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Nghi HT, Shahmohammadi S, Ebrahimi KH. Ancient complexes of iron and sulfur modulate oncogenes and oncometabolism. Curr Opin Chem Biol 2023; 76:102338. [PMID: 37295349 DOI: 10.1016/j.cbpa.2023.102338] [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: 03/21/2023] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 06/12/2023]
Abstract
Inorganic complexes of iron and sulfur, that is, iron-sulfur [FeS] clusters, have played a fundamental role in life on Earth since the prebiotic period. These clusters were involved in elementary reactions leading to the emergence of life and, since then, gained function in processes, such as respiration, replication, transcription, and the immune response. We discuss how three [FeS] proteins involved in the innate immune response play a role in oncogene expression/function and oncometabolism. Our analysis highlights the importance of future research into understanding the [FeS] clusters' roles in cancer progression and proliferation. The outcomes of these studies will help identify new targets and develop new anticancer therapeutics.
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Affiliation(s)
- Hoang Thao Nghi
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Sciences, King's College London, London, United Kingdom
| | - Sayeh Shahmohammadi
- Institute of Pharmaceutical Chemistry, Interdisciplinary Excellence Center and Stereochemistry Research Group, Eötvös Loránd Research Network, Faculty of Pharmacy, University of Szeged, H-6720, Szeged, Hungary
| | - Kourosh H Ebrahimi
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Sciences, King's College London, London, United Kingdom.
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2
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Wilson MR, Harkins S, Reske JJ, Siwicki RA, Adams M, Bae-Jump VL, Teixeira JM, Chandler RL. PIK3CA mutation in endometriotic epithelial cells promotes viperin-dependent inflammatory response to insulin. Reprod Biol Endocrinol 2023; 21:43. [PMID: 37170094 PMCID: PMC10173629 DOI: 10.1186/s12958-023-01094-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/30/2023] [Indexed: 05/13/2023] Open
Abstract
Endometrial epithelia are known to harbor cancer driver mutations in the absence of any pathologies, including mutations in PIK3CA. Insulin plays an important role in regulating uterine metabolism during pregnancy, and hyperinsulinemia is associated with conditions impacting fertility. Hyperinsulinemia also promotes cancer, but the direct action of insulin on mutated endometrial epithelial cells is unknown. Here, we treated 12Z endometriotic epithelial cells carrying the PIK3CAH1047R oncogene with insulin and examined transcriptomes by RNA-seq. While cells naively responded to insulin, the magnitude of differential gene expression (DGE) was nine times greater in PIK3CAH1047R cells, representing a synergistic effect between insulin signaling and PIK3CAH1047R expression. Interferon signaling and the unfolded protein response (UPR) were enriched pathways among affected genes. Insulin treatment in wild-type cells activated normal endoplasmic reticulum stress (ERS) response programs, while PIK3CAH1047R cells activated programs necessary to avoid ERS-induced apoptosis. PIK3CAH1047R expression alone resulted in overexpression (OE) of Viperin (RSAD2), which is involved in viral response and upregulated in the endometrium during early pregnancy. The transcriptional changes induced by insulin in PIK3CAH1047R cells were rescued by knockdown of Viperin, while Viperin OE alone was insufficient to induce a DGE response to insulin, suggesting that Viperin is necessary but not sufficient for the synergistic effect of PIK3CAH1047R and insulin treatment. We identified interferon signaling, viral response, and protein targeting pathways that are induced by insulin but dependent on Viperin in PIK3CAH1047R mutant cells. These results suggest that response to insulin signaling is altered in mutated endometriotic epithelial cells.
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Affiliation(s)
- Mike R Wilson
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI, 49503, USA
| | - Shannon Harkins
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI, 49503, USA
| | - Jake J Reske
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI, 49503, USA
| | - Rebecca A Siwicki
- Genomics Core Facility, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Marie Adams
- Genomics Core Facility, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Victoria L Bae-Jump
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Division of Gynecologic Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jose M Teixeira
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI, 49503, USA
- Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, 48824, USA
| | - Ronald L Chandler
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI, 49503, USA.
- Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, 48824, USA.
- Department for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, 49503, USA.
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Ji Y, Wei L, Da A, Stark H, Hagedoorn PL, Ciofi-Baffoni S, Cowley SA, Louro RO, Todorovic S, Mroginski MA, Nicolet Y, Roessler MM, Le Brun NE, Piccioli M, James WS, Hagen WR, Ebrahimi KH. Radical-SAM dependent nucleotide dehydratase (SAND), rectification of the names of an ancient iron-sulfur enzyme using NC-IUBMB recommendations. Front Mol Biosci 2022; 9:1032220. [PMID: 36387278 PMCID: PMC9642334 DOI: 10.3389/fmolb.2022.1032220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 10/07/2022] [Indexed: 11/27/2022] Open
Affiliation(s)
- Yuxuan Ji
- Institute of Pharmaceutical Science, King’s College London, London, United Kingdom
| | - Li Wei
- Institute of Pharmaceutical Science, King’s College London, London, United Kingdom
| | - Anqi Da
- Institute of Pharmaceutical Science, King’s College London, London, United Kingdom
| | - Holger Stark
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-University Düsseldorf, Duesseldorf, Germany
| | | | - Simone Ciofi-Baffoni
- Magnetic Resonance Center (CERM), University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Florence, and Department of Chemistry, University of Florence, Florence, Italy
| | - Sally A. Cowley
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Ricardo O. Louro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República–EAN, Oeiras, Portugal
| | - Smilja Todorovic
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República–EAN, Oeiras, Portugal
| | | | | | - Maxie M. Roessler
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom
| | - Nick E. Le Brun
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, United Kingdom
| | - Mario Piccioli
- Magnetic Resonance Center (CERM), University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Florence, and Department of Chemistry, University of Florence, Florence, Italy
| | - William S. James
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Wilfred R. Hagen
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Kourosh H. Ebrahimi
- Institute of Pharmaceutical Science, King’s College London, London, United Kingdom
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4
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Iron–sulfur clusters as inhibitors and catalysts of viral replication. Nat Chem 2022; 14:253-266. [DOI: 10.1038/s41557-021-00882-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 12/15/2021] [Indexed: 12/11/2022]
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Guo Y, Esfahani F, Shao X, Srinivasan V, Thomo A, Xing L, Zhang X. Integrative COVID-19 biological network inference with probabilistic core decomposition. Brief Bioinform 2022; 23:6425808. [PMID: 34791019 PMCID: PMC8689992 DOI: 10.1093/bib/bbab455] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/15/2021] [Accepted: 10/07/2021] [Indexed: 12/15/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for millions of deaths around the world. To help contribute to the understanding of crucial knowledge and to further generate new hypotheses relevant to SARS-CoV-2 and human protein interactions, we make use of the information abundant Biomine probabilistic database and extend the experimentally identified SARS-CoV-2-human protein-protein interaction (PPI) network in silico. We generate an extended network by integrating information from the Biomine database, the PPI network and other experimentally validated results. To generate novel hypotheses, we focus on the high-connectivity sub-communities that overlap most with the integrated experimentally validated results in the extended network. Therefore, we propose a new data analysis pipeline that can efficiently compute core decomposition on the extended network and identify dense subgraphs. We then evaluate the identified dense subgraph and the generated hypotheses in three contexts: literature validation for uncovered virus targeting genes and proteins, gene function enrichment analysis on subgraphs and literature support on drug repurposing for identified tissues and diseases related to COVID-19. The major types of the generated hypotheses are proteins with their encoding genes and we rank them by sorting their connections to the integrated experimentally validated nodes. In addition, we compile a comprehensive list of novel genes, and proteins potentially related to COVID-19, as well as novel diseases which might be comorbidities. Together with the generated hypotheses, our results provide novel knowledge relevant to COVID-19 for further validation.
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Affiliation(s)
- Yang Guo
- Department of Mathematics and Statistics, University of Victoria, 3800 Finnerty Road, V8P 5C2, Victoria, BC, Canada
| | - Fatemeh Esfahani
- Department of Computer Science, University of Victoria, 3800 Finnerty Road, V8P 5C2, Victoria, BC, Canada
| | - Xiaojian Shao
- Digital Technologies Research Centre, National Research Council Canada, 1200 Montreal Road, K1A 0R6, Ottawa, ON, Canada
| | - Venkatesh Srinivasan
- Department of Computer Science, University of Victoria, 3800 Finnerty Road, V8P 5C2, Victoria, BC, Canada
| | - Alex Thomo
- Department of Computer Science, University of Victoria, 3800 Finnerty Road, V8P 5C2, Victoria, BC, Canada
| | - Li Xing
- Department of Mathematics and Statistics, University of Saskatchewan, 110 Science Place, S7N 5A2, Saskatoon, SK, Canada
| | - Xuekui Zhang
- Corresponding author: Xuekui Zhang, Department of Mathematics and Statistics, University of Victoria, 3800 Finnerty Road, V8P 5C2, Victoria, BC, Canada.
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A lipidomic view of SARS-CoV-2. Biosci Rep 2021; 41:229396. [PMID: 34313294 PMCID: PMC8350433 DOI: 10.1042/bsr20210953] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/20/2021] [Accepted: 07/27/2021] [Indexed: 02/07/2023] Open
Abstract
The global pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which started in late 2019, has caused huge social and economic losses. A growing number of investigators are focusing on understanding the interaction of SARS-CoV-2 with host cellular processes to find therapeutic approaches. New data suggest that lipid metabolism may play a significant role in regulating the response of immune cells like macrophages to viral infection, thereby affecting the outcome of the disease. Therefore, understanding the role of lipid metabolism could help develop new therapeutic approaches to mitigate the social and economic cost of coronavirus disease 2019 (COVID-19).
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