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Lebedev TD, Khabusheva ER, Mareeva SR, Ivanenko KA, Morozov AV, Spirin PV, Rubtsov PM, Snezhkina AV, Kudryavtseva AV, Sorokin MI, Buzdin AA, Prassolov VS. Identification of cell type-specific correlations between ERK activity and cell viability upon treatment with ERK1/2 inhibitors. J Biol Chem 2022; 298:102226. [PMID: 35787369 PMCID: PMC9358475 DOI: 10.1016/j.jbc.2022.102226] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 12/05/2022] Open
Abstract
Increased MAPK signaling is a hallmark of various cancers and is a central regulator of cell survival. Direct ERK1/2 inhibition is considered a promising approach to avoid ERK1/2 reactivation caused by upstream kinases BRAF, MEK1/2, and KRAS, as well as by receptor tyrosine kinase inhibitors, but the dynamics and selectivity of ERK1/2 inhibitors are much less studied compared with BRAF or MEK inhibitors. Using ERK1/2 and downstream kinase ELK1 reporter cell lines of lung cancer (H1299; NRASQ61K), colon cancer (HCT-116; KRASG13D), neuroblastoma (SH-SY5Y), and leukemia (U937), we examined the relationship between ERK inhibition and drug-induced toxicity for five ERK inhibitors: SCH772984, ravoxertinib, LY3214996, ulixertinib, and VX-11e, as well as one MEK inhibitor, PD0325901. Comparing cell viability and ERK inhibition revealed different ERK dependencies for these cell lines. We identify several drugs, such as SCH772984 and VX-11e, which induce excessive toxicity not directly related to ERK1/2 inhibition in specific cell lines. We also show that PD0325901, LY3214996, and ulixertinib are prone to ERK1/2 reactivation over time. We distinguished two types of ERK1/2 reactivation: the first could be reversed by adding a fresh dose of inhibitors, while the second persists even after additional treatments. We also showed that cells that became resistant to the MEK1/2 inhibitor PD0325901 due to ERK1/2 reactivation remained sensitive to ERK1/2 inhibitor ulixertinib. Our data indicate that correlation of ERK inhibition with drug-induced toxicity in multiple cell lines may help to find more selective and effective ERK1/2 inhibitors.
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Affiliation(s)
- Timofey D Lebedev
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
| | - Elmira R Khabusheva
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Sofia R Mareeva
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia; Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Moscow Region, Russia
| | - Karina A Ivanenko
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexey V Morozov
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Pavel V Spirin
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Petr M Rubtsov
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anastasiya V Snezhkina
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anna V Kudryavtseva
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Maxim I Sorokin
- Institute of Personalized Oncology, Sechenov First Moscow State Medical University, Moscow, Russia; Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia; Department of Bioinformatics and Molecular Networks, OmicsWay Corp, Walnut, California, USA
| | - Anton A Buzdin
- Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Moscow Region, Russia; Institute of Personalized Oncology, Sechenov First Moscow State Medical University, Moscow, Russia; Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia; Department of Bioinformatics and Molecular Networks, OmicsWay Corp, Walnut, California, USA
| | - Vladimir S Prassolov
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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Lebedev TD, Vagapova ER, Prassolov VS. The Different Impact of ERK Inhibition on Neuroblastoma, Astrocytoma, and Rhabdomyosarcoma Cell Differentiation. Acta Naturae 2021; 13:69-77. [PMID: 35127149 PMCID: PMC8807533 DOI: 10.32607/actanaturae.11461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 08/02/2021] [Indexed: 12/02/2022] Open
Abstract
Aberrant ERK activity can lead to uncontrolled cell proliferation,
immortalization, and impaired cell differentiation. Impairment of normal cell
differentiation is one of the critical stages in malignant cell transformation.
In this study, we investigated a relationship between ERK tyrosine kinase
activity and the main differentiation features (changes in cell morphology and
expression of genes encoding differentiation markers and growth factor
receptors) in SH-SY5Y neuroblastoma, U-251 astrocytoma, and TE-671
rhabdomyosarcoma cells. ERK activity was assessed using a reporter system that
enabled live measurements of ERK activity in single cells. We demonstrated that
suppression of ERK activity by selective ERK inhibitors, in contrast to a
commonly used differentiation inducer, retinoic acid, leads to significant
changes in TE-671 cell morphology and expression of the myogenic
differentiation marker genes PROM1, MYOG, and PAX7. There was a relationship
between ERK activity and morphological changes at an individual cell level. In
this case, SH-SY5Y cell differentiation induced by retinoic acid was
ERK-independent. We showed that ERK inhibition increases the sensitivity of
TE-671 cells to the EGF, IGF-1, and NGF growth factors, presumably by reducing
basal ERK activity, and to the BDNF growth factor, by increasing expression of
the TrkB receptor.
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Affiliation(s)
- T. D. Lebedev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - E. R. Vagapova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - V. S. Prassolov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
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3
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Spirin P, Shyrokova E, Lebedev T, Vagapova E, Smirnova P, Kantemirov A, Dyshlovoy SA, von Amsberg G, Zhidkov M, Prassolov V. Cytotoxic Marine Alkaloid 3,10-Dibromofascaplysin Induces Apoptosis and Synergizes with Cytarabine Resulting in Leukemia Cell Death. Mar Drugs 2021; 19:md19090489. [PMID: 34564151 PMCID: PMC8468638 DOI: 10.3390/md19090489] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 01/24/2023] Open
Abstract
Myeloid leukemia is a hematologic neoplasia characterized by a clonal proliferation of hematopoietic stem cell progenitors. Patient prognosis varies depending on the subtype of leukemia as well as eligibility for intensive treatment regimens and allogeneic stem cell transplantation. Although significant progress has been made in the therapy of patients including novel targeted treatment approaches, there is still an urgent need to optimize treatment outcome. The most common therapy is based on the use of chemotherapeutics cytarabine and anthrayclines. Here, we studied the effect of the recently synthesized marine alkaloid 3,10-dibromofascaplysin (DBF) in myeloid leukemia cells. Unsubstituted fascaplysin was early found to affect cell cycle via inhibiting CDK4/6, thus we compared the activity of DBF and other brominated derivatives with known CDK4/6 inhibitor palbociclib, which was earlier shown to be a promising candidate to treat leukemia. Unexpectedly, the effect DBF on cell cycle differs from palbociclib. In fact, DBF induced leukemic cells apoptosis and decreased the expression of genes responsible for cancer cell survival. Simultaneously, DBF was found to activate the E2F1 transcription factor. Using bioinformatical approaches we evaluated the possible molecular mechanisms, which may be associated with DBF-induced activation of E2F1. Finally, we found that DBF synergistically increase the cytotoxic effect of cytarabine in different myeloid leukemia cell lines. In conclusion, DBF is a promising drug candidate, which may be used in combinational therapeutics approaches to reduce leukemia cell growth.
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Affiliation(s)
- Pavel Spirin
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, 119991 Moscow, Russia; (E.S.); (T.L.); (E.V.); (V.P.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, 119991 Moscow, Russia
- Correspondence:
| | - Elena Shyrokova
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, 119991 Moscow, Russia; (E.S.); (T.L.); (E.V.); (V.P.)
- Moscow Institute of Physics and Technology (National Research University), Institutskiy Per. 9, 141701 Dolgoprudny, Russia
| | - Timofey Lebedev
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, 119991 Moscow, Russia; (E.S.); (T.L.); (E.V.); (V.P.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, 119991 Moscow, Russia
| | - Elmira Vagapova
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, 119991 Moscow, Russia; (E.S.); (T.L.); (E.V.); (V.P.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, 119991 Moscow, Russia
| | - Polina Smirnova
- School of Natural Sciences, Far Eastern Federal University, FEFU Campus, Ajax Bay 10, Russky Island, 690922 Vladivostok, Russia; (P.S.); (A.K.); (M.Z.)
| | - Alexey Kantemirov
- School of Natural Sciences, Far Eastern Federal University, FEFU Campus, Ajax Bay 10, Russky Island, 690922 Vladivostok, Russia; (P.S.); (A.K.); (M.Z.)
| | - Sergey A. Dyshlovoy
- Laboratory of Experimental Oncology, Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald-Tumorzentrum, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20251 Hamburg, Germany; (S.A.D.); (G.v.A.)
- Martini-Klinik, Prostate Cancer Center, University Hospital Hamburg-Eppendorf, Martinistrasse 52, 20251 Hamburg, Germany
- Laboratory of Pharmacology, A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Palchevskogo Str. 17, 690041 Vladivostok, Russia
| | - Gunhild von Amsberg
- Laboratory of Experimental Oncology, Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald-Tumorzentrum, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20251 Hamburg, Germany; (S.A.D.); (G.v.A.)
- Martini-Klinik, Prostate Cancer Center, University Hospital Hamburg-Eppendorf, Martinistrasse 52, 20251 Hamburg, Germany
| | - Maxim Zhidkov
- School of Natural Sciences, Far Eastern Federal University, FEFU Campus, Ajax Bay 10, Russky Island, 690922 Vladivostok, Russia; (P.S.); (A.K.); (M.Z.)
| | - Vladimir Prassolov
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, 119991 Moscow, Russia; (E.S.); (T.L.); (E.V.); (V.P.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, 119991 Moscow, Russia
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Li X, Zhang CT, Ma W, Xie X, Huang Q. Oridonin: A Review of Its Pharmacology, Pharmacokinetics and Toxicity. Front Pharmacol 2021; 12:645824. [PMID: 34295243 PMCID: PMC8289702 DOI: 10.3389/fphar.2021.645824] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 06/18/2021] [Indexed: 12/17/2022] Open
Abstract
Oridonin, as a natural terpenoids found in traditional Chinese herbal medicine Isodon rubescens (Hemsl.) H.Hara, is widely present in numerous Chinese medicine preparations. The purpose of this review focuses on providing the latest and comprehensive information on the pharmacology, pharmacokinetics and toxicity of oridonin, to excavate the therapeutic potential and explore promising ways to balance toxicity and efficacy of this natural compound. Information concerning oridonin was systematically collected from the authoritative internet database of PubMed, Elsevier, Web of Science, Wiley Online Library and Europe PMC applying a combination of keywords involving "pharmacology," "pharmacokinetics," and "toxicology". New evidence shows that oridonin possesses a wide range of pharmacological properties, including anticancer, anti-inflammatory, hepatorenal activities as well as cardioprotective protective activities and so on. Although significant advancement has been witnessed in this field, some basic and intricate issues still exist such as the specific mechanism of oridonin against related diseases not being clear. Moreover, several lines of evidence indicated that oridonin may exhibit adverse effects, even toxicity under specific circumstances, which sparked intense debate and concern about security of oridonin. Based on the current progress, future research directions should emphasize on 1) investigating the interrelationship between concentration and pharmacological effects as well as toxicity, 2) reducing pharmacological toxicity, and 3) modifying the structure of oridonin-one of the pivotal approaches to strengthen pharmacological activity and bioavailability. We hope that this review can provide some inspiration for the research of oridonin in the future.
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Affiliation(s)
- Xiang Li
- Department of Ophthalmology, School of Pharmacy, College of Medical Technology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Department of Respiratory, School of Pharmacy, College of Medical Technology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Chuan-Tao Zhang
- Department of Ophthalmology, School of Pharmacy, College of Medical Technology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Department of Respiratory, School of Pharmacy, College of Medical Technology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Wei Ma
- Department of Ophthalmology, School of Pharmacy, College of Medical Technology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Department of Respiratory, School of Pharmacy, College of Medical Technology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xin Xie
- Department of Ophthalmology, School of Pharmacy, College of Medical Technology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Department of Respiratory, School of Pharmacy, College of Medical Technology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Qun Huang
- Department of Ophthalmology, School of Pharmacy, College of Medical Technology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Department of Respiratory, School of Pharmacy, College of Medical Technology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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5
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Using proteomic and transcriptomic data to assess activation of intracellular molecular pathways. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 127:1-53. [PMID: 34340765 DOI: 10.1016/bs.apcsb.2021.02.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Analysis of molecular pathway activation is the recent instrument that helps to quantize activities of various intracellular signaling, structural, DNA synthesis and repair, and biochemical processes. This may have a deep impact in fundamental research, bioindustry, and medicine. Unlike gene ontology analyses and numerous qualitative methods that can establish whether a pathway is affected in principle, the quantitative approach has the advantage of exactly measuring the extent of a pathway up/downregulation. This results in emergence of a new generation of molecular biomarkers-pathway activation levels, which reflect concentration changes of all measurable pathway components. The input data can be the high-throughput proteomic or transcriptomic profiles, and the output numbers take both positive and negative values and positively reflect overall pathway activation. Due to their nature, the pathway activation levels are more robust biomarkers compared to the individual gene products/protein levels. Here, we review the current knowledge of the quantitative gene expression interrogation methods and their applications for the molecular pathway quantization. We consider enclosed bioinformatic algorithms and their applications for solving real-world problems. Besides a plethora of applications in basic life sciences, the quantitative pathway analysis can improve molecular design and clinical investigations in pharmaceutical industry, can help finding new active biotechnological components and can significantly contribute to the progressive evolution of personalized medicine. In addition to the theoretical principles and concepts, we also propose publicly available software for the use of large-scale protein/RNA expression data to assess the human pathway activation levels.
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Shyrokova EY, Prassolov VS, Spirin PV. The Role of the MCTS1 and DENR Proteins in Regulating the Mechanisms Associated with Malignant Cell Transformation. Acta Naturae 2021; 13:98-105. [PMID: 34377560 PMCID: PMC8327141 DOI: 10.32607/actanaturae.11181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 09/28/2020] [Indexed: 02/05/2023] Open
Abstract
The mutations associated with malignant cell transformation are believed to disrupt the expression of a significant number of normal, non-mutant genes. The proteins encoded by these genes are involved in the regulation of many signaling pathways that are responsible for differentiation and proliferation, as well as sensitivity to apoptotic signals, growth factors, and cytokines. Abnormalities in the balance of signaling pathways can lead to the transformation of a normal cell, which results in tumor formation. Detection of the target genes and the proteins they encode and that are involved in the malignant transformation is one of the major evolutions in anti-cancer biomedicine. Currently, there is an accumulation of data that shed light on the role of the MCTS1 and DENR proteins in oncogenesis.
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Affiliation(s)
- E. Y. Shyrokova
- Engelhardt Institute of Molecular Biology, Russian Academy of Science, Moscow, 119991 Russia
- Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Moscow Region, 141701 Russia
| | - V. S. Prassolov
- Engelhardt Institute of Molecular Biology, Russian Academy of Science, Moscow, 119991 Russia
| | - P. V. Spirin
- Engelhardt Institute of Molecular Biology, Russian Academy of Science, Moscow, 119991 Russia
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Hu X, Wang Y, Gao X, Xu S, Zang L, Xiao Y, Li Z, Hua H, Xu J, Li D. Recent Progress of Oridonin and Its Derivatives for the Treatment of Acute Myelogenous Leukemia. Mini Rev Med Chem 2020; 20:483-497. [PMID: 31660811 DOI: 10.2174/1389557519666191029121809] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 03/13/2019] [Accepted: 09/06/2019] [Indexed: 01/03/2023]
Abstract
First stage human clinical trial (CTR20150246) for HAO472, the L-alanine-(14-oridonin) ester trifluoroacetate, was conducted by a Chinese company, Hengrui Medicine Co. Ltd, to develop a new treatment for acute myelogenous leukemia. Two patents, WO2015180549A1 and CN201410047904.X, covered the development of the I-type crystal, stability experiment, conversion rate research, bioavailability experiment, safety assessment, and solubility study. HAO472 hewed out new avenues to explore the therapeutic properties of oridonin derivatives and develop promising treatment of cancer originated from naturally derived drug candidates. Herein, we sought to overview recent progress of the synthetic, physiological, and pharmacological investigations of oridonin and its derivatives, aiming to disclose the therapeutic potentials and broaden the platform for the discovery of new anticancer drugs.
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Affiliation(s)
- Xu Hu
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, and School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, China
| | - Yan Wang
- Valiant Co. Ltd., 11 Wuzhishan Road, YEDA Yantai, Shandong 264006, China
| | - Xiang Gao
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, and School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, China
| | - Shengtao Xu
- Department of Medicinal Chemistry and State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjia Xiang, Nanjing 210009, China
| | - Linghe Zang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, China
| | - Yan Xiao
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, and School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, China
| | - Zhanlin Li
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, and School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, China
| | - Huiming Hua
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, and School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, China
| | - Jinyi Xu
- Department of Medicinal Chemistry and State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjia Xiang, Nanjing 210009, China
| | - Dahong Li
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, and School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, China
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Karpov DS, Spirin PV, Zheltukhin AO, Tutyaeva VV, Zinovieva OL, Grineva EN, Matrosova VA, Krasnov GS, Snezhkina AV, Kudryavtseva AV, Prassolov VS, Mashkova TD, Lisitsyn NA. LINC00973 Induces Proliferation Arrest of Drug-Treated Cancer Cells by Preventing p21 Degradation. Int J Mol Sci 2020; 21:ijms21218322. [PMID: 33171937 PMCID: PMC7664178 DOI: 10.3390/ijms21218322] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 10/31/2020] [Accepted: 11/04/2020] [Indexed: 12/21/2022] Open
Abstract
Overcoming drug resistance of cancer cells is the major challenge in molecular oncology. Here, we demonstrate that long non-coding RNA LINC00973 is up-regulated in normal and cancer cells of different origins upon treatment with different chemotherapeutics. Bioinformatics analysis shows that this is a consequence of DNA damage response pathway activation or mitotic arrest. Knockdown of LINC0973 decreases p21 levels, activates cellular proliferation of cancer cells, and suppresses apoptosis of drug-treated cells. We have found that LINC00973 strongly increases p21 protein content, possibly by blocking its degradation. Besides, we have found that ectopic over-expression of LINC00973 inhibits formation of the pro-survival p53-Ser15-P isoform, which preserves chromosome integrity. These results might open a new approach to the development of more efficient anti-cancer drugs.
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Affiliation(s)
- Dmitry S. Karpov
- Engelhard Institute of Molecular Biology, Russian Academy of Sciences, 111991 Moscow, Russia; (D.S.K.); (P.V.S.); (A.O.Z.); (V.V.T.); (O.L.Z.); (E.N.G.); (V.A.M.); (G.S.K.); (A.V.S.); (A.V.K.); (V.S.P.); (T.D.M.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhard Institute of Molecular Biology, 111991 Moscow, Russia
| | - Pavel V. Spirin
- Engelhard Institute of Molecular Biology, Russian Academy of Sciences, 111991 Moscow, Russia; (D.S.K.); (P.V.S.); (A.O.Z.); (V.V.T.); (O.L.Z.); (E.N.G.); (V.A.M.); (G.S.K.); (A.V.S.); (A.V.K.); (V.S.P.); (T.D.M.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhard Institute of Molecular Biology, 111991 Moscow, Russia
| | - Andrey O. Zheltukhin
- Engelhard Institute of Molecular Biology, Russian Academy of Sciences, 111991 Moscow, Russia; (D.S.K.); (P.V.S.); (A.O.Z.); (V.V.T.); (O.L.Z.); (E.N.G.); (V.A.M.); (G.S.K.); (A.V.S.); (A.V.K.); (V.S.P.); (T.D.M.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhard Institute of Molecular Biology, 111991 Moscow, Russia
| | - Vera V. Tutyaeva
- Engelhard Institute of Molecular Biology, Russian Academy of Sciences, 111991 Moscow, Russia; (D.S.K.); (P.V.S.); (A.O.Z.); (V.V.T.); (O.L.Z.); (E.N.G.); (V.A.M.); (G.S.K.); (A.V.S.); (A.V.K.); (V.S.P.); (T.D.M.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhard Institute of Molecular Biology, 111991 Moscow, Russia
| | - Olga L. Zinovieva
- Engelhard Institute of Molecular Biology, Russian Academy of Sciences, 111991 Moscow, Russia; (D.S.K.); (P.V.S.); (A.O.Z.); (V.V.T.); (O.L.Z.); (E.N.G.); (V.A.M.); (G.S.K.); (A.V.S.); (A.V.K.); (V.S.P.); (T.D.M.)
| | - Evgenia N. Grineva
- Engelhard Institute of Molecular Biology, Russian Academy of Sciences, 111991 Moscow, Russia; (D.S.K.); (P.V.S.); (A.O.Z.); (V.V.T.); (O.L.Z.); (E.N.G.); (V.A.M.); (G.S.K.); (A.V.S.); (A.V.K.); (V.S.P.); (T.D.M.)
| | - Vera A. Matrosova
- Engelhard Institute of Molecular Biology, Russian Academy of Sciences, 111991 Moscow, Russia; (D.S.K.); (P.V.S.); (A.O.Z.); (V.V.T.); (O.L.Z.); (E.N.G.); (V.A.M.); (G.S.K.); (A.V.S.); (A.V.K.); (V.S.P.); (T.D.M.)
| | - George S. Krasnov
- Engelhard Institute of Molecular Biology, Russian Academy of Sciences, 111991 Moscow, Russia; (D.S.K.); (P.V.S.); (A.O.Z.); (V.V.T.); (O.L.Z.); (E.N.G.); (V.A.M.); (G.S.K.); (A.V.S.); (A.V.K.); (V.S.P.); (T.D.M.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhard Institute of Molecular Biology, 111991 Moscow, Russia
| | - Anastasiya V. Snezhkina
- Engelhard Institute of Molecular Biology, Russian Academy of Sciences, 111991 Moscow, Russia; (D.S.K.); (P.V.S.); (A.O.Z.); (V.V.T.); (O.L.Z.); (E.N.G.); (V.A.M.); (G.S.K.); (A.V.S.); (A.V.K.); (V.S.P.); (T.D.M.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhard Institute of Molecular Biology, 111991 Moscow, Russia
| | - Anna V. Kudryavtseva
- Engelhard Institute of Molecular Biology, Russian Academy of Sciences, 111991 Moscow, Russia; (D.S.K.); (P.V.S.); (A.O.Z.); (V.V.T.); (O.L.Z.); (E.N.G.); (V.A.M.); (G.S.K.); (A.V.S.); (A.V.K.); (V.S.P.); (T.D.M.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhard Institute of Molecular Biology, 111991 Moscow, Russia
| | - Vladimir S. Prassolov
- Engelhard Institute of Molecular Biology, Russian Academy of Sciences, 111991 Moscow, Russia; (D.S.K.); (P.V.S.); (A.O.Z.); (V.V.T.); (O.L.Z.); (E.N.G.); (V.A.M.); (G.S.K.); (A.V.S.); (A.V.K.); (V.S.P.); (T.D.M.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhard Institute of Molecular Biology, 111991 Moscow, Russia
| | - Tamara D. Mashkova
- Engelhard Institute of Molecular Biology, Russian Academy of Sciences, 111991 Moscow, Russia; (D.S.K.); (P.V.S.); (A.O.Z.); (V.V.T.); (O.L.Z.); (E.N.G.); (V.A.M.); (G.S.K.); (A.V.S.); (A.V.K.); (V.S.P.); (T.D.M.)
| | - Nikolai A. Lisitsyn
- Engelhard Institute of Molecular Biology, Russian Academy of Sciences, 111991 Moscow, Russia; (D.S.K.); (P.V.S.); (A.O.Z.); (V.V.T.); (O.L.Z.); (E.N.G.); (V.A.M.); (G.S.K.); (A.V.S.); (A.V.K.); (V.S.P.); (T.D.M.)
- Correspondence: ; Tel.: +7-916-531-2672
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9
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Liu X, Xu J, Zhou J, Shen Q. Oridonin and its derivatives for cancer treatment and overcoming therapeutic resistance. Genes Dis 2020; 8:448-462. [PMID: 34179309 PMCID: PMC8209342 DOI: 10.1016/j.gendis.2020.06.010] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/23/2020] [Accepted: 06/29/2020] [Indexed: 12/24/2022] Open
Abstract
Cancer is one of the diseases with high morbidity and mortality on a global scale. Chemotherapy remains the primary treatment option for most cancer patients, including patients with progressive, metastatic, and recurrent diseases. To date, hundreds of chemotherapy drugs are used to treat various cancers, however, the anti-cancer efficacy and outcomes are largely hampered by chemotherapy-associated toxicity and acquired therapeutic resistance. The natural product (NP) oridonin has been extensively studied for its anti-cancer efficacy. More recently, oridonin has been shown to overcome drug resistance through multiple mechanisms, with yet-to-be-defined bona fide targets. Hundreds of oridonin derivative analogs (oridonalogs) have been synthesized and screened for improved potency, bioavailability, and other drug properties. Particularly, many of these oridonalogs have been tested against oridonin for tumor growth inhibition, potential for overcoming therapeutic resistance, and immunity modulation. This concise review seeks to summarize the advances in this field in light of identifying clinical-trial level drug candidates with the promise for treating progressive cancers and reversing chemoresistance.
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Affiliation(s)
- Xi Liu
- Department of Genetics, Stanley S. Scott Cancer Center, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, 70112, USA
| | - Jimin Xu
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Jia Zhou
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, TX, 77555, USA
- Corresponding author. Department of Pharmacology and Toxicology, The University of Texas Medical Branch, Basic Science Building, 301 University Blvd., Galveston, TX, 77555, USA.
| | - Qiang Shen
- Department of Genetics, Stanley S. Scott Cancer Center, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, 70112, USA
- Corresponding author. Department of Genetics, Stanley S. Scott Cancer Center, School of Medicine, Louisiana State University Health Sciences Center, 1700 Tulane Avenue, New Orleans, LA, 70112, USA.
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10
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Borisov N, Sorokin M, Garazha A, Buzdin A. Quantitation of Molecular Pathway Activation Using RNA Sequencing Data. Methods Mol Biol 2020; 2063:189-206. [PMID: 31667772 DOI: 10.1007/978-1-0716-0138-9_15] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Intracellular molecular pathways (IMPs) control all major events in the living cell. IMPs are considered hotspots in biomedical sciences and thousands of IMPs have been discovered for humans and model organisms. Knowledge of IMPs activation is essential for understanding biological functions and differences between the biological objects at the molecular level. Here we describe the Oncobox system for accurate quantitative scoring activities of up to several thousand molecular pathways based on high throughput molecular data. Although initially designed for gene expression and mainly RNA sequencing data, Oncobox is now also applicable for quantitative proteomics, microRNA and transcription factor binding sites mapping data. The Oncobox system includes modules of gene expression data harmonization, aggregation and comparison and a recursive algorithm for automatic annotation of molecular pathways. The universal rationale of Oncobox enables scoring of signaling, metabolic, cytoskeleton, immunity, DNA repair, and other pathways in a multitude of biological objects. The Oncobox system can be helpful to all those working in the fields of genetics, biochemistry, interactomics, and big data analytics in molecular biomedicine.
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Affiliation(s)
- Nicolas Borisov
- Laboratory of Clinical Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
- Omicsway Corp., Walnut, CA, USA
| | - Maxim Sorokin
- Laboratory of Clinical Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
- Omicsway Corp., Walnut, CA, USA
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | - Anton Buzdin
- Laboratory of Clinical Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia.
- Omicsway Corp., Walnut, CA, USA.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
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11
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Tkachev V, Sorokin M, Garazha A, Borisov N, Buzdin A. Oncobox Method for Scoring Efficiencies of Anticancer Drugs Based on Gene Expression Data. Methods Mol Biol 2020; 2063:235-255. [PMID: 31667774 DOI: 10.1007/978-1-0716-0138-9_17] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We describe here the Oncobox method for scoring efficiencies of anticancer target drugs (ATDs) using high throughput gene expression data. The method rationale, design, and validation are given along with the examples of its practical applications in biomedicine. The method is based on the analysis of intracellular molecular pathways activation and measuring expressions of molecular target genes for every ATD under consideration. Using Oncobox method requires collection of normal (control) expression profiles and annotated databases of molecular pathways and drug target genes. Both microarray and RNA sequencing profiles are acceptable, although the latter type of data prevails in the most recent applications of this technique.
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Affiliation(s)
| | - Maxim Sorokin
- Omicsway Corp., Walnut, CA, USA
- Laboratory of Clinical Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | | | - Nicolas Borisov
- Omicsway Corp., Walnut, CA, USA
- Laboratory of Clinical Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Anton Buzdin
- Omicsway Corp., Walnut, CA, USA.
- Laboratory of Clinical Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
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12
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Zolotovskaia M, Sorokin M, Garazha A, Borisov N, Buzdin A. Molecular Pathway Analysis of Mutation Data for Biomarkers Discovery and Scoring of Target Cancer Drugs. Methods Mol Biol 2020; 2063:207-234. [PMID: 31667773 DOI: 10.1007/978-1-0716-0138-9_16] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
DNA mutations govern cancer development. Cancer mutation profiles vary dramatically among the individuals. In some cases, they may serve as the predictors of disease progression and response to therapies. However, the biomarker potential of cancer mutations can be dramatically (several orders of magnitude) enhanced by applying molecular pathway-based approach. We developed Oncobox system for calculation of pathway instability (PI) values for the molecular pathways that are aggregated mutation frequencies of the pathway members normalized on gene lengths and on number of genes in the pathway. PI scores can be effective biomarkers in different types of comparisons, for example, as the cancer type biomarkers and as the predictors of tumor response to target therapies. The latter option is implemented using mutation drug score (MDS) values, which algorithmically rank the drugs capacity of interfering with the mutated molecular pathways. Here, describe the mathematical basis and algorithms for PI and MDS values calculation, validation and implementation. The example analysis is provided encompassing 5956 human tumor mutation profiles of 15 cancer types from The Cancer Genome Atlas (TCGA) project, that totally make 2,316,670 mutations in 19,872 genes and 1748 molecular pathways, thus enabling ranking of 128 clinically approved target drugs. Our results evidence that the Oncobox PI and MDS approaches are highly useful for basic and applied aspects of molecular oncology and pharmacology research.
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Affiliation(s)
- Marianna Zolotovskaia
- Omicsway Corp., Walnut, CA, USA
- Department of Oncology, Hematology and Radiotherapy of Pediatric Faculty, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Maxim Sorokin
- Omicsway Corp., Walnut, CA, USA
- Laboratory of Clinical Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | - Nikolay Borisov
- Omicsway Corp., Walnut, CA, USA
- Laboratory of Clinical Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Anton Buzdin
- Omicsway Corp., Walnut, CA, USA.
- Laboratory of Clinical Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
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13
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Buzdin A, Sorokin M, Garazha A, Glusker A, Aleshin A, Poddubskaya E, Sekacheva M, Kim E, Gaifullin N, Giese A, Seryakov A, Rumiantsev P, Moshkovskii S, Moiseev A. RNA sequencing for research and diagnostics in clinical oncology. Semin Cancer Biol 2019; 60:311-323. [PMID: 31412295 DOI: 10.1016/j.semcancer.2019.07.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 07/16/2019] [Indexed: 12/26/2022]
Abstract
Molecular diagnostics is becoming one of the major drivers of personalized oncology. With hundreds of different approved anticancer drugs and regimens of their administration, selecting the proper treatment for a patient is at least nontrivial task. This is especially sound for the cases of recurrent and metastatic cancers where the standard lines of therapy failed. Recent trials demonstrated that mutation assays have a strong limitation in personalized selection of therapeutics, consequently, most of the drugs cannot be ranked and only a small percentage of patients can benefit from the screening. Other approaches are, therefore, needed to address a problem of finding proper targeted therapies. The analysis of RNA expression (transcriptomic) profiles presents a reasonable solution because transcriptomics stands a few steps closer to tumor phenotype than the genome analysis. Several recent studies pioneered using transcriptomics for practical oncology and showed truly encouraging clinical results. The possibility of directly measuring of expression levels of molecular drugs' targets and profiling activation of the relevant molecular pathways enables personalized prioritizing for all types of molecular-targeted therapies. RNA sequencing is the most robust tool for the high throughput quantitative transcriptomics. Its use, potentials, and limitations for the clinical oncology will be reviewed here along with the technical aspects such as optimal types of biosamples, RNA sequencing profile normalization, quality controls and several levels of data analysis.
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Affiliation(s)
- Anton Buzdin
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia; Omicsway Corp., Walnut, CA, USA; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
| | - Maxim Sorokin
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia; Omicsway Corp., Walnut, CA, USA; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | | | - Alex Aleshin
- Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Elena Poddubskaya
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia; Vitamed Oncological Clinics, Moscow, Russia
| | - Marina Sekacheva
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Ella Kim
- Johannes Gutenberg University Mainz, Mainz, Germany
| | - Nurshat Gaifullin
- Lomonosov Moscow State University, Faculty of Medicine, Moscow, Russia
| | | | | | | | - Sergey Moshkovskii
- Institute of Biomedical Chemistry, Moscow, 119121, Russia; Pirogov Russian National Research Medical University (RNRMU), Moscow, 117997, Russia
| | - Alexey Moiseev
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
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14
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Li J, Wu Y, Wang D, Zou L, Fu C, Zhang J, Leung GPH. Oridonin synergistically enhances the anti-tumor efficacy of doxorubicin against aggressive breast cancer via pro-apoptotic and anti-angiogenic effects. Pharmacol Res 2019; 146:104313. [PMID: 31202781 DOI: 10.1016/j.phrs.2019.104313] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 06/12/2019] [Accepted: 06/12/2019] [Indexed: 01/30/2023]
Abstract
The therapeutic outcomes of doxorubicin (Dox) treatment in breast cancer are limited by decreased drug efficiency and cardiotoxicity. The aim of this study was to investigate whether oridonin (Ori), a natural chemical abundant in the Chinese herb Isodon rubescens, might potentiate the anticancer effects, and decrease the adverse cardiotoxic effects, of Dox. On the basis of the optimized drug ratio determined through combination index calculations, we evaluated the synergistic effects and potential mechanisms of combining Dox with Ori to suppress breast cancer growth and angiogenesis both in vitro and in vivo. Dox plus Ori synergistically induced apoptosis in MDA-MB-231 cells, in a manner involving regulation of the Bcl-2/Bax, PARP, Caspase 3 and Survivin signaling pathways. Additionally, Ori increased the intracellular accumulation of Dox in MDA-MB-231 cells. Moreover, Dox plus Ori significantly decreased the proliferation, migration, invasion and tube formation of HUVECs. The underlying anti-angiogenic mechanism may have been due to the inhibition of VEGFR2-mediated signaling. Computational docking analysis further demonstrated that Dox plus Ori had high affinity toward the ATP-binding domain of VEGFR-2 kinase. Consistently with these findings, in vivo studies indicated that Ori enhanced the antitumor effect of Dox via activating apoptosis and inhibiting blood vessel formation at tumor sites. Moreover, Ori reversed the Dox-induced cardiotoxicity in a mouse model. In conclusion, our findings provide strong evidence that Ori may be highly promising in enhancing the efficacy of Dox and decreasing its adverse cardiotoxic effects, thus suggesting that Ori may serve as a potential adjunct therapy during Dox-based chemotherapy.
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Affiliation(s)
- Jingjing Li
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China; Department of Pharmacology and Pharmacy, The University of Hong Kong, 999077, Hong Kong Special Administrative Region
| | - Yihan Wu
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Di Wang
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Liang Zou
- School of Medicine, Chengdu University, Chengdu, 610106, China
| | - Chaomei Fu
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Jinming Zhang
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
| | - George Pak-Heng Leung
- Department of Pharmacology and Pharmacy, The University of Hong Kong, 999077, Hong Kong Special Administrative Region.
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15
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Hydrogen sulfide releasing enmein-type diterpenoid derivatives as apoptosis inducers through mitochondria-related pathways. Bioorg Chem 2019; 82:192-203. [DOI: 10.1016/j.bioorg.2018.10.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/21/2018] [Accepted: 10/04/2018] [Indexed: 01/20/2023]
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16
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Zolotovskaia MA, Sorokin MI, Emelianova AA, Borisov NM, Kuzmin DV, Borger P, Garazha AV, Buzdin AA. Pathway Based Analysis of Mutation Data Is Efficient for Scoring Target Cancer Drugs. Front Pharmacol 2019; 10:1. [PMID: 30728774 PMCID: PMC6351482 DOI: 10.3389/fphar.2019.00001] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 01/03/2019] [Indexed: 12/20/2022] Open
Abstract
Despite the significant achievements in chemotherapy, cancer remains one of the leading causes of death. Target therapy revolutionized this field, but efficiencies of target drugs show dramatic variation among individual patients. Personalization of target therapies remains, therefore, a challenge in oncology. Here, we proposed molecular pathway-based algorithm for scoring of target drugs using high throughput mutation data to personalize their clinical efficacies. This algorithm was validated on 3,800 exome mutation profiles from The Cancer Genome Atlas (TCGA) project for 128 target drugs. The output values termed Mutational Drug Scores (MDS) showed positive correlation with the published drug efficiencies in clinical trials. We also used MDS approach to simulate all known protein coding genes as the putative drug targets. The model used was built on the basis of 18,273 mutation profiles from COSMIC database for eight cancer types. We found that the MDS algorithm-predicted hits frequently coincide with those already used as targets of the existing cancer drugs, but several novel candidates can be considered promising for further developments. Our results evidence that the MDS is applicable to ranking of anticancer drugs and can be applied for the identification of novel molecular targets.
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Affiliation(s)
- Marianna A Zolotovskaia
- Oncobox Ltd., Moscow, Russia.,Department of Oncology, Hematology and Radiotherapy of Pediatric Faculty, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Maxim I Sorokin
- The Laboratory of Clinical Bioinformatics, IM Sechenov First Moscow State Medical University, Moscow, Russia.,Omicsway Corp., Walnut, CA, United States.,Science-Educational Center Department, M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Anna A Emelianova
- Science-Educational Center Department, M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Nikolay M Borisov
- The Laboratory of Clinical Bioinformatics, IM Sechenov First Moscow State Medical University, Moscow, Russia.,Omicsway Corp., Walnut, CA, United States
| | - Denis V Kuzmin
- Science-Educational Center Department, M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Pieter Borger
- Laboratory of the Swiss Hepato-Pancreato-Biliary, Department of Surgery, Transplantation Center, University Hospital Zurich, Zurich, Switzerland
| | | | - Anton A Buzdin
- Oncobox Ltd., Moscow, Russia.,The Laboratory of Clinical Bioinformatics, IM Sechenov First Moscow State Medical University, Moscow, Russia.,Science-Educational Center Department, M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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17
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Molecular pathway activation – New type of biomarkers for tumor morphology and personalized selection of target drugs. Semin Cancer Biol 2018; 53:110-124. [DOI: 10.1016/j.semcancer.2018.06.003] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 06/19/2018] [Accepted: 06/19/2018] [Indexed: 02/06/2023]
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18
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Oncobox Bioinformatical Platform for Selecting Potentially Effective Combinations of Target Cancer Drugs Using High-Throughput Gene Expression Data. Cancers (Basel) 2018; 10:cancers10100365. [PMID: 30274248 PMCID: PMC6209915 DOI: 10.3390/cancers10100365] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 09/24/2018] [Accepted: 09/25/2018] [Indexed: 12/22/2022] Open
Abstract
Sequential courses of anticancer target therapy lead to selection of drug-resistant cells, which results in continuous decrease of clinical response. Here we present a new approach for predicting effective combinations of target drugs, which act in a synergistic manner. Synergistic combinations of drugs may prevent or postpone acquired resistance, thus increasing treatment efficiency. We cultured human ovarian carcinoma SKOV-3 and neuroblastoma NGP-127 cancer cell lines in the presence of Tyrosine Kinase Inhibitors (Pazopanib, Sorafenib, and Sunitinib) and Rapalogues (Temsirolimus and Everolimus) for four months and obtained cell lines demonstrating increased drug resistance. We investigated gene expression profiles of intact and resistant cells by microarrays and analyzed alterations in 378 cancer-related signaling pathways using the bioinformatical platform Oncobox. This revealed numerous pathways linked with development of drug resistant phenotypes. Our approach is based on targeting proteins involved in as many as possible signaling pathways upregulated in resistant cells. We tested 13 combinations of drugs and/or selective inhibitors predicted by Oncobox and 10 random combinations. Synergy scores for Oncobox predictions were significantly higher than for randomly selected drug combinations. Thus, the proposed approach significantly outperforms random selection of drugs and can be adopted to enhance discovery of new synergistic combinations of anticancer target drugs.
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19
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Novel enmein-type diterpenoid hybrids coupled with nitrogen mustards: Synthesis of promising candidates for anticancer therapeutics. Eur J Med Chem 2018; 146:588-598. [DOI: 10.1016/j.ejmech.2018.01.069] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Revised: 01/18/2018] [Accepted: 01/19/2018] [Indexed: 12/20/2022]
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20
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Vagapova ER, Spirin PV, Lebedev TD, Prassolov VS. The Role of TAL1 in Hematopoiesis and Leukemogenesis. Acta Naturae 2018; 10:15-23. [PMID: 29713515 PMCID: PMC5916730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
TAL1 (SCL/TAL1, T-cell acute leukemia protein 1) is a transcription factor that is involved in the process of hematopoiesis and leukemogenesis. It participates in blood cell formation, forms mesoderm in early embryogenesis, and regulates hematopoiesis in adult organisms. TAL1 is essential in maintaining the multipotency of hematopoietic stem cells (HSC) and keeping them in quiescence (stage G0). TAL1 forms complexes with various transcription factors, regulating hematopoiesis (E2A/HEB, GATA1-3, LMO1-2, Ldb1, ETO2, RUNX1, ERG, FLI1). In these complexes, TAL1 regulates normal myeloid differentiation, controls the proliferation of erythroid progenitors, and determines the choice of the direction of HSC differentiation. The transcription factors TAL1, E2A, GATA1 (or GATA2), LMO2, and Ldb1 are the major components of the SCL complex. In addition to normal hematopoiesis, this complex may also be involved in the process of blood cell malignant transformation. Upregulation of C-KIT expression is one of the main roles played by the SCL complex. Today, TAL1 and its partners are considered promising therapeutic targets in the treatment of T-cell acute lymphoblastic leukemia.
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Affiliation(s)
- E. R. Vagapova
- The Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str. 32, Moscow,119991, Russia
| | - P. V. Spirin
- The Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str. 32, Moscow,119991, Russia
| | - T. D. Lebedev
- The Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str. 32, Moscow,119991, Russia
| | - V. S. Prassolov
- The Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str. 32, Moscow,119991, Russia
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