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Shahini E, Pasculli G, Mastropietro A, Stolfi P, Tieri P, Vergni D, Cozzolongo R, Pesce F, Giannelli G. Network Proximity-Based Drug Repurposing Strategy for Early and Late Stages of Primary Biliary Cholangitis. Biomedicines 2022; 10:1694. [PMID: 35884999 PMCID: PMC9312896 DOI: 10.3390/biomedicines10071694] [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: 04/23/2022] [Revised: 06/03/2022] [Accepted: 07/11/2022] [Indexed: 11/30/2022] Open
Abstract
Primary biliary cholangitis (PBC) is a chronic, cholestatic, immune-mediated, and progressive liver disorder. Treatment to preventing the disease from advancing into later and irreversible stages is still an unmet clinical need. Accordingly, we set up a drug repurposing framework to find potential therapeutic agents targeting relevant pathways derived from an expanded pool of genes involved in different stages of PBC. Starting with updated human protein-protein interaction data and genes specifically involved in the early and late stages of PBC, a network medicine approach was used to provide a PBC "proximity" or "involvement" gene ranking using network diffusion algorithms and machine learning models. The top genes in the proximity ranking, when combined with the original PBC-related genes, resulted in a final dataset of the genes most involved in PBC disease. Finally, a drug repurposing strategy was implemented by mining and utilizing dedicated drug-gene interaction and druggable genome information knowledge bases (e.g., the DrugBank repository). We identified several potential drug candidates interacting with PBC pathways after performing an over-representation analysis on our initial 1121-seed gene list and the resulting disease-associated (algorithm-obtained) genes. The mechanism and potential therapeutic applications of such drugs were then thoroughly discussed, with a particular emphasis on different stages of PBC disease. We found that interleukin/EGFR/TNF-alpha inhibitors, branched-chain amino acids, geldanamycin, tauroursodeoxycholic acid, genistein, antioestrogens, curcumin, antineovascularisation agents, enzyme/protease inhibitors, and antirheumatic agents are promising drugs targeting distinct stages of PBC. We developed robust and transparent selection mechanisms for prioritizing already approved medicinal products or investigational products for repurposing based on recognized unmet medical needs in PBC, as well as solid preliminary data to achieve this goal.
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Affiliation(s)
- Endrit Shahini
- National Institute of Research IRCCS “Saverio De Bellis”, Castellana Grotte, 70013 Bari, Italy; (R.C.); (G.G.)
| | - Giuseppe Pasculli
- Department of Computer, Control and Management Engineering Antonio Ruberti (DIAG), Sapienza University of Rome, 00185 Rome, Italy; (G.P.); (A.M.)
| | - Andrea Mastropietro
- Department of Computer, Control and Management Engineering Antonio Ruberti (DIAG), Sapienza University of Rome, 00185 Rome, Italy; (G.P.); (A.M.)
| | - Paola Stolfi
- National Research Council (CNR), Institute for Applied Computing (IAC), 00185 Rome, Italy; (P.S.); (P.T.); (D.V.)
| | - Paolo Tieri
- National Research Council (CNR), Institute for Applied Computing (IAC), 00185 Rome, Italy; (P.S.); (P.T.); (D.V.)
| | - Davide Vergni
- National Research Council (CNR), Institute for Applied Computing (IAC), 00185 Rome, Italy; (P.S.); (P.T.); (D.V.)
| | - Raffaele Cozzolongo
- National Institute of Research IRCCS “Saverio De Bellis”, Castellana Grotte, 70013 Bari, Italy; (R.C.); (G.G.)
| | - Francesco Pesce
- Department of Emergency and Organ Transplantation, Nephrology, Dialysis and Transplantation Unit, University of Bari “A. Moro”, 70121 Bari, Italy;
| | - Gianluigi Giannelli
- National Institute of Research IRCCS “Saverio De Bellis”, Castellana Grotte, 70013 Bari, Italy; (R.C.); (G.G.)
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Cao Y, Lu X, Wang J, Zhang H, Liu Z, Xu S, Wang T, Ning S, Xiao B, Wang L. Construction of an miRNA-regulated drug-pathway network reveals drug repurposing candidates for myasthenia gravis. Int J Mol Med 2017; 39:268-278. [PMID: 28075449 PMCID: PMC5358695 DOI: 10.3892/ijmm.2017.2853] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 01/04/2017] [Indexed: 12/31/2022] Open
Abstract
Myasthenia gravis (MG) is a rare debilitating autoimmune neuromuscular disorder. Many studies have focused on the mechanism and treatment strategies of MG. However, the exact pathogenesis of MG and effective treatment strategies remain unclear. Recent studies have indicated that microRNAs (miRNAs or miRs) can regulate the pathological pathways of MG, suggesting their potential role in novel treatments. In the present study, we created a comprehensive catalog of experimentally confirmed MG risk genes and miRNAs by manually mining published literature and public databases. Based on these genes and miRNAs, we identified 41 MG risk pathways and 105 approved drugs that can affect these pathways. Some important MG-related pathways, such as hsa04060 (cytokine-cytokine receptor interaction) and hsa05200 (pathway in cancer), were found to be regulated by MG risk miRNAs and drugs. Furthermore, we constructed an miRNA-regulated drug-pathway network and identified miRNAs and drugs that synergistically regulate key MG pathways and biological processes. We developed a drug repurposing strategy to identify 25 drug repurposing candidates for MG; several of these drugs, such as rituximab, adalimumab, sunitinib, and muromonab, have the potential to be novel MG treatment drugs. This study provides novel insight into the pathogenesis of MG and potential drug candidates for MG were identified.
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Affiliation(s)
- Yuze Cao
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Xiaoyan Lu
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Jianjian Wang
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Huixue Zhang
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Zhaojun Liu
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Si Xu
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Tianfeng Wang
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Bo Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Lihua Wang
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
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Abstract
1. Despite highly potent immunosuppression regimens, there is a small cohort of patients at risk of graft failure due to rejection. 2. Steroid-resistant rejection is managed by the escalation of immunosuppression, but only one-third of patients with chronic rejection respond to this approach. 3. Interferon therapy for recurrent hepatitis C may induce an immunoreactive state and increase rejection rates. 4. Cyclosporine reduces the risk of recurrence of primary biliary cirrhosis but does not alter survival rates. 5. Patterns of primary sclerosing cholangitis recurrence are not affected by immunosuppression. 6. Autoimmune hepatitis recurrence and de novo autoimmune hepatitis are corticosteroid-responsive in most cases.
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Affiliation(s)
- John O'Grady
- Institute of Liver Studies, King's College Hospital, London, United Kingdom. john.o'
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