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Cartas‐Cejudo P, Cortés A, Lachén‐Montes M, Anaya‐Cubero E, Puerta E, Solas M, Fernández‐Irigoyen J, Santamaría E. Neuropathological stage-dependent proteome mapping of the olfactory tract in Alzheimer's disease: From early olfactory-related omics signatures to computational repurposing of drug candidates. Brain Pathol 2024; 34:e13252. [PMID: 38454090 PMCID: PMC11189775 DOI: 10.1111/bpa.13252] [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: 09/27/2023] [Accepted: 02/21/2024] [Indexed: 03/09/2024] Open
Abstract
Alzheimer's disease (AD) is the most common form of dementia, characterized by an early olfactory dysfunction, progressive memory loss, and behavioral deterioration. Albeit substantial progress has been made in characterizing AD-associated molecular and cellular events, there is an unmet clinical need for new therapies. In this study, olfactory tract proteotyping performed in controls and AD subjects (n = 17/group) showed a Braak stage-dependent proteostatic impairment accompanied by the progressive modulation of amyloid precursor protein and tau functional interactomes. To implement a computational repurposing of drug candidates with the capacity to reverse early AD-related olfactory omics signatures (OMSs), we generated a consensual OMSs database compiling differential omics datasets obtained by mass-spectrometry or RNA-sequencing derived from initial AD across the olfactory axis. Using the Connectivity Map-based drug repurposing approach, PKC, EGFR, Aurora kinase, Glycogen synthase kinase, and CDK inhibitors were the top pharmacologic classes capable to restore multiple OMSs, whereas compounds with targeted activity to inhibit PI3K, Insulin-like growth factor 1 (IGF-1), microtubules, and Polo-like kinase (PLK) represented a family of drugs with detrimental potential to induce olfactory AD-associated gene expression changes. To validate the potential therapeutic effects of the proposed drugs, in vitro assays were performed. These validation experiments revealed that pretreatment of human neuron-like SH-SY5Y cells with the EGFR inhibitor AG-1478 showed a neuroprotective effect against hydrogen peroxide-induced damage while the pretreatment with the Aurora kinase inhibitor Reversine reduced amyloid-beta (Aβ)-induced neurotoxicity. Taken together, our data pointed out that OMSs may be useful as substrates for drug repurposing to propose novel neuroprotective treatments against AD.
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Affiliation(s)
- Paz Cartas‐Cejudo
- Clinical Neuroproteomics Unit, Proteomics Platform, Navarrabiomed, Hospitalario Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Navarra Institute for Health ResearchPamplonaSpain
| | - Adriana Cortés
- Clinical Neuroproteomics Unit, Proteomics Platform, Navarrabiomed, Hospitalario Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Navarra Institute for Health ResearchPamplonaSpain
| | - Mercedes Lachén‐Montes
- Clinical Neuroproteomics Unit, Proteomics Platform, Navarrabiomed, Hospitalario Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Navarra Institute for Health ResearchPamplonaSpain
| | - Elena Anaya‐Cubero
- Clinical Neuroproteomics Unit, Proteomics Platform, Navarrabiomed, Hospitalario Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Navarra Institute for Health ResearchPamplonaSpain
| | - Elena Puerta
- Department of Pharmacology and ToxicologyUniversity of Navarra, IdiSNAPamplonaSpain
| | - Maite Solas
- Department of Pharmacology and ToxicologyUniversity of Navarra, IdiSNAPamplonaSpain
| | - Joaquín Fernández‐Irigoyen
- Clinical Neuroproteomics Unit, Proteomics Platform, Navarrabiomed, Hospitalario Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Navarra Institute for Health ResearchPamplonaSpain
| | - Enrique Santamaría
- Clinical Neuroproteomics Unit, Proteomics Platform, Navarrabiomed, Hospitalario Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Navarra Institute for Health ResearchPamplonaSpain
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2
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Kumar V, Roy K. Protein-protein interaction network analysis for the identification of novel multi-target inhibitors and target miRNAs against Alzheimer's disease. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 139:405-467. [PMID: 38448142 DOI: 10.1016/bs.apcsb.2023.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
This study presents a strategy for extracting significant gene complexes and then provides prospective therapeutics for AD. In this research, a total of 7905 reports published from 1981 to 2022 were retrieved. Following a review of all those articles, only the genetic association studies on AD were considered. Finally, there is a list of 453 Alzheimer-related genes in our dataset for network analysis. To this end, an experimentally derived protein-protein interaction (PPI) network from the String database was utilized to extract four meaningful gene complexes functionally interconnected using Cytoscape v3.9.1 software. The acquired gene complexes were subjected to an enrichment analysis using the ClueGO v2.5.9 tool to emphasize the most significant biological processes and pathways. Afterward, extracted gene complexes were used to extract the drugs related to AD from DGI v3.0 database and introduce some new drugs which may be helpful for this disease. Finally, a comprehensive network that included every gene connected to each gene complex group as well as the drug targets for each gene has been shown. Moreover, molecular docking studies have been performed with the selected compounds to identify the interaction pattern with the respective targets. Finally, we proposed a list of 62 compounds as multi-targeted directed drug-like compounds with a degree value between 2 and 5 and 30 compounds as target-specific drug-like compounds, which have not been proclaimed as AD-related drugs in prior scientific and medical investigations. Then, new drugs were suggested that can be experimentally examined for future work. In addition to this, four bipartite networks representing each group's genes and target miRNAs were established to introduce target miRNAs by using the miRWalk v3 server.
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Affiliation(s)
- Vinay Kumar
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Kunal Roy
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India.
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3
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Chen C, Khanthiyong B, Thaweetee-Sukjai B, Charoenlappanit S, Roytrakul S, Thanoi S, Reynolds GP, Nudmamud-Thanoi S. Proteomic association with age-dependent sex differences in Wisconsin Card Sorting Test performance in healthy Thai subjects. Sci Rep 2023; 13:20238. [PMID: 37981639 PMCID: PMC10658079 DOI: 10.1038/s41598-023-46750-4] [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: 02/16/2023] [Accepted: 11/04/2023] [Indexed: 11/21/2023] Open
Abstract
Sex differences in cognitive function exist, but they are not stable and undergo dynamic change during the lifespan. However, our understanding of how sex-related neural information transmission evolves with age is still in its infancy. This study utilized the Wisconsin Card Sorting Test (WCST) and the label-free proteomics method with bioinformatic analysis to investigate the molecular mechanisms underlying age-related sex differences in cognitive performance in 199 healthy Thai subjects (aged 20-70 years), as well as explore the sex-dependent protein complexes for predicting cognitive aging. The results showed that males outperformed females in two of the five WCST sub-scores: %Corrects and %Errors. Sex differences in these scores were related to aging, becoming noticeable in those over 60. At the molecular level, differently expressed individual proteins and protein complexes between both sexes are associated with the potential N-methyl-D-aspartate type glutamate receptor (NMDAR)-mediated excitotoxicity, with the NMDAR complex being enriched exclusively in elderly female samples. These findings provided a preliminary indication that healthy Thai females might be more susceptible to such neurotoxicity, as evidenced by their cognitive performance. NMDAR protein complex enrichment in serum could be proposed as a potential indication for predicting cognitive aging in healthy Thai females.
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Affiliation(s)
- Chen Chen
- Medical Science Graduate Program, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | | | | | - Sawanya Charoenlappanit
- National Centre for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Sittiruk Roytrakul
- National Centre for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Samur Thanoi
- School of Medical Sciences, University of Phayao, Phayao, Thailand.
| | - Gavin P Reynolds
- Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield, UK
- Centre of Excellence in Medical Biotechnology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Sutisa Nudmamud-Thanoi
- Centre of Excellence in Medical Biotechnology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand.
- Department of Anatomy, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand.
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Cingiz MÖ. k- Strong Inference Algorithm: A Hybrid Information Theory Based Gene Network Inference Algorithm. Mol Biotechnol 2023:10.1007/s12033-023-00929-2. [PMID: 37950851 DOI: 10.1007/s12033-023-00929-2] [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: 02/23/2023] [Accepted: 10/05/2023] [Indexed: 11/13/2023]
Abstract
Gene networks allow researchers to understand the underlying mechanisms between diseases and genes while reducing the need for wet lab experiments. Numerous gene network inference (GNI) algorithms have been presented in the literature to infer accurate gene networks. We proposed a hybrid GNI algorithm, k-Strong Inference Algorithm (ksia), to infer more reliable and robust gene networks from omics datasets. To increase reliability, ksia integrates Pearson correlation coefficient (PCC) and Spearman rank correlation coefficient (SCC) scores to determine mutual information scores between molecules to increase diversity of relation predictions. To infer a more robust gene network, ksia applies three different elimination steps to remove redundant and spurious relations between genes. The performance of ksia was evaluated on microbe microarrays database in the overlap analysis with other GNI algorithms, namely ARACNE, C3NET, CLR, and MRNET. Ksia inferred less number of relations due to its strict elimination steps. However, ksia generally performed better on Escherichia coli (E.coli) and Saccharomyces cerevisiae (yeast) gene expression datasets due to F- measure and precision values. The integration of association estimator scores and three elimination stages slightly increases the performance of ksia based gene networks. Users can access ksia R package and user manual of package via https://github.com/ozgurcingiz/ksia .
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Affiliation(s)
- Mustafa Özgür Cingiz
- Computer Engineering Department, Faculty of Engineering and Natural Sciences, Bursa Technical University, Mimar Sinan Campus, Yildirim, 16310, Bursa, Turkey.
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Bourdakou MM, Fernández-Ginés R, Cuadrado A, Spyrou GM. Drug repurposing on Alzheimer's disease through modulation of NRF2 neighborhood. Redox Biol 2023; 67:102881. [PMID: 37696195 PMCID: PMC10500459 DOI: 10.1016/j.redox.2023.102881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 08/30/2023] [Accepted: 09/06/2023] [Indexed: 09/13/2023] Open
Abstract
Alzheimer's disease (AD) is an age-dependent neurodegenerative disorder and the most common cause of cognitive decline. The alarming epidemiological features of Alzheimer's disease, combined with the high failure rate of candidate drugs tested in the preclinical phase, impose more intense investigations for new curative treatments. NRF2 (Nuclear factor-erythroid factor 2-related factor 2) plays a critical role in the inflammatory response and in the cellular redox homeostasis and provides cytoprotection in several diseases including those in the neurodegeneration spectrum. These roles suggest that NRF2 and its directly associated proteins may be novel attractive therapeutic targets in the fight against AD. In this study, through a systemics perspective, we propose an in silico drug repurposing approach for AD, based on the NRF2 interactome and regulome, with the aim of highlighting possible repurposed drugs for AD. Using publicly available information based on differential expressions of the NRF2-neighborhood in AD and through a computational drug repurposing pipeline, we derived to a short list of candidate repurposed drugs and small molecules that affect the expression levels of the majority of NRF2-partners. The relevance of these findings was assessed in a four-step computational meta-analysis including i) structural similarity comparisons with currently ongoing NRF2-related drugs in clinical trials ii) evaluation based on the NRF2-diseasome iii) comparison of relevance between targeted pathways of shortlisted drugs and NRF2-related drugs in clinical trials and iv) further comparison with existing knowledge on AD and NRF2-related drugs in clinical trials based on their known modes of action. Overall, our analysis yielded in 5 candidate repurposed drugs for AD. In cell culture, these 5 candidates activated a luciferase reporter for NRF2 activity and in hippocampus derived TH22 cells they increased NRF2 protein levels and the NRF2 transcriptional signatures as determined by increased expression of its downstream target heme oxygenase 1. We expect that our proposed candidate repurposed drugs will be useful for further research and clinical translation for AD.
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Affiliation(s)
- Marilena M Bourdakou
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Raquel Fernández-Ginés
- Instituto de Investigaciones Biomédicas "Alberto Sols" UAM-CSIC, Instituto de Investigación Sanitaria La Paz (IdiPaz), Department of Biochemistry, Faculty of Medicine, Autonomous University of Madrid, Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), ISCIII, Madrid, Spain
| | - Antonio Cuadrado
- Instituto de Investigaciones Biomédicas "Alberto Sols" UAM-CSIC, Instituto de Investigación Sanitaria La Paz (IdiPaz), Department of Biochemistry, Faculty of Medicine, Autonomous University of Madrid, Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), ISCIII, Madrid, Spain
| | - George M Spyrou
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.
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Tabrizi-Nezhadi P, MotieGhader H, Maleki M, Sahin S, Nematzadeh S, Torkamanian-Afshar M. Application of Protein-Protein Interaction Network Analysis in Order to Identify Cervical Cancer miRNA and mRNA Biomarkers. ScientificWorldJournal 2023; 2023:6626279. [PMID: 37746664 PMCID: PMC10513823 DOI: 10.1155/2023/6626279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/28/2023] [Accepted: 09/04/2023] [Indexed: 09/26/2023] Open
Abstract
Cervical cancer (CC) is one of the world's most common and severe cancers. This cancer includes two histological types: squamous cell carcinoma (SCC) and adenocarcinoma (ADC). The current study aims at identifying novel potential candidate mRNA and miRNA biomarkers for SCC based on a protein-protein interaction (PPI) and miRNA-mRNA network analysis. The current project utilized a transcriptome profile for normal and SCC samples. First, the PPI network was constructed for the 1335 DEGs, and then, a significant gene module was extracted from the PPI network. Next, a list of miRNAs targeting module's genes was collected from the experimentally validated databases, and a miRNA-mRNA regulatory network was formed. After network analysis, four driver genes were selected from the module's genes including MCM2, MCM10, POLA1, and TONSL and introduced as potential candidate biomarkers for SCC. In addition, two hub miRNAs, including miR-193b-3p and miR-615-3p, were selected from the miRNA-mRNA regulatory network and reported as possible candidate biomarkers. In summary, six potential candidate RNA-based biomarkers consist of four genes containing MCM2, MCM10, POLA1, and TONSL, and two miRNAs containing miR-193b-3p and miR-615-3p are opposed as potential candidate biomarkers for CC.
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Affiliation(s)
| | - Habib MotieGhader
- Department of Biology, Tabriz Branch, Islamic Azad University, Tabriz, Iran
- Department of Health Ecosystem, Medical Faculty, Nisantasi University, Istanbul, Turkey
| | - Masoud Maleki
- Department of Biology, Tabriz Branch, Islamic Azad University, Tabriz, Iran
| | - Soner Sahin
- Department of Health Ecosystem, Medical Faculty, Nisantasi University, Istanbul, Turkey
| | - Sajjad Nematzadeh
- Software Engineering Department, Engineering Faculty, Topkapi University, Istanbul, Turkey
| | - Mahsa Torkamanian-Afshar
- Department of Computer Engineering, Faculty of Engineering and Architecture, Nisantasi University, Istanbul, Turkey
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7
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Grabowska ME, Huang A, Wen Z, Li B, Wei WQ. Drug repurposing for Alzheimer's disease from 2012-2022-a 10-year literature review. Front Pharmacol 2023; 14:1257700. [PMID: 37745051 PMCID: PMC10512468 DOI: 10.3389/fphar.2023.1257700] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 08/28/2023] [Indexed: 09/26/2023] Open
Abstract
Background: Alzheimer's disease (AD) is a debilitating neurodegenerative condition with few treatment options available. Drug repurposing studies have sought to identify existing drugs that could be repositioned to treat AD; however, the effectiveness of drug repurposing for AD remains unclear. This review systematically analyzes the progress made in drug repurposing for AD throughout the last decade, summarizing the suggested drug candidates and analyzing changes in the repurposing strategies used over time. We also examine the different types of data that have been leveraged to validate suggested drug repurposing candidates for AD, which to our knowledge has not been previous investigated, although this information may be especially useful in appraising the potential of suggested drug repurposing candidates. We ultimately hope to gain insight into the suggested drugs representing the most promising repurposing candidates for AD. Methods: We queried the PubMed database for AD drug repurposing studies published between 2012 and 2022. 124 articles were reviewed. We used RxNorm to standardize drug names across the reviewed studies, map drugs to their constituent ingredients, and identify prescribable drugs. We used the Anatomical Therapeutic Chemical (ATC) Classification System to group drugs. Results: 573 unique drugs were proposed for repurposing in AD over the last 10 years. These suggested repurposing candidates included drugs acting on the nervous system (17%), antineoplastic and immunomodulating agents (16%), and drugs acting on the cardiovascular system (12%). Clozapine, a second-generation antipsychotic medication, was the most frequently suggested repurposing candidate (N = 6). 61% (76/124) of the reviewed studies performed a validation, yet only 4% (5/124) used real-world data for validation. Conclusion: A large number of potential drug repurposing candidates for AD has accumulated over the last decade. However, among these drugs, no single drug has emerged as the top candidate, making it difficult to establish research priorities. Validation of drug repurposing hypotheses is inconsistently performed, and real-world data has been critically underutilized for validation. Given the urgent need for new AD therapies, the utility of real-world data in accelerating identification of high-priority candidates for AD repurposing warrants further investigation.
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Affiliation(s)
- Monika E. Grabowska
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Annabelle Huang
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Zhexing Wen
- Departments of Psychiatry and Behavioral Sciences, Cell Biology, and Neurology, Emory University School of Medicine, Atlanta, GA, United States
| | - Bingshan Li
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States
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8
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Robin V, Bodein A, Scott-Boyer MP, Leclercq M, Périn O, Droit A. Overview of methods for characterization and visualization of a protein-protein interaction network in a multi-omics integration context. Front Mol Biosci 2022; 9:962799. [PMID: 36158572 PMCID: PMC9494275 DOI: 10.3389/fmolb.2022.962799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/16/2022] [Indexed: 11/26/2022] Open
Abstract
At the heart of the cellular machinery through the regulation of cellular functions, protein-protein interactions (PPIs) have a significant role. PPIs can be analyzed with network approaches. Construction of a PPI network requires prediction of the interactions. All PPIs form a network. Different biases such as lack of data, recurrence of information, and false interactions make the network unstable. Integrated strategies allow solving these different challenges. These approaches have shown encouraging results for the understanding of molecular mechanisms, drug action mechanisms, and identification of target genes. In order to give more importance to an interaction, it is evaluated by different confidence scores. These scores allow the filtration of the network and thus facilitate the representation of the network, essential steps to the identification and understanding of molecular mechanisms. In this review, we will discuss the main computational methods for predicting PPI, including ones confirming an interaction as well as the integration of PPIs into a network, and we will discuss visualization of these complex data.
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Affiliation(s)
- Vivian Robin
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Antoine Bodein
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Marie-Pier Scott-Boyer
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Mickaël Leclercq
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Olivier Périn
- Digital Sciences Department, L'Oréal Advanced Research, Aulnay-sous-bois, France
| | - Arnaud Droit
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
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9
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MotieGhader H, Tabrizi-Nezhadi P, Deldar Abad Paskeh M, Baradaran B, Mokhtarzadeh A, Hashemi M, Lanjanian H, Jazayeri SM, Maleki M, Khodadadi E, Nematzadeh S, Kiani F, Maghsoudloo M, Masoudi-Nejad A. Drug repositioning in non-small cell lung cancer (NSCLC) using gene co-expression and drug–gene interaction networks analysis. Sci Rep 2022; 12:9417. [PMID: 35676421 PMCID: PMC9177601 DOI: 10.1038/s41598-022-13719-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/16/2022] [Indexed: 12/14/2022] Open
Abstract
Lung cancer is the most common cancer in men and women. This cancer is divided into two main types, namely non-small cell lung cancer (NSCLC) and small cell lung cancer (SCLC). Around 85 to 90 percent of lung cancers are NSCLC. Repositioning potent candidate drugs in NSCLC treatment is one of the important topics in cancer studies. Drug repositioning (DR) or drug repurposing is a method for identifying new therapeutic uses of existing drugs. The current study applies a computational drug repositioning method to identify candidate drugs to treat NSCLC patients. To this end, at first, the transcriptomics profile of NSCLC and healthy (control) samples was obtained from the GEO database with the accession number GSE21933. Then, the gene co-expression network was reconstructed for NSCLC samples using the WGCNA, and two significant purple and magenta gene modules were extracted. Next, a list of transcription factor genes that regulate purple and magenta modules' genes was extracted from the TRRUST V2.0 online database, and the TF–TG (transcription factors–target genes) network was drawn. Afterward, a list of drugs targeting TF–TG genes was obtained from the DGIdb V4.0 database, and two drug–gene interaction networks, including drug-TG and drug-TF, were drawn. After analyzing gene co-expression TF–TG, and drug–gene interaction networks, 16 drugs were selected as potent candidates for NSCLC treatment. Out of 16 selected drugs, nine drugs, namely Methotrexate, Olanzapine, Haloperidol, Fluorouracil, Nifedipine, Paclitaxel, Verapamil, Dexamethasone, and Docetaxel, were chosen from the drug-TG sub-network. In addition, nine drugs, including Cisplatin, Daunorubicin, Dexamethasone, Methotrexate, Hydrocortisone, Doxorubicin, Azacitidine, Vorinostat, and Doxorubicin Hydrochloride, were selected from the drug-TF sub-network. Methotrexate and Dexamethasone are common in drug-TG and drug-TF sub-networks. In conclusion, this study proposed 16 drugs as potent candidates for NSCLC treatment through analyzing gene co-expression, TF–TG, and drug–gene interaction networks.
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Oláh J, Szénási T, Lehotzky A, Norris V, Ovádi J. Challenges in Discovering Drugs That Target the Protein-Protein Interactions of Disordered Proteins. Int J Mol Sci 2022; 23:ijms23031550. [PMID: 35163473 PMCID: PMC8835748 DOI: 10.3390/ijms23031550] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 01/25/2022] [Accepted: 01/27/2022] [Indexed: 12/17/2022] Open
Abstract
Protein–protein interactions (PPIs) outnumber proteins and are crucial to many fundamental processes; in consequence, PPIs are associated with several pathological conditions including neurodegeneration and modulating them by drugs constitutes a potentially major class of therapy. Classically, however, the discovery of small molecules for use as drugs entails targeting individual proteins rather than targeting PPIs. This is largely because discovering small molecules to modulate PPIs has been seen as extremely challenging. Here, we review the difficulties and limitations of strategies to discover drugs that target PPIs directly or indirectly, taking as examples the disordered proteins involved in neurodegenerative diseases.
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Affiliation(s)
- Judit Oláh
- Institute of Enzymology, Research Centre for Natural Sciences, ELKH, 1117 Budapest, Hungary; (J.O.); (T.S.); (A.L.)
| | - Tibor Szénási
- Institute of Enzymology, Research Centre for Natural Sciences, ELKH, 1117 Budapest, Hungary; (J.O.); (T.S.); (A.L.)
| | - Attila Lehotzky
- Institute of Enzymology, Research Centre for Natural Sciences, ELKH, 1117 Budapest, Hungary; (J.O.); (T.S.); (A.L.)
| | - Victor Norris
- Laboratory of Microbiology Signals and Microenvironment, University of Rouen, 76821 Mont Saint Aignan, France;
| | - Judit Ovádi
- Institute of Enzymology, Research Centre for Natural Sciences, ELKH, 1117 Budapest, Hungary; (J.O.); (T.S.); (A.L.)
- Correspondence:
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