubiquitination. Additionally, the protective effect of gramine on cardiac injury was almost abolished by overexpressing NF-κB p105. CONCLUSION Gramine is a promising bioactive small molecule for treating sepsis-induced myocardial dysfunction, which acts by docking to NF-κB p105 and inhibiting NF-κB p105 ubiquitination, thus preventing its processing to NF-κB p50. Therefore, gramine holds potential as a clinical drug for treating myocardial depression during sepsis.
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Affiliation(s)
- Ling Dao
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, No.1 Jianshe East Road, Zhengzhou, Henan 450052, China
| | - Hengdao Liu
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, No.1 Jianshe East Road, Zhengzhou, Henan 450052, China
| | - Ruizhen Xiu
- Department of Radiology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Tianbao Yao
- Department of Cardiology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Renyang Tong
- Department of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine, Beijing Chao-Yang Hospital, Capital Medical University, No. 8 Gongtinan Road, Beijing 100020, China.
| | - Longwei Xu
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, No.1 Jianshe East Road, Zhengzhou, Henan 450052, China.
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Song JH, Kim HJ, Lee J, Hong SP, Chung MY, Lee YG, Park JH, Choi HK, Hwang JT. Robinetin Alleviates Metabolic Failure in Liver through Suppression of p300-CD38 Axis. Biomol Ther (Seoul) 2024; 32:214-223. [PMID: 38298012 PMCID: PMC10902699 DOI: 10.4062/biomolther.2023.061] [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: 03/22/2023] [Revised: 09/22/2023] [Accepted: 10/10/2023] [Indexed: 02/02/2024] Open
Abstract
Metabolic abnormalities in the liver are closely associated with diverse metabolic diseases such as non-alcoholic fatty liver disease, type 2 diabetes, and obesity. The aim of this study was to evaluate the ameliorating effect of robinetin (RBN) on the significant pathogenic features of metabolic failure in the liver and to identify the underlying molecular mechanism. RBN significantly decreased triglyceride (TG) accumulation by downregulating lipogenesis-related transcription factors in AML-12 murine hepatocyte cell line. In addition, mice fed with Western diet (WD) containing 0.025% or 0.05% RBN showed reduced liver mass and lipid droplet size, as well as improved plasma insulin levels and homeostatic model assessment of insulin resistance (HOMA-IR) values. CD38 was identified as a target of RBN using the BioAssay database, and its expression was increased in OPA-treated AML-12 cells and liver tissues of WD-fed mice. Furthermore, RBN elicited these effects through its anti-histone acetyltransferase (HAT) activity. Computational simulation revealed that RBN can dock into the HAT domain pocket of p300, a histone acetyltransferase, which leads to the abrogation of its catalytic activity. Additionally, knock-down of p300 using siRNA reduced CD38 expression. The chromatin immunoprecipitation (ChIP) assay showed that p300 occupancy on the promoter region of CD38 was significantly decreased, and H3K9 acetylation levels were diminished in lipid-accumulated AML-12 cells treated with RBN. RBN improves the pathogenic features of metabolic failure by suppressing the p300-CD38 axis through its anti-HAT activity, which suggests that RBN can be used as a new phytoceutical candidate for preventing or improving this condition.
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Affiliation(s)
- Ji-Hye Song
- Korea Food Research Institute, Wanju 55365, Republic of Korea
| | - Hyo-Jin Kim
- Korea Food Research Institute, Wanju 55365, Republic of Korea
| | - Jangho Lee
- Korea Food Research Institute, Wanju 55365, Republic of Korea
| | - Seung-Pyo Hong
- Department of Molecular Biology, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Min-Yu Chung
- Department of Food and Nutrition, Gangseo University, Seoul 07661, Republic of Korea
| | - Yu-Geun Lee
- Korea Food Research Institute, Wanju 55365, Republic of Korea
| | - Jae Ho Park
- Korea Food Research Institute, Wanju 55365, Republic of Korea
| | - Hyo-Kyoung Choi
- Korea Food Research Institute, Wanju 55365, Republic of Korea
| | - Jin-Taek Hwang
- Korea Food Research Institute, Wanju 55365, Republic of Korea
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24
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Shen T, Li S, Wang XS, Wang D, Wu S, Xia J, Zhang L. Deep reinforcement learning enables better bias control in benchmark for virtual screening. Comput Biol Med 2024; 171:108165. [PMID: 38402838 DOI: 10.1016/j.compbiomed.2024.108165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/07/2024] [Accepted: 02/14/2024] [Indexed: 02/27/2024]
Abstract
Virtual screening (VS) has been incorporated into the paradigm of modern drug discovery. This field is now undergoing a new wave of revolution driven by artificial intelligence and more specifically, machine learning (ML). In terms of those out-of-the-box datasets for model training or benchmarking, their data volume and applicability domain are limited. They are suffering from the biases constantly reported in the ML application. To address these issues, we present a novel benchmark named MUBDsyn. The utilization of synthetic decoys (i.e., presumed inactives) is the main feature of MUBDsyn, where deep reinforcement learning was leveraged for bias control during decoy generation. Then, we carried out extensive validations on this new benchmark. First, we confirmed that MUBDsyn was superior to the classical benchmarks in control of domain bias, artificial enrichment bias and analogue bias. Moreover, we found that the assessment of ML models based on MUBDsyn was less biased as revealed by the analysis of asymmetric validation embedding bias. In addition, MUBDsyn showed better setting of benchmarking challenge for deep learning models compared with NRLiSt-BDB. Overall, we have proven that MUBDsyn is the close-to-ideal benchmark for VS. The computational tool is publicly available for the easy extension of MUBDsyn.
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Affiliation(s)
- Tao Shen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Shan Li
- College of Economics and Management, Nanjing University of Aeronautics and Astronautics, Nanjing, 211106, China
| | - Xiang Simon Wang
- Artificial Intelligence and Drug Discovery Core Laboratory for District of Columbia Center for AIDS Research (DC CFAR), Department of Pharmaceutical Sciences, College of Pharmacy, Howard University, USA
| | - Dongmei Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
| | - Song Wu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
| | - Jie Xia
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
| | - Liangren Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
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25
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Zhu J, Wei J, Lin Y, Tang Y, Su Z, Li L, Liu B, Cai X. Inhibition of IL-17 signaling in macrophages underlies the anti-arthritic effects of halofuginone hydrobromide: Network pharmacology, molecular docking, and experimental validation. BMC Complement Med Ther 2024; 24:105. [PMID: 38413973 PMCID: PMC10900594 DOI: 10.1186/s12906-024-04397-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 02/11/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Rheumatoid arthritis (RA) is a prevalent autoimmune disease marked by chronic synovitis as well as cartilage and bone destruction. Halofuginone hydrobromide (HF), a bioactive compound derived from the Chinese herbal plant Dichroa febrifuga Lour., has demonstrated substantial anti-arthritic effects in RA. Nevertheless, the molecular mechanisms responsible for the anti-RA effects of HF remain unclear. METHODS This study employed a combination of network pharmacology, molecular docking, and experimental validation to investigate potential targets of HF in RA. RESULTS Network pharmacology analyses identified 109 differentially expressed genes (DEGs) resulting from HF treatment in RA. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses unveiled a robust association between these DEGs and the IL-17 signaling pathway. Subsequently, a protein-protein interaction (PPI) network analysis revealed 10 core DEGs, that is, EGFR, MMP9, TLR4, ESR1, MMP2, PPARG, MAPK1, JAK2, STAT1, and MAPK8. Among them, MMP9 displayed the greatest binding energy for HF. In an in vitro assay, HF significantly inhibited the activity of inflammatory macrophages, and regulated the IL-17 signaling pathway by decreasing the levels of IL-17 C, p-NF-κB, and MMP9. CONCLUSION In summary, these findings suggest that HF has the potential to inhibit the activation of inflammatory macrophages through its regulation of the IL-17 signaling pathway, underscoring its potential in the suppression of immune-mediated inflammation in RA.
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Affiliation(s)
- Junping Zhu
- Department of Rheumatology, First Hospital, School of Chinese Medical Sciences, Hunan University of Chinese Medicine, Changsha, Hunan, 410208, China
| | - Jiaming Wei
- Department of Rheumatology, First Hospital, School of Chinese Medical Sciences, Hunan University of Chinese Medicine, Changsha, Hunan, 410208, China
| | - Ye Lin
- Department of Rheumatology, First Hospital, School of Chinese Medical Sciences, Hunan University of Chinese Medicine, Changsha, Hunan, 410208, China
| | - Yuanyuan Tang
- Department of Rheumatology, First Hospital, School of Chinese Medical Sciences, Hunan University of Chinese Medicine, Changsha, Hunan, 410208, China
- College of Biology, Hunan University, Changsha, Hunan, 410082, China
| | - Zhaoli Su
- Department of Rheumatology, First Hospital, School of Chinese Medical Sciences, Hunan University of Chinese Medicine, Changsha, Hunan, 410208, China
- The Central Research Laboratory, Hunan Traditional Chinese Medical College, Zhuzhou, China
- Guangxi Provincial Key Laboratory of Preventive and Therapeutic Research in Prevalent Diseases in West Guangxi, Youjiang Medical University for Nationalities, Baise, Guangxi, 533000, China
| | - Liqing Li
- The Central Research Laboratory, Hunan Traditional Chinese Medical College, Zhuzhou, China.
- Guangxi Provincial Key Laboratory of Preventive and Therapeutic Research in Prevalent Diseases in West Guangxi, Youjiang Medical University for Nationalities, Baise, Guangxi, 533000, China.
| | - Bin Liu
- College of Biology, Hunan University, Changsha, Hunan, 410082, China.
| | - Xiong Cai
- Department of Rheumatology, First Hospital, School of Chinese Medical Sciences, Hunan University of Chinese Medicine, Changsha, Hunan, 410208, China.
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Martinez-Mayorga K, Rosas-Jiménez JG, Gonzalez-Ponce K, López-López E, Neme A, Medina-Franco JL. The pursuit of accurate predictive models of the bioactivity of small molecules. Chem Sci 2024; 15:1938-1952. [PMID: 38332817 PMCID: PMC10848664 DOI: 10.1039/d3sc05534e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/09/2024] [Indexed: 02/10/2024] Open
Abstract
Property prediction is a key interest in chemistry. For several decades there has been a continued and incremental development of mathematical models to predict properties. As more data is generated and accumulated, there seems to be more areas of opportunity to develop models with increased accuracy. The same is true if one considers the large developments in machine and deep learning models. However, along with the same areas of opportunity and development, issues and challenges remain and, with more data, new challenges emerge such as the quality and quantity and reliability of the data, and model reproducibility. Herein, we discuss the status of the accuracy of predictive models and present the authors' perspective of the direction of the field, emphasizing on good practices. We focus on predictive models of bioactive properties of small molecules relevant for drug discovery, agrochemical, food chemistry, natural product research, and related fields.
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Affiliation(s)
- Karina Martinez-Mayorga
- Institute of Chemistry, Merida Unit, National Autonomous University of Mexico Merida-Tetiz Highway, Km. 4.5 Ucu Yucatan Mexico
- Institute for Applied Mathematics and Systems, Merida Research Unit, National Autonomous University of Mexico Sierra Papacal Merida Yucatan Mexico
| | - José G Rosas-Jiménez
- Department of Theoretical Biophysics, IMPRS on Cellular Biophysics Max-von-Laue Strasse 3 Frankfurt am Main 60438 Germany
| | - Karla Gonzalez-Ponce
- Institute of Chemistry, Merida Unit, National Autonomous University of Mexico Merida-Tetiz Highway, Km. 4.5 Ucu Yucatan Mexico
| | - Edgar López-López
- Department of Chemistry and Graduate Program in Pharmacology, Center for Research and Advanced Studies of the National Polytechnic Institute Mexico City 07000 Mexico
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry National Autonomous University of Mexico Mexico City 04510 Mexico
| | - Antonio Neme
- Institute for Applied Mathematics and Systems, Merida Research Unit, National Autonomous University of Mexico Sierra Papacal Merida Yucatan Mexico
| | - José L Medina-Franco
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry National Autonomous University of Mexico Mexico City 04510 Mexico
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Yao J, Liang X, Xu S, Liu Y, Shui L, Li S, Guo H, Xiao Z, Zhao Y, Zheng M. TRAF2 inhibits senescence in hepatocellular carcinoma cells via regulating the ROMO1/ NAD +/SIRT3/SOD2 axis. Free Radic Biol Med 2024; 211:47-62. [PMID: 38043870 DOI: 10.1016/j.freeradbiomed.2023.11.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/16/2023] [Accepted: 11/28/2023] [Indexed: 12/05/2023]
Abstract
The suppression of tumor proliferation via cellular senescence has emerged as a promising approach for anti-tumor therapy. Tumor necrosis factor receptor-associated factor 2 (TRAF2), an adaptor protein involved in the NF-κB signaling pathway and reactive oxygen species (ROS) production, has been implicated in hepatocellular carcinoma (HCC) proliferation. However, little is currently known about whether TRAF2 promotes HCC development by inhibiting cellular senescence. Replicative senescence model and IR-induced mouse model demonstrated that TRAF2 expression was decrease in senescence cells or liver tissues. Depletion of TRAF2 could inhibit proliferation and arrest the cell cycle via activating p53/p21WAF1 and p16INK4a/pRb signaling pathways in HCC cells and eventually lead to cellular senescence. Mechanistically, TRAF2 deficiency increased the expression of mitochondrial protein reactive oxygen species modulator 1 (ROMO1) and subsequently activated the NAD+/SIRT3/SOD2 pathway to promote the production of ROS and cause mitochondrial dysfunction, which eventually contributed to DNA damage response (DDR). Our findings demonstrate that TRAF2 deficiency inhibits the proliferation of HCC by promoting senescence. Therefore, targeting TRAF2 through various approaches holds therapeutic potential for treating HCC.
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Affiliation(s)
- Jiping Yao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310003, China; Department of Gastroenterology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, 310014, China
| | - Xue Liang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310003, China; Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Siduo Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310003, China
| | - Yanning Liu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310003, China
| | - Liyan Shui
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310003, China
| | - Shuangshuang Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310003, China
| | - Huiting Guo
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310003, China
| | - Zhengyun Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310003, China
| | - Yongchao Zhao
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310003, China; Cancer Center, Zhejiang University, Hangzhou, China; Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310029, China.
| | - Min Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310003, China.
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Teng Z, Pan X, Liu Y, You J, Zhang H, Zhao Z, Qiao Z, Rao Z. Engineering serine hydroxymethyltransferases for efficient synthesis of L-serine in Escherichia coli. BIORESOURCE TECHNOLOGY 2024; 393:130153. [PMID: 38052329 DOI: 10.1016/j.biortech.2023.130153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/01/2023] [Accepted: 12/02/2023] [Indexed: 12/07/2023]
Abstract
L-serine is a high-value amino acid widely used in the food, medicine, and cosmetic industries. However, the low yield of L-serine has limited its industrial production. In this study, a cellular factory for efficient synthesis of L-serine was obtained by engineering the serine hydroxymethyltransferases (SHMT). Firstly, after screening the SHMT from Alcanivorax dieselolei by genome mining, a mutant AdSHMTE266M with high thermal stability was identified through rational design. Subsequently, an iterative saturating mutant library was constructed by using coevolutionary analysis, and a mutant AdSHMTE160L/E193Q with enzyme activity 1.35 times higher than AdSHMT was identified. Additionally, the target protein AdSHMTE160L/E193Q/E266M was efficiently overexpressed by improving its mRNA stability. Finally, combining the substrate addition strategy and system optimization, the optimized strain BL21/pET28a-AdSHMTE160L/E193Q/E266M-5'UTR-REP3S16 produced 106.06 g/L L-serine, which is the highest production to date. This study provides new ideas and insights for the engineering design of SHMT and the industrial production of L-serine.
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Affiliation(s)
- Zixin Teng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Xuewei Pan
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Yunran Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Jiajia You
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Hengwei Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Zhenqiang Zhao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Zhina Qiao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Zhiming Rao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China.
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Hong J, Wang X, Jin H, Chen Y, Jiang Y, Du K, Chen D, Zheng S, Cao L. Environment relevant exposure of perfluorooctanoic acid accelerates the growth of hepatocellular carcinoma cells through mammalian target of rapamycin (mTOR) signal pathway. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 341:122910. [PMID: 37967710 DOI: 10.1016/j.envpol.2023.122910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 10/25/2023] [Accepted: 11/08/2023] [Indexed: 11/17/2023]
Abstract
Perfluorooctanoic acid (PFOA), a synthetic alkyl chain fluorinated compound, has emerged as a persistent organic pollutant of grave concern, casting a shadow over both ecological integrity and humans. Its insidious presence raises alarms due to its capacity to bioaccumulate within the human liver, potentially paving the treacherous path toward liver cancer. Yet, the intricate mechanisms underpinning PFOA's role in promoting the growth of hepatocellular carcinoma (HCC) remain shrouded in ambiguity. Here, we determined the proliferation and transcription changes of HCC after PFOA exposure through integrated experiments including cell culture, nude mice tests, and colony-forming assays. Based on our findings, PFOA effectively promotes the proliferation of HCC cells within the experimental range of concentrations, both in vivo and in vitro. The proliferation efficiency of HCC cells was observed to increase by approximately 10% due to overexposure to PFOA. Additionally, the cancer weight of tumor-bearing nude mice increased by 87.0% (p < 0.05). We systematically evaluated the effects of PFOA on HCC cells and found that PFOA's exposure can selectively activate the PI3K/AKT/mTOR/4E-BP1 signaling pathway, thereby playing a pro-cancer effect on HCC cells Confirmation echoed through western blot assays and inhibitor combination analyses. These insights summon a response to PFOA's dual nature as both an environmental threat and a promoter of liver cancer. Our work illuminates the obscured domain of PFOA-induced hepatoxicity, shedding light on its ties to hepatocellular carcinoma progression.
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Affiliation(s)
- Jiawei Hong
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, PR China; Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310003, PR China; NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, 310003, PR China
| | - Xiaoyan Wang
- Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310003, PR China
| | - Hangbiao Jin
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang, 310032, PR China
| | - Yuanchen Chen
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang, 310032, PR China
| | - Yifan Jiang
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, PR China; Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310003, PR China; NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, 310003, PR China
| | - Keyi Du
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, PR China; Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310003, PR China; NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, 310003, PR China
| | - Diyu Chen
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, PR China; Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310003, PR China; NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, 310003, PR China
| | - Shusen Zheng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, PR China; Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310003, PR China; NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, 310003, PR China
| | - Linping Cao
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, PR China; Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310003, PR China; NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, 310003, PR China.
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Shi Y, Wu S, Zhang X, Cao Y, Zhang L. Lipid metabolism-derived FAAH is a sensitive marker for the prognosis and immunotherapy of osteosarcoma patients. Heliyon 2024; 10:e23499. [PMID: 38169921 PMCID: PMC10758879 DOI: 10.1016/j.heliyon.2023.e23499] [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: 08/16/2023] [Revised: 10/17/2023] [Accepted: 12/05/2023] [Indexed: 01/05/2024] Open
Abstract
Lipid metabolism in cancer refers to the alterations in how cancer cells process and utilize lipids, a type of fat molecule. It was investigated how lipid metabolism relates to osteosarcoma. Genes relevant to lipid metabolism were gathered to create lipid metabolism-associated clusters and locate the dangerous marker. We investigated FAAH's prognostic significance, route annotation, immunotherapy response, and medication prediction. Besides, FAAH is proven to be a potent, dangerous marker that may promote growth and migration and inhibit the apoptosis of osteosarcoma. FAAH exhibits higher expression levels in tumor tissues as compared to normal tissues. In conclusion, FAAH is identified in this work as a potentially dangerous gene and immunotherapy determinant. This study requires more investigation to determine how FAAH influences the immune response in osteosarcoma.
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Affiliation(s)
- Yanbin Shi
- Department of Orthopaedics, The 3rd Xiangya Hospital, Central South University, Changsha, China
| | - Song Wu
- Department of Orthopaedics, The 3rd Xiangya Hospital, Central South University, Changsha, China
| | - Xiaolin Zhang
- The 3rd Xiangya Hospital, Central South University, Changsha, China
| | - Yangbo Cao
- Department of Orthopaedics, The 3rd Xiangya Hospital, Central South University, Changsha, China
| | - Lina Zhang
- Hunan Provincial People's Hospital, Changsha, China
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Meng J, Li S, Niu Z, Bao Z, Niu L. The efficacy of sorafenib against hepatocellular carcinoma is enhanced by 5-aza-mediated inhibition of ID1 promoter methylation. FEBS Open Bio 2024; 14:127-137. [PMID: 37964494 PMCID: PMC10761934 DOI: 10.1002/2211-5463.13734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 09/14/2023] [Accepted: 11/06/2023] [Indexed: 11/16/2023] Open
Abstract
Sorafenib resistance greatly restricts its clinical application in patients with hepatocellular carcinoma (HCC). Numerous studies have reported that ID1 exerts a crucial effect in cancer initiation and development. Our previous research revealed an inhibitory role of ID1 in sorafenib resistance. However, the upstream regulatory mechanism of ID1 expression is unclear. Here, we discovered that ID1 expression is negatively correlated with promoter methylation, which is regulated by DNMT3B. Knockdown of DNMT3B significantly inhibited ID1 methylation status and resulted in an increase of ID1 expression. The demethylating agent 5-aza-2'-deoxycytidine (5-aza) remarkably upregulated ID1 expression. The combination of 5-aza with sorafenib showed a synergistic effect on the inhibition of cell viability.
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Affiliation(s)
- Jing Meng
- Department of Clinical LaboratoryThe Second Hospital of Shandong University, Shandong UniversityJinanChina
| | - Shi Li
- Department of GastroenterologyPeople's Hospital of WeihaiweiWeihaiChina
| | - Zhao‐qing Niu
- Department of Clinical LaboratoryThe Second Hospital of Shandong University, Shandong UniversityJinanChina
| | - Zheng‐qiang Bao
- Cancer CenterThe Second Hospital of Shandong University, Shandong UniversityJinanChina
| | - Lei‐lei Niu
- Department of Clinical LaboratoryThe Second Hospital of Shandong University, Shandong UniversityJinanChina
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Lu S, Liang Y, Li L, Liao S, Zou Y, Yang C, Ouyang D. Inferring circRNA-drug sensitivity associations via dual hierarchical attention networks and multiple kernel fusion. BMC Genomics 2023; 24:796. [PMID: 38129810 PMCID: PMC10734204 DOI: 10.1186/s12864-023-09899-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
Increasing evidence has shown that the expression of circular RNAs (circRNAs) can affect the drug sensitivity of cells and significantly influence drug efficacy. Therefore, research into the relationships between circRNAs and drugs can be of great significance in increasing the comprehension of circRNAs function, as well as contributing to the discovery of new drugs and the repurposing of existing drugs. However, it is time-consuming and costly to validate the function of circRNA with traditional medical research methods. Therefore, the development of efficient and accurate computational models that can assist in discovering the potential interactions between circRNAs and drugs is urgently needed. In this study, a novel method is proposed, called DHANMKF , that aims to predict potential circRNA-drug sensitivity interactions for further biomedical screening and validation. Firstly, multimodal networks were constructed by DHANMKF using multiple sources of information on circRNAs and drugs. Secondly, comprehensive intra-type and inter-type node representations were learned using bi-typed multi-relational heterogeneous graphs, which are attention-based encoders utilizing a hierarchical process. Thirdly, the multi-kernel fusion method was used to fuse intra-type embedding and inter-type embedding. Finally, the Dual Laplacian Regularized Least Squares method (DLapRLS) was used to predict the potential circRNA-drug sensitivity associations using the combined kernel in circRNA and drug spaces. Compared with the other methods, DHANMKF obtained the highest AUC value on two datasets. Code is available at https://github.com/cuntjx/DHANMKF .
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Affiliation(s)
- Shanghui Lu
- Faculty of Innovation Enginee, Macau University of Science and Technology, Avenida Wai Long, Taipa, 999078, Macao, Macao Special Administrative Region of China, China
- School of Mathematics and Physics, Hechi University, No.42, Longjiang, 546300, Guangxi, China
| | - Yong Liang
- Faculty of Innovation Enginee, Macau University of Science and Technology, Avenida Wai Long, Taipa, 999078, Macao, Macao Special Administrative Region of China, China.
- Peng Cheng Laboratory, Shenzhen, 518055, Guangdong, China.
| | - Le Li
- Faculty of Innovation Enginee, Macau University of Science and Technology, Avenida Wai Long, Taipa, 999078, Macao, Macao Special Administrative Region of China, China
| | - Shuilin Liao
- Faculty of Innovation Enginee, Macau University of Science and Technology, Avenida Wai Long, Taipa, 999078, Macao, Macao Special Administrative Region of China, China
| | - Yongfu Zou
- School of Mathematics and Physics, Hechi University, No.42, Longjiang, 546300, Guangxi, China
| | - Chengjun Yang
- School of Artificial Intelligence and Manufacturing, Hechi University, No.42, Longjiang, 546300, Guangxi, China
| | - Dong Ouyang
- Faculty of Innovation Enginee, Macau University of Science and Technology, Avenida Wai Long, Taipa, 999078, Macao, Macao Special Administrative Region of China, China
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Wang C, Ouyang S, Zhu X, Jiang Y, Lu Z, Gong P. Myricetin suppresses traumatic brain injury-induced inflammatory response via EGFR/AKT/STAT pathway. Sci Rep 2023; 13:22764. [PMID: 38123650 PMCID: PMC10733425 DOI: 10.1038/s41598-023-50144-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023] Open
Abstract
Traumatic brain injury (TBI) is a common disease in neurosurgery with a high fatality and disability rate which imposes a huge burden on society and patient's family. Inhibition of neuroinflammation caused by microglia activation is a reasonable strategy to promote neurological recovery after TBI. Myricetin is a natural flavonoid that has shown good therapeutic effects in a variety of neurological disease models, but its therapeutic effect on TBI is not clear. We demonstrated that intraperitoneal injection of appropriate doses of myricetin significantly improved recovery of neurological function after TBI in Sprague Dawley rats and inhibited excessive inflammatory responses around the lesion site. Myricetin dramatically reduced the expression of toxic microglia markers generated by TBI and LPS, according to the outcomes of in vivo and in vitro tests. In particular, the expression of inducible nitric oxide synthase, cyclooxygenase 2, and some pro-inflammatory cytokines was reduced, which protected learning and memory functions in TBI rats. Through network pharmacological analysis, we found that myricetin may inhibit microglia hyperactivation through the EGFR-AKT/STAT pathway. These findings imply that myricetin is a promising treatment option for the management of neuroinflammation following TBI.
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Affiliation(s)
- Chenxing Wang
- Department of Neurosurgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, Jiangsu, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China
| | - Siguang Ouyang
- Department of Neurosurgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, Jiangsu, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China
| | - Xingjia Zhu
- Department of Neurosurgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, Jiangsu, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China
| | - Yi Jiang
- Department of Neurosurgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, Jiangsu, China
| | - Zhichao Lu
- Department of Neurosurgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, Jiangsu, China.
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China.
| | - Peipei Gong
- Department of Neurosurgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, Jiangsu, China.
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Li G, Zeng F, Luo J, Liang C, Xiao Q. MNCLCDA: predicting circRNA-drug sensitivity associations by using mixed neighbourhood information and contrastive learning. BMC Med Inform Decis Mak 2023; 23:291. [PMID: 38110886 PMCID: PMC10729363 DOI: 10.1186/s12911-023-02384-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 12/01/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND circRNAs play an important role in drug resistance and cancer development. Recently, many studies have shown that the expressions of circRNAs in human cells can affect the sensitivity of cells to therapeutic drugs, thus significantly influencing the therapeutic effects of these drugs. Traditional biomedical experiments required to verify this sensitivity relationship are not only time-consuming but also expensive. Hence, the development of an efficient computational approach that can accurately predict the novel associations between drug sensitivities and circRNAs is a crucial and pressing need. METHODS In this research, we present a novel computational framework called MNCLCDA, which aims to predict the potential associations between drug sensitivities and circRNAs to assist with medical research. First, MNCLCDA quantifies the similarity between the given drug and circRNA using drug structure information, circRNA gene sequence information, and GIP kernel information. Due to the existence of noise in similarity information, we employ a preprocessing approach based on random walk with restart for similarity networks to efficiently capture the useful features of circRNAs and drugs. Second, we use a mixed neighbourhood graph convolutional network to obtain the neighbourhood information of nodes. Then, a graph-based contrastive learning method is used to enhance the robustness of the model, and finally, a double Laplace-regularized least-squares method is used to predict potential circRNA-drug associations through the kernel matrices in the circRNA and drug spaces. RESULTS Numerous experimental results show that MNCLCDA outperforms six other advanced methods. In addition, the excellent performance of our proposed model in case studies illustrates that MNCLCDA also has the ability to predict the associations between drug sensitivity and circRNA in practical situations. CONCLUSIONS After a large number of experiments, it is illustrated that MNCLCDA is an efficient tool for predicting the potential associations between drug sensitivities and circRNAs, thereby can provide some guidance for clinical trials.
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Affiliation(s)
- Guanghui Li
- School of Information Engineering, East China Jiaotong University, Nanchang, China.
| | - Feifan Zeng
- School of Information Engineering, East China Jiaotong University, Nanchang, China
| | - Jiawei Luo
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China.
| | - Cheng Liang
- School of Information Science and Engineering, Shandong Normal University, Jinan, China
| | - Qiu Xiao
- College of Information Science and Engineering, Hunan Normal University, Changsha, China
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Azemin WA, Ishak NF, Saedin MAA, Shamsir MS, Razali SA. Molecular docking and simulation studies of Chloroquine, Rimantadine and CAP-1 as potential repurposed antivirals for decapod iridescent virus 1 (DIV1). FISH AND SHELLFISH IMMUNOLOGY REPORTS 2023; 5:100120. [PMID: 37854946 PMCID: PMC10579962 DOI: 10.1016/j.fsirep.2023.100120] [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] [Indexed: 10/20/2023] Open
Abstract
Drug repurposing is a methodology of identifying new therapeutic use for existing drugs. It is a highly efficient, time and cost-saving strategy that offers an alternative approach to the traditional drug discovery process. Past in-silico studies involving molecular docking have been successful in identifying potential repurposed drugs for the various treatment of diseases including aquaculture diseases. The emerging shrimp hemocyte iridescent virus (SHIV) or Decapod iridescent virus 1 (DIV1) is a viral pathogen that causes severe disease and high mortality (80 %) in farmed shrimps caused serious economic losses and presents a new threat to the shrimp farming industry. Therefore, effective antiviral drugs are critically needed to control DIV1 infections. The aim of this study is to investigate the interaction of potential existing antiviral drugs, Chloroquine, Rimantadine, and CAP-1 with DIV1 major capsid protein (MCP) with the intention of exploring the potential of drug repurposing. The interaction of the DIV1 MCP and three antivirals were characterised and analysed using molecular docking and molecular dynamics simulation. The results showed that CAP-1 is a more promising candidate against DIV1 with the lowest binding energy of -8.46 kcal/mol and is more stable compared to others. We speculate that CAP-1 binding may induce the conformational changes in the DIV1 MCP structure by phosphorylating multiple residues (His123, Tyr162, and Thr395) and ultimately block the viral assembly and maturation of DIV1 MCP. To the best of our knowledge, this is the first report regarding the structural characterisation of DIV1 MCP docked with repurposing drugs.
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Affiliation(s)
- Wan-Atirah Azemin
- School of Biological Sciences, Universiti Sains Malaysia, Pulau, Minden, Pinang 11800, Malaysia
| | - Nur Farahin Ishak
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Nerus, Kuala, Terengganu 21030, Malaysia
| | - Mohamad Amirul Asyraf Saedin
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Nerus, Kuala, Terengganu 21030, Malaysia
| | - Mohd Shahir Shamsir
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, UTM, Johor Bahru 81310, Malaysia
| | - Siti Aisyah Razali
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Nerus, Kuala, Terengganu 21030, Malaysia
- Biological Security and Sustainability Research Interest Group (BIOSES), Universiti Malaysia Terengganu, Nerus, Kuala, Terengganu 21030, Malaysia
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Sun Q, Jin H, Li W, Tong P, Yuan W. Study of the curative effect of Zhang's Xibi formula and its underlying mechanism involving inhibition of inflammatory responses and delay of knee osteoarthritis. J Orthop Surg Res 2023; 18:963. [PMID: 38098028 PMCID: PMC10722826 DOI: 10.1186/s13018-023-04453-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 12/07/2023] [Indexed: 12/17/2023] Open
Abstract
OBJECTIVE To verify the clinical efficacy of Zhang's Xibi formula (ZSXBF) and explain the mechanism underlying its therapeutic effect. METHODS Preliminary elucidation of the clinical efficacy of ZSXBF in treating KOA in self-control studies, exploration of its mechanism of action with network pharmacology methods, and validation in animal experiments. RESULTS In clinical studies, ZSXBF administration effectively improved patient quality of life and reduce pain. Network pharmacology was used to explore the possible mechanisms underlying its treatment effect, and after verification in clinical experience and animal experiments, it was found that ZSXBF regulated the expression of immune-related proteins such as IL-17, ERK1, and TP53 in mouse knee joints. CONCLUSION ZSXBF, which is a traditional Chinese medicine compound that is used to clear heat and detoxify, can effectively improve the clinical symptoms of KOA patients, and its underlying mechanism includes the regulation of human immune-related proteins.
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Affiliation(s)
- Qi Sun
- Institute of Orthopedics and Traumatology of Zhejiang Province, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Zhejiang Chinese Medical University, Hangzhou, China
- Fuyang TCM Hospital of Orthopedics Affiliated to Zhejiang, Chinese Medical University (Hangzhou Fuyang Hospital of Orthopedics of Traditional Chinese Medicine), Hangzhou, China
- Department of Orthopedic, Luoyang Orthopedic Hospital of Henan Province, Luoyang, China
| | - Hongting Jin
- Institute of Orthopedics and Traumatology of Zhejiang Province, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Zhejiang Chinese Medical University, Hangzhou, China
| | - Wuyin Li
- Department of Orthopedic, Luoyang Orthopedic Hospital of Henan Province, Luoyang, China
| | - Peijian Tong
- Institute of Orthopedics and Traumatology of Zhejiang Province, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Zhejiang Chinese Medical University, Hangzhou, China
| | - Wenhua Yuan
- Institute of Orthopedics and Traumatology of Zhejiang Province, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Zhejiang Chinese Medical University, Hangzhou, China.
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Visonà G, Duroux D, Miranda L, Sükei E, Li Y, Borgwardt K, Oliver C. Multimodal learning in clinical proteomics: enhancing antimicrobial resistance prediction models with chemical information. Bioinformatics 2023; 39:btad717. [PMID: 38001023 PMCID: PMC10724849 DOI: 10.1093/bioinformatics/btad717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 11/08/2023] [Accepted: 11/23/2023] [Indexed: 11/26/2023] Open
Abstract
MOTIVATION Large-scale clinical proteomics datasets of infectious pathogens, combined with antimicrobial resistance outcomes, have recently opened the door for machine learning models which aim to improve clinical treatment by predicting resistance early. However, existing prediction frameworks typically train a separate model for each antimicrobial and species in order to predict a pathogen's resistance outcome, resulting in missed opportunities for chemical knowledge transfer and generalizability. RESULTS We demonstrate the effectiveness of multimodal learning over proteomic and chemical features by exploring two clinically relevant tasks for our proposed deep learning models: drug recommendation and generalized resistance prediction. By adopting this multi-view representation of the pathogenic samples and leveraging the scale of the available datasets, our models outperformed the previous single-drug and single-species predictive models by statistically significant margins. We extensively validated the multi-drug setting, highlighting the challenges in generalizing beyond the training data distribution, and quantitatively demonstrate how suitable representations of antimicrobial drugs constitute a crucial tool in the development of clinically relevant predictive models. AVAILABILITY AND IMPLEMENTATION The code used to produce the results presented in this article is available at https://github.com/BorgwardtLab/MultimodalAMR.
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Affiliation(s)
- Giovanni Visonà
- Department of Empirical Inference, Max Planck Institute for Intelligent Systems, Max-Planck-Ring 4, Tübingen 72076, Germany
| | - Diane Duroux
- BIO3—GIGA-R Medical Genomics, University of Liège, Avenue de l’Hôpital 11, Liège 4000, Belgium
- ETH AI Center, ETH Zürich, Andreasstrasse 5, Zürich 8092, Switzerland
| | - Lucas Miranda
- Research Group Statistical Genetics, Max Planck Institute of Psychiatry, Kraepelinstraße 10, München 80804, Germany
| | - Emese Sükei
- Department of Signal Theory and Communications, Universidad Carlos III de Madrid, Leganés 28911, Spain
| | - Yiran Li
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - Karsten Borgwardt
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
- Swiss Institute for Bioinformatics (SIB), Amphipôle, Quartier UNIL-Sorge, Lausanne 1015, Switzerland
- Department of Machine Learning and Systems Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Carlos Oliver
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
- Swiss Institute for Bioinformatics (SIB), Amphipôle, Quartier UNIL-Sorge, Lausanne 1015, Switzerland
- Department of Machine Learning and Systems Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
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Elmaidomy AH, El Zawily A, Salem AK, Altemani FH, Algehainy NA, Altemani AH, Rateb ME, Abdelmohsen UR, Shady NH. New cytotoxic dammarane type saponins from Ziziphus spina-christi. Sci Rep 2023; 13:20612. [PMID: 37996449 PMCID: PMC10667233 DOI: 10.1038/s41598-023-46841-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 11/06/2023] [Indexed: 11/25/2023] Open
Abstract
Cancer is the world's second-leading cause of death. Drug development efforts frequently focus on medicinal plants since they are a valuable source of anticancer medications. A phytochemical investigation of the edible Ziziphus spina-christi (F. Rhamnaceae) leaf extract afforded two new dammarane type saponins identified as christinin E and F (1, 2), along with the known compound christinin A (3). Different cancer cell lines, such as lung cancer (A549), glioblastoma (U87), breast cancer (MDA-MB-231), and colorectal carcinoma (CT-26) cell lines, were used to investigate the extracted compounds' cytotoxic properties. Our findings showed significant effects on all the tested cell lines at varying concentrations (1, 5, 10, and 20 µg/mL). The three compounds exhibited potent activity at low concentrations (< 10 μg/mL), as evidenced by their low IC50 values. To further investigate the complex relationships between these identified cancer-relevant biological targets and to identify critical targets in the pathogenesis of the disease, we turned to network pharmacology and in silico-based investigations. Following this, in silico-based analysis (e.g., inverse docking, ΔG calculation, and molecular dynamics simulation) was performed on the structures of the isolated compounds to identify additional potential targets for these compounds and their likely interactions with various signalling pathways relevant to this disease. Based on our findings, Z. spina-christi's compounds showed promise as potential anti-cancer therapeutic leads in the future.
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Affiliation(s)
- Abeer H Elmaidomy
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62511, Egypt
| | - Amr El Zawily
- Department of Plant and Microbiology, Faculty of Science, Damanhour University, Damanhour, 22511, Egypt.
- Division of Pharmaceutics and Translational Therapeutics, College of Pharmacy, University of Iowa, Iowa City, IA, 52242, USA.
| | - Aliasger K Salem
- Division of Pharmaceutics and Translational Therapeutics, College of Pharmacy, University of Iowa, Iowa City, IA, 52242, USA
| | - Faisal H Altemani
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, 71491, Tabuk, Saudi Arabia
| | - Naseh A Algehainy
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, 71491, Tabuk, Saudi Arabia
| | - Abdullah H Altemani
- Department of Family and Community Medicine, Faculty of Medicine, University of Tabuk, 71491, Tabuk, Saudi Arabia
| | - Mostafa E Rateb
- School of Computing, Engineering & Physical Sciences, University of the West of Scotland, Paisley, PA1 2BE, UK
| | - Usama Ramadan Abdelmohsen
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia, 61519, Egypt.
- Department of Pharmacognosy, Faculty of Pharmacy, Deraya University, Universities Zone, New Minia, 61111, Egypt.
| | - Nourhan Hisham Shady
- Department of Pharmacognosy, Faculty of Pharmacy, Deraya University, Universities Zone, New Minia, 61111, Egypt
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Jia X, Wang T, Zhu H. Advancing Computational Toxicology by Interpretable Machine Learning. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:17690-17706. [PMID: 37224004 PMCID: PMC10666545 DOI: 10.1021/acs.est.3c00653] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 05/05/2023] [Accepted: 05/05/2023] [Indexed: 05/26/2023]
Abstract
Chemical toxicity evaluations for drugs, consumer products, and environmental chemicals have a critical impact on human health. Traditional animal models to evaluate chemical toxicity are expensive, time-consuming, and often fail to detect toxicants in humans. Computational toxicology is a promising alternative approach that utilizes machine learning (ML) and deep learning (DL) techniques to predict the toxicity potentials of chemicals. Although the applications of ML- and DL-based computational models in chemical toxicity predictions are attractive, many toxicity models are "black boxes" in nature and difficult to interpret by toxicologists, which hampers the chemical risk assessments using these models. The recent progress of interpretable ML (IML) in the computer science field meets this urgent need to unveil the underlying toxicity mechanisms and elucidate the domain knowledge of toxicity models. In this review, we focused on the applications of IML in computational toxicology, including toxicity feature data, model interpretation methods, use of knowledge base frameworks in IML development, and recent applications. The challenges and future directions of IML modeling in toxicology are also discussed. We hope this review can encourage efforts in developing interpretable models with new IML algorithms that can assist new chemical assessments by illustrating toxicity mechanisms in humans.
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Affiliation(s)
- Xuelian Jia
- Department
of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Tong Wang
- Department
of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Hao Zhu
- Department
of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
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40
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Qiao H, Li H. PLP2 Could Be a Prognostic Biomarker and Potential Treatment Target in Glioblastoma Multiforme. Pharmgenomics Pers Med 2023; 16:991-1009. [PMID: 37964785 PMCID: PMC10642424 DOI: 10.2147/pgpm.s425251] [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: 07/09/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023] Open
Abstract
Objective This study aimed to discern the association between PLP2 expression, its biological significance, and the extent of immune infiltration in human GBM. Methods Utilizing the GEPIA2 and TCGA databases, we contrasted the expression levels of PLP2 in GBM against normal tissue. We utilized GEPIA2 and LinkedOmics for survival analysis, recognized genes co-expressed with PLP2 via cBioPortal and GEPIA2, and implemented GO and KEGG analyses. The STRING database facilitated the construction of protein-protein interaction networks. We evaluated the relationship of PLP2 with tumor immune infiltrates using ssGSEA and the TIMER 2.0 database. An IHC assay assessed PLP2 and PDL-1 expression in GBM tissue, and the Drugbank database aided in identifying potential PLP2-targeting compounds. Molecular docking was accomplished using Autodock Vina 1.2.2. Results PLP2 expression was markedly higher in GBM tissues in comparison to normal tissues. High PLP2 expression correlated with a decrease in overall survival across two databases. Functional analyses highlighted a focus of PLP2 functions within leukocyte. Discrepancies in PLP2 expression were evident in immune infiltration, impacting CD4+ T cells, neutrophils, myeloid dendritic cells, and macrophages. There was a concomitant increase in PLP2 and PD-L1 expression in GBM tissues, revealing a link between the two. Molecular docking with ethosuximide and praziquantel yielded scores of -7.441 and -4.295 kcal/mol, correspondingly. Conclusion PLP2's upregulation in GBM may adversely influence the lifespan of GBM patients. The involvement of PLP2 in pathways linked to leukocyte function is suggested. The positive correlation between PLP2 and PD-L1 could provide insights into PLP2's role in glioma modulation. Our research hints at PLP2's potential as a therapeutic target for GBM, with ethosuximide and praziquantel emerging as potential treatment candidates, especially emphasizing the potential of these compounds in GBM treatment targeting PLP2.
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Affiliation(s)
- Hao Qiao
- The Affiliated Hospital of Qingdao University, Qingdao, Shandong, People’s Republic of China
| | - Huanting Li
- The Affiliated Hospital of Qingdao University, Qingdao, Shandong, People’s Republic of China
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Júnior MA, Silva LC, Rocha OB, Oliveira AA, Portis IG, Alonso A, Alonso L, Silva KS, Gomes MN, Andrade CH, Soares CM, Pereira M. Proteomic identification of metabolic changes in Paracoccidioides brasiliensis induced by a nitroheteroarylchalcone. Future Microbiol 2023; 18:1077-1093. [PMID: 37424510 DOI: 10.2217/fmb-2022-0150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2023] Open
Abstract
Aim: To access the metabolic changes caused by a chalcone derivative (LabMol-75) through a proteomic approach. Methods: Proteomic analysis was performed after 9 h of Paracoccidioides brasiliensis yeast (Pb18) cell incubation with the LabMol-75 at MIC. The proteomic findings were validated through in vitro and in silico assays. Results: Exposure to the compound led to the downregulation of proteins associated with glycolysis and gluconeogenesis, β-oxidation, the citrate cycle and the electron transport chain. Conclusion: LabMol-75 caused an energetic imbalance in the fungus metabolism and deep oxidative stress. Additionally, the in silico molecular docking approach pointed to this molecule as a putative competitive inhibitor of DHPS.
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Affiliation(s)
- Marcos Abc Júnior
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Lívia C Silva
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Olivia B Rocha
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Amanda A Oliveira
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Igor G Portis
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Antonio Alonso
- Institute of Physics, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Lais Alonso
- Institute of Physics, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Kleber Sf Silva
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Marcelo N Gomes
- InsiChem, Goiás State University, Anápolis, Goiás, Brazil
- Faculdade Metropolitana de Anápolis, Anápolis, Goiás, Brazil
| | - Carolina H Andrade
- Laboratory for Molecular Modeling & Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Célia Ma Soares
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Maristela Pereira
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
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Zhu W, Huang J, Wu J, Wu C, Ye F, Li X, Lai W. Inflammation-related signature for prognostic prediction, tumor immune, genomic heterogeneity, and drug choices in prostate cancer: Integrated analysis of bulk and single-cell RNA-sequencing. Heliyon 2023; 9:e21174. [PMID: 37920511 PMCID: PMC10618505 DOI: 10.1016/j.heliyon.2023.e21174] [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: 04/24/2023] [Revised: 09/10/2023] [Accepted: 10/17/2023] [Indexed: 11/04/2023] Open
Abstract
Background Prostate cancer (PCa) ranks as the second most prevalent malignancy among males on a global scale. Accumulating evidence suggests that inflammation has an intricate relationship with tumorigenesis, tumor progression and tumor immune microenvironment. However, the overall impact of inflammation-related genes on the clinical prognosis and tumor immunity in PCa remains unclear. Methods Machine learning methods were utilized to construct and validate a signature using The Cancer Genome Atlas (TCGA) for training, while the Memorial Sloan Kettering Cancer Center (MSKCC) and GSE70769 cohorts for independent validation. The efficacy of the signature in predicting outcomes and its clinical utility were assessed through a series of investigations encompassing in vitro experiments, survival analysis, and nomogram development. The association between the signature and precision medicine was explored via tumor immunity, genomic heterogeneity, therapeutic response, and molecular docking analyses, using bulk and single-cell RNA-sequencing data. Results We identified 7 inflammation-related genes with prognostic significance and developed an inflammation-related prognostic signature (IRPS) with 6 genes. Furthermore, we demonstrated that both the IRPS and a nomogram integrating risk score and pathologic T stage exhibited excellent predictive ability for the survival outcomes in PCa patients. Moreover, the IRPS was found to be significantly associated with the tumor immune, genomic heterogeneity, therapeutic response, and drug selection. Conclusion IRPS can serve as a reliable predictor for PCa patients. The signature may provide clinicians with valuable information on the efficacy of therapy and help personalize treatment for PCa patients.
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Affiliation(s)
- Weian Zhu
- Department of Urology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
| | - Jiongduan Huang
- Department of Urology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
| | - Jianjie Wu
- Department of Urology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
| | - Chenglun Wu
- Department of Urology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
| | - Fengxi Ye
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Xiang Li
- Department of Emergency Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Wenjie Lai
- Department of Urology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
- Laboratory of Biomaterials and Translational Medicine, Center for Nanomedicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
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43
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Shi Y, Zhu R. Analysis of damage-associated molecular patterns in amyotrophic lateral sclerosis based on ScRNA-seq and bulk RNA-seq data. Front Neurosci 2023; 17:1259742. [PMID: 37942135 PMCID: PMC10628000 DOI: 10.3389/fnins.2023.1259742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 10/11/2023] [Indexed: 11/10/2023] Open
Abstract
Background Amyotrophic Lateral Sclerosis (ALS) is a devastating neurodegenerative disorder characterized by the progressive loss of motor neurons. Despite extensive research, the exact etiology of ALS remains elusive. Emerging evidence highlights the critical role of the immune system in ALS pathogenesis and progression. Damage-Associated Molecular Patterns (DAMPs) are endogenous molecules released by stressed or damaged cells, acting as danger signals and activating immune responses. However, their specific involvement in ALS remains unclear. Methods We obtained single-cell RNA sequencing (scRNA-seq) data of ALS from the primary motor cortex in the Gene Expression Omnibus (GEO) database. To better understand genes associated with DAMPs, we performed analyses on cell-cell communication and trajectory. The abundance of immune-infiltrating cells was assessed using the single-sample Gene Set Enrichment Analysis (ssGSEA) method. We performed univariate Cox analysis to construct the risk model and utilized the least absolute shrinkage and selection operator (LASSO) analysis. Finally, we identified potential small molecule drugs targeting ALS by screening the Connectivity Map database (CMap) and confirmed their potential through molecular docking analysis. Results Our study annotated 10 cell types, with the expression of genes related to DAMPs predominantly observed in microglia. Analysis of intercellular communication revealed 12 ligand-receptor pairs in the pathways associated with DAMPs, where microglial cells acted as ligands. Among these pairs, the SPP1-CD44 pair demonstrated the greatest contribution. Furthermore, trajectory analysis demonstrated distinct differentiation fates of different microglial states. Additionally, we constructed a risk model incorporating four genes (TRPM2, ROCK1, HSP90AA1, and HSPA4). The validity of the risk model was supported by multivariate analysis. Moreover, external validation from dataset GSE112681 confirmed the predictive power of the model, which yielded consistent results with datasets GSE112676 and GSE112680. Lastly, the molecular docking analysis suggested that five compounds, namely mead-acid, nifedipine, nifekalant, androstenol, and hydrastine, hold promise as potential candidates for the treatment of ALS. Conclusion Taken together, our study demonstrated that DAMP entities were predominantly observed in microglial cells within the context of ALS. The utilization of a prognostic risk model can accurately predict ALS patient survival. Additionally, genes related to DAMPs may present viable drug targets for ALS therapy.
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Affiliation(s)
| | - Ruixia Zhu
- Department of Neurology, The First Affiliated Hospital of China Medical University, Shenyang, China
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Ou S, Chen H, Wang H, Ye J, Liu H, Tao Y, Ran S, Mu X, Liu F, Zhu S, Luo K, Guan Z, Jin Y, Huang R, Song Y, Liu SL. Fusobacterium nucleatum upregulates MMP7 to promote metastasis-related characteristics of colorectal cancer cell via activating MAPK(JNK)-AP1 axis. J Transl Med 2023; 21:704. [PMID: 37814323 PMCID: PMC10561506 DOI: 10.1186/s12967-023-04527-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 09/15/2023] [Indexed: 10/11/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is the third most common malignant tumor. Fusobacterium nucleatum (F. nucleatum) is overabundant in CRC and associated with metastasis, but the role of F. nucleatum in CRC cell migration and metastasis has not been fully elucidated. METHODS Differential gene analysis, protein-protein interaction, robust rank aggregation analysis, functional enrichment analysis, and gene set variation analysis were used to figure out the potential vital genes and biological functions affected by F. nucleatum infection. The 16S rDNA sequencing and q-PCR were used to detect the abundance of F. nucleatum in tissues and stools. Then, we assessed the effect of F. nucleatum on CRC cell migration by wound healing and transwell assays, and confirmed the role of Matrix metalloproteinase 7 (MMP7) induced by F. nucleatum in cell migration. Furthermore, we dissected the mechanisms involved in F. nucleatum induced MMP7 expression. We also investigated the MMP7 expression in clinical samples and its correlation with prognosis in CRC patients. Finally, we screened out potential small molecular drugs that targeted MMP7 using the HERB database and molecular docking. RESULTS F. nucleatum infection altered the gene expression profile and affected immune response, inflammation, biosynthesis, metabolism, adhesion and motility related biological functions in CRC. F. nucleatum was enriched in CRC and promoted the migration of CRC cell by upregulating MMP7 in vitro. MMP7 expression induced by F. nucleatum infection was mediated by the MAPK(JNK)-AP1 axis. MMP7 was highly expressed in CRC and correlated with CMS4 and poor clinical prognosis. Small molecular drugs such as δ-tocotrienol, 3,4-benzopyrene, tea polyphenols, and gallic catechin served as potential targeted therapeutic drugs for F. nucleatum induced MMP7 in CRC. CONCLUSIONS Our study showed that F. nucleatum promoted metastasis-related characteristics of CRC cell by upregulating MMP7 via MAPK(JNK)-AP1 axis. F. nucleatum and MMP7 may serve as potential therapeutic targets for repressing CRC advance and metastasis.
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Affiliation(s)
- Suwen Ou
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Haipeng Chen
- Department of Colorectal Surgery, National Clinical Research Center of Cancer/Cancer Hospital, National Cancer Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Hufei Wang
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - Jinhua Ye
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - Huidi Liu
- Genomics Research Center (Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
- Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University-University of Calgary, Harbin Medical University, Harbin, 150081, China
| | - Yangbao Tao
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - Songlin Ran
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - Xiaoqin Mu
- Genomics Research Center (Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
- Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University-University of Calgary, Harbin Medical University, Harbin, 150081, China
| | - Fangzhou Liu
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - Shuang Zhu
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - Kangjia Luo
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
- Department of Gastrointestinal Surgery, The Affiliated Hospital of Medical School of Ningbo University, Ningbo, 315020, China
| | - Zilong Guan
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150000, China
| | - Yinghu Jin
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - Rui Huang
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China.
| | - Yanni Song
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China.
| | - Shu-Lin Liu
- Genomics Research Center (Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province), College of Pharmacy, Harbin Medical University, Harbin, 150081, China.
- Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University-University of Calgary, Harbin Medical University, Harbin, 150081, China.
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, T2N 4N1, Canada.
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Zhong Y, Zheng H, Chen X, Zhao Y, Gao T, Dong H, Luo H, Weng Z. DDI-GCN: Drug-drug interaction prediction via explainable graph convolutional networks. Artif Intell Med 2023; 144:102640. [PMID: 37783544 DOI: 10.1016/j.artmed.2023.102640] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 03/21/2023] [Accepted: 08/20/2023] [Indexed: 10/04/2023]
Abstract
Drug-drug interactions (DDI) may lead to unexpected side effects, which is a growing concern in both academia and industry. Many DDIs have been reported, but the underlying mechanisms are not well understood. Predicting and understanding DDIs can help researchers to improve drug safety and protect patient health. Here, we introduce DDI-GCN, a method that utilizes graph convolutional networks (GCN) to predict DDIs based on chemical structures. We demonstrate that this method achieves state-of-the-art prediction performance on the independent hold-out set. It can also provide visualization of structural features associated with DDIs, which can help us to study the underlying mechanisms. To make it easy and accessible to use, we developed a web server for DDI-GCN, which is freely available at http://wengzq-lab.cn/ddi/.
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Affiliation(s)
- Yi Zhong
- The Center for Big Data Research in Burns and Trauma, College of Computer and Data Science/College of Software, Fuzhou University, Fujian Province, China
| | - Houbing Zheng
- Department of Plastic Surgery, the First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Xiaoming Chen
- The Center for Big Data Research in Burns and Trauma, College of Computer and Data Science/College of Software, Fuzhou University, Fujian Province, China
| | - Yu Zhao
- The Center for Big Data Research in Burns and Trauma, College of Computer and Data Science/College of Software, Fuzhou University, Fujian Province, China
| | - Tingfang Gao
- College of Biological Science and Engineering, Fuzhou University, Fujian Province, China
| | - Huiqun Dong
- College of Biological Science and Engineering, Fuzhou University, Fujian Province, China
| | - Heng Luo
- The Center for Big Data Research in Burns and Trauma, College of Computer and Data Science/College of Software, Fuzhou University, Fujian Province, China; MetaNovas Biotech Inc., Foster City, CA, USA.
| | - Zuquan Weng
- College of Biological Science and Engineering, Fuzhou University, Fujian Province, China; The Center for Big Data Research in Burns and Trauma, College of Computer and Data Science/College of Software, Fuzhou University, Fujian Province, China; Department of Plastic Surgery, the First Affiliated Hospital of Fujian Medical University, Fuzhou, China.
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Zhang C, Lei D, Zhou Y, Zhong T, Li X, Ai W, Zheng B, Liu J, Piao Y, Yan Z, Lai Z. Identifying a baicalein-related prognostic signature contributes to prognosis prediction and tumor microenvironment of pancreatic cancer. Front Immunol 2023; 14:1223650. [PMID: 37575248 PMCID: PMC10416623 DOI: 10.3389/fimmu.2023.1223650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 07/12/2023] [Indexed: 08/15/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most malignant and lethal human cancers in the world due to its high metastatic potential, and patients with PDAC have a poor prognosis, yet quite little is understood regarding the underlying biological mechanisms of its high metastatic capacity. Baicalein has a dramatic anti-tumor function in the treatment of different types of cancer. However, the therapeutic effects of baicalein on human PDAC and its mechanisms of action have not been extensively understood. In order to explore the biological characteristic, molecular mechanisms, and potential clinical value of baicalein in inhibiting the metastatic capacity of PDAC. We performed several in vitro, in vivo, and in silico studies. We first examined the potential regulation of baicalein in the metastatic capacity of PDAC cells. We showed that baicalein could dramatically suppress liver metastasis of PDAC cells with highly metastatic potential in mice model. The high-throughput sequencing analysis was employed to explore the biological roles of baicalein in PDAC cells. We found that baicalein might be involved in the infiltration of Cancer-Associated Fibroblasts (CAF) in PDAC. Moreover, a baicalein-related risk model and a lncRNA-related model were built by Cox analysis according to the data set of PDAC from TCGA database which suggested a clinical value of baicalein. Finally, we revealed a potential downstream target of baicalein in PDAC, we proposed that baicalein might contribute to the infiltration of CAF via FGFBP1. Thus, we uncovered a novel role for baicalein in regulation of PDAC liver metastasis that may contribute to its anti-cancer effect. We proposed that baicalein might suppress PDAC liver metastasis via regulation of FGFBP1-mediated CAF infiltration. Our results provide a new perspective on clinical utility of baicalein and open new avenues for the inhibition of liver-metastasis of PDAC.
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Affiliation(s)
- Citing Zhang
- Department of Pharmacy, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University, Shenzhen, Guangdong, China
| | - Defeng Lei
- Department of Hepatobiliary Surgery, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Yan Zhou
- Department of Obstetrics & Carson International Cancer Research Center, Shenzhen University General Hospital and Shenzhen University Clinical Medical Academy, Shenzhen, Guangdong, China
| | - Tongning Zhong
- Department of Hepatobiliary Surgery, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Xuefei Li
- College of Stomatology, Dalian Medical University, Dalian, Liaoning, China
| | - Weipeng Ai
- Department of Pharmacy, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University, Shenzhen, Guangdong, China
| | - Biao Zheng
- Department of Surgery, The First Dongguan Affiliated Hospital, Guangdong Medical University. Dongguan, Guangdong, China
| | - Jikui Liu
- Department of Hepatobiliary Surgery, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Yicui Piao
- Department of Critical Care Medicine, National Cancer Center, Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, Guangdong, China
| | - Zilong Yan
- Department of Hepatobiliary Surgery, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Zhengquan Lai
- Department of Pharmacy, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University, Shenzhen, Guangdong, China
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47
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Abdulrahman N, Honda TJ, Ali A, Abdulrahman N, Vrinceanu D, Shishodia S. Impacts of Indoor Dust Exposure on Human Colonic Cell Viability, Cytotoxicity and Apoptosis. TOXICS 2023; 11:633. [PMID: 37505597 PMCID: PMC10383473 DOI: 10.3390/toxics11070633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/09/2023] [Accepted: 07/18/2023] [Indexed: 07/29/2023]
Abstract
INTRODUCTION Environmental exposure to indoor dust is known to be associated with myriad health conditions, especially among children. Established routes of exposure include inhalation and non-dietary ingestion, which result in the direct exposure of gastrointestinal epithelia to indoor dust. Despite this, little prior research is available on the impacts of indoor dust on the health of human gastrointestinal tissue. METHODS Cultured human colonic (CCD841) cells were exposed for 24 h to standard trace metal dust (TMD) and organic contaminant dust (OD) samples at the following concentrations: 0, 10, 25, 50, 75, 100, 250, and 500 µg/mL. Cell viability was assessed using an MTT assay and protease analysis (glycyl-phenylalanyl-aminofluorocoumarin (GF-AFC)); cytotoxicity was assessed with a lactate dehydrogenase release assay, and apoptosis was assessed using a Caspase-Glo 3/7 activation assay. RESULTS TMD and OD decreased cellular metabolic and protease activity and increased apoptosis and biomarkers of cell membrane damage (LDH) in CCD841 human colonic epithelial cells. Patterns appeared to be, in general, dose-dependent, with the highest TMD and OD exposures associated with the largest increases in apoptosis and LDH, as well as with the largest decrements in metabolic and protease activities. CONCLUSIONS TMD and OD exposure were associated with markers of reduced viability and increased cytotoxicity and apoptosis in human colonic cells. These findings add important information to the understanding of the physiologic effects of indoor dust exposure on human health. The doses used in our study represent a range of potential exposure levels, and the effects observed at the higher doses may not necessarily occur under typical exposure conditions. The effects of long-term, low-dose exposure to indoor dust are still not fully understood and warrant further investigation. Future research should explore these physiological mechanisms to further our understanding and inform public health interventions.
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Affiliation(s)
- Noura Abdulrahman
- Department of Environmental and Interdisciplinary Sciences, Texas Southern University, Houston, TX 77004, USA
| | - Trenton J Honda
- School of Clinical and Rehabilitation Sciences, Northeastern University, Boston, MA 02115, USA
| | - Ayat Ali
- Department of Environmental and Interdisciplinary Sciences, Texas Southern University, Houston, TX 77004, USA
| | - Nabras Abdulrahman
- Department of Environmental and Interdisciplinary Sciences, Texas Southern University, Houston, TX 77004, USA
| | - Daniel Vrinceanu
- Department of Physics, Texas Southern University, Houston, TX 77004, USA
| | - Shishir Shishodia
- Department of Environmental and Interdisciplinary Sciences, Texas Southern University, Houston, TX 77004, USA
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Kawashima H, Watanabe R, Esaki T, Kuroda M, Nagao C, Natsume-Kitatani Y, Ohashi R, Komura H, Mizuguchi K. DruMAP: A Novel Drug Metabolism and Pharmacokinetics Analysis Platform. J Med Chem 2023. [PMID: 37449459 PMCID: PMC10388294 DOI: 10.1021/acs.jmedchem.3c00481] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
We developed a novel drug metabolism and pharmacokinetics (DMPK) analysis platform named DruMAP. This platform consists of a database for DMPK parameters and programs that can predict many DMPK parameters based on the chemical structure of a compound. The DruMAP database includes curated DMPK parameters from public sources and in-house experimental data obtained under standardized conditions; it also stores predicted DMPK parameters produced by our prediction programs. Users can predict several DMPK parameters simultaneously for novel compounds not found in the database. Furthermore, the highly flexible search system enables users to search for compounds as they desire. The current version of DruMAP comprises more than 30,000 chemical compounds, about 40,000 activity values (collected from public databases and in-house data), and about 600,000 predicted values. Our platform provides a simple tool for searching and predicting DMPK parameters and is expected to contribute to the acceleration of new drug development. DruMAP can be freely accessed at: https://drumap.nibiohn.go.jp/.
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Affiliation(s)
- Hitoshi Kawashima
- Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Settsu, Osaka 566-0002, Japan
| | - Reiko Watanabe
- Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Settsu, Osaka 566-0002, Japan
- Laboratory for Computational Biology, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Tsuyoshi Esaki
- Data Science and AI Innovation Research Promotion Center, Shiga University, Hikone, Shiga 522-8522, Japan
| | - Masataka Kuroda
- Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Settsu, Osaka 566-0002, Japan
- Discovery Technology Laboratories, Mitsubishi Tanabe Pharma Corporation, Yokohama, Kanagawa 227-0033, Japan
| | - Chioko Nagao
- Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Settsu, Osaka 566-0002, Japan
- Laboratory for Computational Biology, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yayoi Natsume-Kitatani
- Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Settsu, Osaka 566-0002, Japan
- Institute of Advanced Medical Sciences, Tokushima University, Tokushima, Tokushima 770-8503, Japan
| | - Rikiya Ohashi
- Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Settsu, Osaka 566-0002, Japan
| | - Hiroshi Komura
- University Research Administration Center, Osaka Metropolitan University, Osaka, Osaka 545-0051, Japan
| | - Kenji Mizuguchi
- Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Settsu, Osaka 566-0002, Japan
- Laboratory for Computational Biology, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
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Wu F, Li G, Shen H, Huang J, Liu Z, Zhu Y, Zhong Q, Ou R, Zhang Q, Liu S. Pan-Cancer Analysis Reveals CENPI as a Potential Biomarker and Therapeutic Target in Adrenocortical Carcinoma. J Inflamm Res 2023; 16:2907-2928. [PMID: 37465344 PMCID: PMC10350421 DOI: 10.2147/jir.s408358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/06/2023] [Indexed: 07/20/2023] Open
Abstract
Background Centromere protein I (CENPI) has been shown to affect the tumorigenesis of breast and colorectal cancers. However, its biological role and prognostic value in other kinds of cancer, especially adrenocortical carcinoma (ACC), remained to be further investigated. Methods Various bioinformatics tools were adopted for exploring the significance of differential expression of CENPI in several malignant tumors from databases such as Depmap portal, GTEx, and TCGA. ACC was selected for further analyzed, and information such as clinicopathological features, the prognostic outcome of diverse subgroups, differentially expressed genes (DEGs), co-expression genes, as well as levels of tumor-infiltrating immune cells (TIIC), was extracted from multiple databases. To verify the possibility of CENPI as a therapeutic target in ACC, drug sensitivity assay and si-RNA mediate knockdown of CENPI were carried out. Results The pan-cancer analyses showed that the CENPI mRNA expression levels differed significantly among most cancer types. Additionally, a high precision in cancer prediction and close relation with cancer survival indicated that CENPI could be a potential candidate biomarker to diagnose and predict cancer prognosis. In ACC, CENPI was closely related to multiple clinical characteristics, such as pathological stage and primary therapy outcome. High CENPI levels predicted poor overall survival (OS), progression-free interval (PFI), and disease-specific survival (DSS) of ACC patients, particularly for different clinical subgroups. Moreover, the expression of CENPI showed positive relationship to Th2 cells but negatively related to most of the TIICs. Furthermore, drug sensitivity assay showed that vorinostat inhibit CENPI expression and ACC cell growth. Additionally, si-RNA mediated knockdown of CENPI inhibited ACC cell growth and invasion and showed synergistic anti-proliferation effect with AURKB inhibitor barasertib. Conclusion Pan-cancer analysis demonstrated that CENPI is a potential diagnostic and prognostic biomarker in various cancers as well as an anti-ACC therapeutic target.
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Affiliation(s)
- Feima Wu
- Department of Hematology, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, People’s Republic of China
| | - Guangchao Li
- Department of Hematology, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, People’s Republic of China
| | - Huijuan Shen
- Department of Hematology, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, People’s Republic of China
| | - Jing Huang
- Department of Hematology, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, People’s Republic of China
| | - Zhi Liu
- Department of Hematology, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, People’s Republic of China
| | - Yangmin Zhu
- Department of Hematology, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, People’s Republic of China
| | - Qi Zhong
- Department of Hematology, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, People’s Republic of China
| | - Ruiming Ou
- Department of Hematology, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, People’s Republic of China
| | - Qing Zhang
- Department of Hematology, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, People’s Republic of China
| | - Shuang Liu
- Department of Hematology, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, People’s Republic of China
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50
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Qureshi R, Irfan M, Gondal TM, Khan S, Wu J, Hadi MU, Heymach J, Le X, Yan H, Alam T. AI in drug discovery and its clinical relevance. Heliyon 2023; 9:e17575. [PMID: 37396052 PMCID: PMC10302550 DOI: 10.1016/j.heliyon.2023.e17575] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 06/17/2023] [Accepted: 06/21/2023] [Indexed: 07/04/2023] Open
Abstract
The COVID-19 pandemic has emphasized the need for novel drug discovery process. However, the journey from conceptualizing a drug to its eventual implementation in clinical settings is a long, complex, and expensive process, with many potential points of failure. Over the past decade, a vast growth in medical information has coincided with advances in computational hardware (cloud computing, GPUs, and TPUs) and the rise of deep learning. Medical data generated from large molecular screening profiles, personal health or pathology records, and public health organizations could benefit from analysis by Artificial Intelligence (AI) approaches to speed up and prevent failures in the drug discovery pipeline. We present applications of AI at various stages of drug discovery pipelines, including the inherently computational approaches of de novo design and prediction of a drug's likely properties. Open-source databases and AI-based software tools that facilitate drug design are discussed along with their associated problems of molecule representation, data collection, complexity, labeling, and disparities among labels. How contemporary AI methods, such as graph neural networks, reinforcement learning, and generated models, along with structure-based methods, (i.e., molecular dynamics simulations and molecular docking) can contribute to drug discovery applications and analysis of drug responses is also explored. Finally, recent developments and investments in AI-based start-up companies for biotechnology, drug design and their current progress, hopes and promotions are discussed in this article.
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Affiliation(s)
- Rizwan Qureshi
- College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
- Department of Imaging Physics, MD Anderson Cancer Center, The University of Texas, Houston, USA
| | - Muhammad Irfan
- Faculty of Electrical Engineering, Ghulam Ishaq Khan Institute of Engineering Sciences and Technology, Swabi, Pakistan
| | | | - Sheheryar Khan
- School of Professional Education & Executive Development, The Hong Kong Polytechnic University, Hong Kong
| | - Jia Wu
- Department of Imaging Physics, MD Anderson Cancer Center, The University of Texas, Houston, USA
| | | | - John Heymach
- Department of Thoracic Head and Neck Medical Oncology, Division of Cancer Medicine, The University of Texas, MD Anderson Cancer Center, Houston, USA
| | - Xiuning Le
- Department of Thoracic Head and Neck Medical Oncology, Division of Cancer Medicine, The University of Texas, MD Anderson Cancer Center, Houston, USA
| | - Hong Yan
- Department of Electrical Engineering, City University of Hong Kong, Kowloon, Hong Kong
| | - Tanvir Alam
- College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
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