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Kravchuk EV, Ashniev GA, Gladkova MG, Orlov AV, Vasileva AV, Boldyreva AV, Burenin AG, Skirda AM, Nikitin PI, Orlova NN. Experimental Validation and Prediction of Super-Enhancers: Advances and Challenges. Cells 2023; 12:cells12081191. [PMID: 37190100 DOI: 10.3390/cells12081191] [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: 03/07/2023] [Revised: 04/07/2023] [Accepted: 04/14/2023] [Indexed: 05/17/2023] Open
Abstract
Super-enhancers (SEs) are cis-regulatory elements of the human genome that have been widely discussed since the discovery and origin of the term. Super-enhancers have been shown to be strongly associated with the expression of genes crucial for cell differentiation, cell stability maintenance, and tumorigenesis. Our goal was to systematize research studies dedicated to the investigation of structure and functions of super-enhancers as well as to define further perspectives of the field in various applications, such as drug development and clinical use. We overviewed the fundamental studies which provided experimental data on various pathologies and their associations with particular super-enhancers. The analysis of mainstream approaches for SE search and prediction allowed us to accumulate existing data and propose directions for further algorithmic improvements of SEs' reliability levels and efficiency. Thus, here we provide the description of the most robust algorithms such as ROSE, imPROSE, and DEEPSEN and suggest their further use for various research and development tasks. The most promising research direction, which is based on topic and number of published studies, are cancer-associated super-enhancers and prospective SE-targeted therapy strategies, most of which are discussed in this review.
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Affiliation(s)
- Ekaterina V Kravchuk
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Leninskiye Gory, MSU, 1-12, 119991 Moscow, Russia
| | - German A Ashniev
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Leninskiye Gory, MSU, 1-12, 119991 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, GSP-1, Leninskiye Gory, MSU, 1-73, 119234 Moscow, Russia
| | - Marina G Gladkova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, GSP-1, Leninskiye Gory, MSU, 1-73, 119234 Moscow, Russia
| | - Alexey V Orlov
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia
| | - Anastasiia V Vasileva
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia
| | - Anna V Boldyreva
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia
| | - Alexandr G Burenin
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia
| | - Artemiy M Skirda
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia
| | - Petr I Nikitin
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia
| | - Natalia N Orlova
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia
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Lebedev TD, Vagapova ER, Astashkova OO, Spirin PV, Prassolov VS. Inhibition of Non-Receptor Tyrosine Kinase JAK2 Reduces Neuroblastoma Cell Growth and Enhances the Action of Doxorubicin. Mol Biol 2020. [DOI: 10.1134/s0026893320020119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Lebedev TD, Vagapova ER, Popenko VI, Leonova OG, Spirin PV, Prassolov VS. Two Receptors, Two Isoforms, Two Cancers: Comprehensive Analysis of KIT and TrkA Expression in Neuroblastoma and Acute Myeloid Leukemia. Front Oncol 2019; 9:1046. [PMID: 31681584 PMCID: PMC6813278 DOI: 10.3389/fonc.2019.01046] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 09/26/2019] [Indexed: 01/04/2023] Open
Abstract
Pediatric cancers represent a wide variety of different tumors, though they have unique features that distinguish them from adult cancers. Receptor tyrosine kinases KIT and TrkA functions in AML and NB, respectively, are well-characterized. Though expression of these receptors is found in both tumors, little is known about KIT function in NB and TrkA in AML. By combining gene enrichment analysis with multidimensional scaling we showed that pediatric AMLs with t(8;21) or inv16 and high KIT expression levels stand out from other AML subtypes as they share prominent transcriptomic features exclusively with KIT-overexpressing NBs. We showed that AML cell lines had a predominant expression of an alternative TrkAIII isoform, which reportedly has oncogenic features, while NB cell lines had dominating TrkAI-II isoforms. NB cells, on the other hand, had an abnormal ratio of KIT isoforms as opposed to AML cells. Both SCF and NGF exerted protective action against doxorubicin and cytarabine for t(8;21) AML and NB cells. We identified several gene sets both unique and common for pediatric AML and NB, and this expression is associated with KIT or TrkA levels. NMU, DUSP4, RET, SUSD5, NOS1, and GABRA5 genes are differentially expressed in NBs with high KIT expression and are associated with poor survival in NB. We identified HOXA10, BAG3, and MARCKS genes that are connected with TrkA expression and are marker genes of poor outcome in AML. We also report that SLC18A2, PLXNC1, and MRPL33 gene expression is associated with TrkA or KIT expression levels in both AML and NB, and these genes have a prognostic value for both cancers. Thus, we have provided a comprehensive characterization of TrkA and KIT expression along with the oncogenic signatures of these genes across two pediatric tumors.
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Affiliation(s)
- Timofey D Lebedev
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia
| | - Elmira R Vagapova
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia
| | - Vladimir I Popenko
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia
| | - Olga G Leonova
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia
| | - Pavel V Spirin
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia
| | - Vladimir S Prassolov
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia
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Kholodenko IV, Kalinovsky DV, Doronin II, Deyev SM, Kholodenko RV. Neuroblastoma Origin and Therapeutic Targets for Immunotherapy. J Immunol Res 2018; 2018:7394268. [PMID: 30116755 PMCID: PMC6079467 DOI: 10.1155/2018/7394268] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 05/27/2018] [Indexed: 01/30/2023] Open
Abstract
Neuroblastoma is a pediatric solid cancer of heterogeneous clinical behavior. The unique features of this type of cancer frequently hamper the process of determining clinical presentation and predicting therapy effectiveness. The tumor can spontaneously regress without treatment or actively develop and give rise to metastases despite aggressive multimodal therapy. In recent years, immunotherapy has become one of the most promising approaches to the treatment of neuroblastoma. Still, only one drug for targeted immunotherapy of neuroblastoma, chimeric monoclonal GD2-specific antibodies, is used in the clinic today, and its application has significant limitations. In this regard, the development of effective and safe GD2-targeted immunotherapies and analysis of other potential molecular targets for the treatment of neuroblastoma represents an important and topical task. The review summarizes biological characteristics of the origin and development of neuroblastoma and outlines molecular markers of neuroblastoma and modern immunotherapy approaches directed towards these markers.
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Affiliation(s)
- Irina V. Kholodenko
- Orekhovich Institute of Biomedical Chemistry, 10 Pogodinskaya St., Moscow 119121, Russia
| | - Daniel V. Kalinovsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., Moscow 117997, Russia
| | - Igor I. Doronin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., Moscow 117997, Russia
- Real Target LLC, 16/10 Miklukho-Maklaya St., Moscow 117997, Russia
| | - Sergey M. Deyev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., Moscow 117997, Russia
- Institute of Engineering Physics for Biomedicine (PhysBio), National Research Nuclear University “MEPhI”, Moscow 115409, Russia
| | - Roman V. Kholodenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., Moscow 117997, Russia
- Real Target LLC, 16/10 Miklukho-Maklaya St., Moscow 117997, Russia
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