1
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Goleij P, Pourali G, Raisi A, Ravaei F, Golestan S, Abed A, Razavi ZS, Zarepour F, Taghavi SP, Ahmadi Asouri S, Rafiei M, Mousavi SM, Hamblin MR, Talei S, Sheida A, Mirzaei H. Role of Non-coding RNAs in the Response of Glioblastoma to Temozolomide. Mol Neurobiol 2024:10.1007/s12035-024-04316-z. [PMID: 39023794 DOI: 10.1007/s12035-024-04316-z] [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: 11/27/2023] [Accepted: 06/16/2024] [Indexed: 07/20/2024]
Abstract
Chemotherapy and radiotherapy are widely used in clinical practice across the globe as cancer treatments. Intrinsic or acquired chemoresistance poses a significant problem for medical practitioners and researchers, causing tumor recurrence and metastasis. The most dangerous kind of malignant brain tumor is called glioblastoma multiforme (GBM) that often recurs following surgery. The most often used medication for treating GBM is temozolomide chemotherapy; however, most patients eventually become resistant. Researchers are studying preclinical models that accurately reflect human disease and can be used to speed up drug development to overcome chemoresistance in GBM. Non-coding RNAs (ncRNAs) have been shown to be substantial in regulating tumor development and facilitating treatment resistance in several cancers, such as GBM. In this work, we mentioned the mechanisms of how different ncRNAs (microRNAs, long non-coding RNAs, circular RNAs) can regulate temozolomide chemosensitivity in GBM. We also address the role of these ncRNAs encapsulated inside secreted exosomes.
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Affiliation(s)
- Pouya Goleij
- Department of Genetics, Faculty of Biology, Sana Institute of Higher Education, Sari, Iran
- USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ghazaleh Pourali
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Arash Raisi
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Fatemeh Ravaei
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Shahin Golestan
- Department of Ophthalmology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Atena Abed
- Department of Medical Biotechnology, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Zahra Sadat Razavi
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Fatemeh Zarepour
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Seyed Pouya Taghavi
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Sahar Ahmadi Asouri
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Moein Rafiei
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Seyed Mojtaba Mousavi
- Department of Neuroscience and Addiction Studies, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Michael R Hamblin
- Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein, 2028, South Africa
| | - Sahand Talei
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
| | - Amirhossein Sheida
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran.
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran.
| | - Hamed Mirzaei
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran.
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran.
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2
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Thompson PE, Shortt J. Defeating MYC with drug combinations or dual-targeting drugs. Trends Pharmacol Sci 2024; 45:490-502. [PMID: 38782688 DOI: 10.1016/j.tips.2024.04.008] [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: 03/11/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 05/25/2024]
Abstract
Members of the MYC family of proteins are a major target for cancer drug discovery, but the development of drugs that block MYC-driven cancers has not yet been successful. Approaches to achieve success may include the development of combination therapies or dual-acting drugs that target MYC at multiple nodes. Such treatments hold the possibility of additive or synergistic activity, potentially reducing side effect profiles and the emergence of resistance. In this review, we examine the prominent MYC-related targets and highlight those that have been targeted in combination and/or dual-target approaches. Finally, we explore the challenges of combination and dual-target approaches from a drug development perspective.
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Affiliation(s)
- Philip E Thompson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia.
| | - Jake Shortt
- Blood Cancer Therapeutics Laboratory, School of Clinical Sciences at Monash Health, Faculty of Medicine Nursing and Health Sciences, Monash University, Melbourne, Victoria 3168, Australia; Monash Hematology, Monash Health, Melbourne, Victoria 3168, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria 3000, Australia
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3
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Wang Y, Hermetz K, Burt A, Kennedy EM, Lesseur C, Panuwet P, Fiedler N, Prapamontol T, Suttiwan P, Naksen W, B Barr D, Hao K, Chen J, Marsit CJ. Placental transcriptome variation associated with season, location, and urinary prenatal pyrethroid metabolites of Thai farm-working women. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 349:123873. [PMID: 38554839 PMCID: PMC11070292 DOI: 10.1016/j.envpol.2024.123873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 03/21/2024] [Accepted: 03/24/2024] [Indexed: 04/02/2024]
Abstract
Prenatal exposure to pyrethroids is linked to adverse health effects in early life and proper placental function is critical to fetal development. This study explores the impact of prenatal pyrethroid exposure, as well as factors impacting exposure and effect, on the placental transcriptome, to understand pyrethroid exposures' relationship to placental function. The study of Asian Women and their Offspring's Development and Environmental Exposures (SAWASDEE) recruited pregnant farm-working women from two agricultural districts in the Chiang Mai province of Thailand between 2017 and 2019. This cohort was predominantly exposed to cypermethrin (type II), alongside pyrethroids such as cyfluthrin (type II) and permethrin (type I). In 253 participants, maternal urinary pyrethroid metabolites, 3-phenoxybenzoic acid (PBA), cis-3-(2,2-Dichlorovinyl)-2,2-dimethylcyclopropane carboxylic acid (CDCCA), and trans-3-(2,2-Dichlorovinyl)-2,2-dimethylcyclopropane carboxylic acid (TDCCA) were measured in early, middle, and late pregnancy and adjusted for urinary creatinine. The placental transcriptome was analyzed using RNA-Seq. Using generalized linear regression, we identified differentially expressed genes (DEGs) associated with the sum of each metabolite across pregnancy, as well as those associated with location of residence and season of birth. Pathway and upstream transcription factor analyses were performed to examine potential mechanisms associated with DEGs. Notably, TDCCA and CDCCA levels peaked in late pregnancy, with significant regional differences, particularly higher levels in the Fang region. Placental gene expression analysis showed no DEGs associated with individual metabolites at FDR<0.05. However, 251 DEGs by location, implicating immune response and oxidative phosphorylation pathways, were identified, while season of birth was associated with 2585 DEGs, over-represented in fibrosis signaling and metabolism pathways. Finally, transcription factor analysis identified 226 and 282 transcription factors associated with location and season, respectively, related to cell proliferation, differentiation, and the immune system. These alterations may have significant implications for fetal development and other pathologic processes, highlighting the importance of monitoring environmental exposures during pregnancy.
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Affiliation(s)
- Yewei Wang
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Karen Hermetz
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Amber Burt
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Elizabeth M Kennedy
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Corina Lesseur
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Parinya Panuwet
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Nancy Fiedler
- Rutgers University School of Public Health, Environmental and Occupational Health Sciences Institute, Piscataway, NJ, USA
| | - Tippawan Prapamontol
- Research Institute for Health Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Panrapee Suttiwan
- Life Di Center, Faculty of Psychology, Chulalongkorn University, Bangkok, Thailand
| | - Warangkana Naksen
- Faculty of Public Health, Chiang Mai University, Chiang Mai, Thailand
| | - Dana B Barr
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Ke Hao
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jia Chen
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carmen J Marsit
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA.
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4
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Lama D, Vosselman T, Sahin C, Liaño-Pons J, Cerrato CP, Nilsson L, Teilum K, Lane DP, Landreh M, Arsenian Henriksson M. A druggable conformational switch in the c-MYC transactivation domain. Nat Commun 2024; 15:1865. [PMID: 38424045 PMCID: PMC10904854 DOI: 10.1038/s41467-024-45826-7] [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: 01/12/2023] [Accepted: 02/06/2024] [Indexed: 03/02/2024] Open
Abstract
The c-MYC oncogene is activated in over 70% of all human cancers. The intrinsic disorder of the c-MYC transcription factor facilitates molecular interactions that regulate numerous biological pathways, but severely limits efforts to target its function for cancer therapy. Here, we use a reductionist strategy to characterize the dynamic and structural heterogeneity of the c-MYC protein. Using probe-based Molecular Dynamics (MD) simulations and machine learning, we identify a conformational switch in the c-MYC amino-terminal transactivation domain (termed coreMYC) that cycles between a closed, inactive, and an open, active conformation. Using the polyphenol epigallocatechin gallate (EGCG) to modulate the conformational landscape of coreMYC, we show through biophysical and cellular assays that the induction of a closed conformation impedes its interactions with the transformation/transcription domain-associated protein (TRRAP) and the TATA-box binding protein (TBP) which are essential for the transcriptional and oncogenic activities of c-MYC. Together, these findings provide insights into structure-activity relationships of c-MYC, which open avenues towards the development of shape-shifting compounds to target c-MYC as well as other disordered transcription factors for cancer treatment.
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Affiliation(s)
- Dilraj Lama
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Biomedicum, SE-17165, Stockholm, Sweden.
| | - Thibault Vosselman
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Biomedicum, SE-17165, Stockholm, Sweden
| | - Cagla Sahin
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Biomedicum, SE-17165, Stockholm, Sweden
- Department of Biology, Structural Biology and NMR Laboratory and the Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Judit Liaño-Pons
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Biomedicum, SE-17165, Stockholm, Sweden
| | - Carmine P Cerrato
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Biomedicum, SE-17165, Stockholm, Sweden
| | - Lennart Nilsson
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-14813, Huddinge, Sweden
| | - Kaare Teilum
- Department of Biology, Structural Biology and NMR Laboratory and the Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - David P Lane
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Biomedicum, SE-17165, Stockholm, Sweden
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Biomedicum, SE-17165, Stockholm, Sweden.
- Department of Cell- and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden.
| | - Marie Arsenian Henriksson
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Biomedicum, SE-17165, Stockholm, Sweden.
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, SE-221 00, Lund, Sweden.
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5
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Schütz S, Bergsdorf C, Hänni-Holzinger S, Lingel A, Renatus M, Gossert AD, Jahnke W. Intrinsically Disordered Regions in the Transcription Factor MYC:MAX Modulate DNA Binding via Intramolecular Interactions. Biochemistry 2024. [PMID: 38264995 DOI: 10.1021/acs.biochem.3c00608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
The basic helix-loop-helix leucine zipper (bHLH-LZ) transcription factor (TF) MYC is in large part an intrinsically disordered oncoprotein. In complex with its obligate heterodimerization partner MAX, MYC preferentially binds E-Box DNA sequences (CANNTG). At promoters containing these sequence motifs, MYC controls fundamental cellular processes such as cell cycle progression, metabolism, and apoptosis. A vast network of proteins in turn regulates MYC function via intermolecular interactions. In this work, we establish another layer of MYC regulation by intramolecular interactions. We used nuclear magnetic resonance (NMR) spectroscopy to identify and map multiple binding sites for the C-terminal MYC:MAX DNA-binding domain (DBD) on the intrinsically disordered regions (IDRs) in the MYC N-terminus. We find that these binding events in trans are driven by electrostatic attraction, that they have distinct affinities, and that they are competitive with DNA binding. Thereby, we observe the strongest effects for the N-terminal MYC box 0 (Mb0), a conserved motif involved in MYC transactivation and target gene induction. We prepared recombinant full-length MYC:MAX complex and demonstrate that the interactions identified in this work are also relevant in cis, i.e., as intramolecular interactions. These findings are supported by surface plasmon resonance (SPR) experiments, which revealed that intramolecular IDR:DBD interactions in MYC decelerate the association of MYC:MAX complexes to DNA. Our work offers new insights into how bHLH-LZ TFs are regulated by intramolecular interactions, which open up new possibilities for drug discovery.
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Affiliation(s)
- Stefan Schütz
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Christian Bergsdorf
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Sandra Hänni-Holzinger
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Andreas Lingel
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Martin Renatus
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | | | - Wolfgang Jahnke
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
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6
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Saito M, Fujimoto S, Kawasaki H. Ecdysone and gene expressions for chromatin remodeling, histone modification, and Broad Complex in relation to pupal commitment in Bombyx mori. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2024; 115:e22076. [PMID: 38288490 DOI: 10.1002/arch.22076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/28/2023] [Accepted: 12/08/2023] [Indexed: 02/01/2024]
Abstract
In the present study, we tried to clarify when and how pupal commitment (PT) better to use PC occurs and what is involved in the PT of Bombyx mori. To clarify this, we examined the responsiveness of a wing disc to ecdysone, referring to metamorphosis-related BR-C, development-related Myc and Wnt, and chromatin remodeling-related genes at around the predicted PT stage of the Bombyx wing disc. Wing disc responsiveness to juvenile hormone (JH) and ecdysone was examined using Methoprene and 20-hydroxyecdysone (20E) in vitro. The body weight of B. mori increased after the last larval ecdysis, peaked at Day 5 of the fifth larval instar (D5L5), and then decreased. The responsiveness of the wing disc to JH decreased after the last larval ecdysis up to D3L5. Bmbr-c (the Broad Complex of B. mori) showed enhanced expression in D4L5 wing discs with 20E treatment. Some chromatin remodeler and histone modifier genes (Bmsnr1, Bmutx, and Bmtip60) showed upregulation after being cultured with 20E in D4L5 wing discs. A low concentration of 20E is suggested to induce responsiveness to 20E in D4L5 wing discs. Bmbr-c, Bmsnr1, Bmutx, and Bmtip60 were upregulated after being cultured with a low concentration of 20E in D4L5 wing discs. The expression of Bmmyc and Bmwnt1 did not show a change after being cultured with or without 20E in D4L5 wing discs, while enhanced expression was observed with 20E in D5L5 wing discs. From the present results, we concluded that PT of the wing disc of B. mori occurred beginning on D4L5 with the secretion of low concentrations of ecdysteroids. Bmsnr1, Bmutx, Bmtip60, and BR-C are also involved.
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Affiliation(s)
- Maki Saito
- Department of Bioproductive Science, Faculty of Agriculture, Takasaki University of Health and Welfare, Gunma, Japan
| | - Shota Fujimoto
- Department of Bioproductive Science, Faculty of Agriculture, Takasaki University of Health and Welfare, Gunma, Japan
| | - Hideki Kawasaki
- Department of Bioproductive Science, Faculty of Agriculture, Takasaki University of Health and Welfare, Gunma, Japan
- Faculty of Agriculture, Utsunomiya University, Tochigi, Japan
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Jha RK, Kouzine F, Levens D. MYC function and regulation in physiological perspective. Front Cell Dev Biol 2023; 11:1268275. [PMID: 37941901 PMCID: PMC10627926 DOI: 10.3389/fcell.2023.1268275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/12/2023] [Indexed: 11/10/2023] Open
Abstract
MYC, a key member of the Myc-proto-oncogene family, is a universal transcription amplifier that regulates almost every physiological process in a cell including cell cycle, proliferation, metabolism, differentiation, and apoptosis. MYC interacts with several cofactors, chromatin modifiers, and regulators to direct gene expression. MYC levels are tightly regulated, and deregulation of MYC has been associated with numerous diseases including cancer. Understanding the comprehensive biology of MYC under physiological conditions is an utmost necessity to demark biological functions of MYC from its pathological functions. Here we review the recent advances in biological mechanisms, functions, and regulation of MYC. We also emphasize the role of MYC as a global transcription amplifier.
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Affiliation(s)
| | | | - David Levens
- Gene Regulation Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute (NCI), Bethesda, MD, United States
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8
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Kotekar A, Singh AK, Devaiah BN. BRD4 and MYC: power couple in transcription and disease. FEBS J 2023; 290:4820-4842. [PMID: 35866356 PMCID: PMC9867786 DOI: 10.1111/febs.16580] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/16/2022] [Accepted: 07/20/2022] [Indexed: 01/26/2023]
Abstract
The MYC proto-oncogene and BRD4, a BET family protein, are two cardinal proteins that have a broad influence in cell biology and disease. Both proteins are expressed ubiquitously in mammalian cells and play central roles in controlling growth, development, stress responses and metabolic function. As chromatin and transcriptional regulators, they play a critical role in regulating the expression of a burgeoning array of genes, maintaining chromatin architecture and genome stability. Consequently, impairment of their function or regulation leads to many diseases, with cancer being the most predominant. Interestingly, accumulating evidence indicates that regulation of the expression and functions of MYC are tightly intertwined with BRD4 at both transcriptional and post-transcriptional levels. Here, we review the mechanisms by which MYC and BRD4 are regulated, their functions in governing various molecular mechanisms and the consequences of their dysregulation that lead to disease. We present a perspective of how the regulatory mechanisms for the two proteins could be entwined at multiple points in a BRD4-MYC nexus that leads to the modulation of their functions and disease upon dysregulation.
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Affiliation(s)
- Aparna Kotekar
- Experimental Immunology Branch, NCI, NIH, Bethesda, MD 20892, USA
| | - Amit Kumar Singh
- Experimental Immunology Branch, NCI, NIH, Bethesda, MD 20892, USA
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9
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Agrawal R, Natarajan KN. Oncogenic signaling pathways in pancreatic ductal adenocarcinoma. Adv Cancer Res 2023; 159:251-283. [PMID: 37268398 DOI: 10.1016/bs.acr.2023.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the most common (∼90% cases) pancreatic neoplasm and one of the most lethal cancer among all malignances. PDAC harbor aberrant oncogenic signaling that may result from the multiple genetic and epigenetic alterations such as the mutation in driver genes (KRAS, CDKN2A, p53), genomic amplification of regulatory genes (MYC, IGF2BP2, ROIK3), deregulation of chromatin-modifying proteins (HDAC, WDR5) among others. A key event is the formation of Pancreatic Intraepithelial Neoplasia (PanIN) that often results from the activating mutation in KRAS. Mutated KRAS can direct a variety of signaling pathways and modulate downstream targets including MYC, which play an important role in cancer progression. In this review, we discuss recent literature shedding light on the origins of PDAC from the perspective of major oncogenic signaling pathways. We highlight how MYC directly and indirectly, with cooperation with KRAS, affect epigenetic reprogramming and metastasis. Additionally, we summarize the recent findings from single cell genomic approaches that highlight heterogeneity in PDAC and tumor microenvironment, and provide molecular avenues for PDAC treatment in the future.
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Affiliation(s)
- Rahul Agrawal
- DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
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10
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Bahls B, Aljnadi IM, Emídio R, Mendes E, Paulo A. G-Quadruplexes in c-MYC Promoter as Targets for Cancer Therapy. Biomedicines 2023; 11:biomedicines11030969. [PMID: 36979947 PMCID: PMC10046398 DOI: 10.3390/biomedicines11030969] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/09/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
Cancer is a societal burden demanding innovative approaches. A major problem with the conventional chemotherapeutic agents is their strong toxicity and other side effects due to their poor selectivity. Uncontrolled proliferation of cancer cells is due to mutations, deletions, or amplifications in genes (oncogenes) encoding for proteins that regulate cell growth and division, such as transcription factors, for example, c-MYC. The direct targeting of the c-MYC protein has been attempted but so far unsuccessfully, as it lacks a definite binding site for the modulators. Meanwhile, another approach has been explored since the discovery that G-quadruplex secondary DNA structures formed in the guanine-rich sequences of the c-MYC promoter region can downregulate the transcription of this oncogene. Here, we will overview the major achievements made in the last decades towards the discovery of a new class of anticancer drugs targeting G-quadruplexes in the c-MYC promoter of cancer cells.
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Affiliation(s)
- Bárbara Bahls
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | - Israa M Aljnadi
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | - Rita Emídio
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | - Eduarda Mendes
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | - Alexandra Paulo
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal
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11
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Kawasaki H, Shahin R, Fujimoto S. Proliferative and preparative cell divisions in wing discs of the last larval instar are regulated by different hormones and determine the size and differentiation of the wing of Bombyx mori. JOURNAL OF INSECT PHYSIOLOGY 2023; 145:104476. [PMID: 36623750 DOI: 10.1016/j.jinsphys.2023.104476] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 06/17/2023]
Abstract
Through investigating the two different enhanced cell division stages, we tried to clarify the switch from the growth to differentiation in the wing disc of the last larval instar of Bombyx mori. The response to insulin and 20E in vitro was stage specific. Bmmyc expression in V1 wing discs showed differences after being cultured with and without insulin. Bmmyc expression in V5 wing discs also showed differences after being cultured with and without 20E. Cell cycle-related genes, BmE2F1 and BmcycE, were upregulated with insulin or 20E in cultured wing discs of V1 or V5, respectively. Bmwnt1 and Bmras1 showed upregulation with 20E in cultured wing discs. Bmwnt1 showed upregulation with insulin in cultured wing discs, but Bmras1 did not show clear upregulation with insulin treatment. In contrast, Bmdpp showed upregulation with insulin, but did not show clear upregulation with 20E. The addition of PI3K or TOR inhibitors inhibited the upregulation of Bmmyc expression that was upregulated with insulin or 20E. The upregulation of Bmmyc and Bmwnt1 with insulin or 20E was inhibited with the addition of Myc or Wnt inhibitors, respectively. Genes related to matrix metalloprotease showed upregulation with 20E, and the upregulation was inhibited by the addition of Myc or Wnt inhibitors. From the present results, we concluded that cell division during the feeding stage occurred through PI3K/TOR cascade, and that at the wandering stage occurred through ecdysone and PI3K/TOR cascade; the former is for growth and the latter for differentiation.
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Affiliation(s)
- Hideki Kawasaki
- Department of Bioproductive Science, Faculty of Agriculture, Takasaki University of Health and Welfare, 37-1 Nakaorui-machi, Takasaki-shi, Gunma 370-0033, Japan; Facultyof Agriculture, Utsunomiya University, 350, Mine, Utsunomiya, Tochigi 321-8505, Japan.
| | - Rima Shahin
- Department of Applied Entomology and Zoology, Faculty of Agriculture (El-Shatby), Alexandria University, Alexandria 21545, Egypt
| | - Shota Fujimoto
- Department of Bioproductive Science, Faculty of Agriculture, Takasaki University of Health and Welfare, 37-1 Nakaorui-machi, Takasaki-shi, Gunma 370-0033, Japan
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When Just One Phosphate Is One Too Many: The Multifaceted Interplay between Myc and Kinases. Int J Mol Sci 2023; 24:ijms24054746. [PMID: 36902175 PMCID: PMC10003727 DOI: 10.3390/ijms24054746] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/19/2023] [Accepted: 02/21/2023] [Indexed: 03/06/2023] Open
Abstract
Myc transcription factors are key regulators of many cellular processes, with Myc target genes crucially implicated in the management of cell proliferation and stem pluripotency, energy metabolism, protein synthesis, angiogenesis, DNA damage response, and apoptosis. Given the wide involvement of Myc in cellular dynamics, it is not surprising that its overexpression is frequently associated with cancer. Noteworthy, in cancer cells where high Myc levels are maintained, the overexpression of Myc-associated kinases is often observed and required to foster tumour cells' proliferation. A mutual interplay exists between Myc and kinases: the latter, which are Myc transcriptional targets, phosphorylate Myc, allowing its transcriptional activity, highlighting a clear regulatory loop. At the protein level, Myc activity and turnover is also tightly regulated by kinases, with a finely tuned balance between translation and rapid protein degradation. In this perspective, we focus on the cross-regulation of Myc and its associated protein kinases underlying similar and redundant mechanisms of regulation at different levels, from transcriptional to post-translational events. Furthermore, a review of the indirect effects of known kinase inhibitors on Myc provides an opportunity to identify alternative and combined therapeutic approaches for cancer treatment.
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13
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Luo Y, Pratihar S, Horste EH, Mitschka S, Mey ASJS, Al-Hashimi HM, Mayr C. mRNA interactions with disordered regions control protein activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.18.529068. [PMID: 36824771 PMCID: PMC9949118 DOI: 10.1101/2023.02.18.529068] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
The cytoplasm is compartmentalized into different translation environments. mRNAs use their 3'UTRs to localize to distinct cytoplasmic compartments, including TIS granules (TGs). Many transcription factors, including MYC, are translated in TGs. It was shown that translation of proteins in TGs enables the formation of protein complexes that cannot be established when these proteins are translated in the cytosol, but the mechanism is poorly understood. Here we show that MYC protein complexes that involve binding to the intrinsically disordered region (IDR) of MYC are only formed when MYC is translated in TGs. TG-dependent protein complexes require TG-enriched mRNAs for assembly. These mRNAs bind to a new and widespread RNA-binding domain in neutral or negatively charged IDRs in several transcription factors, including MYC. RNA-IDR interaction changes the conformational ensemble of the IDR, enabling the formation of MYC protein complexes that act in the nucleus and control functions that cannot be accomplished by cytosolically-translated MYC. We propose that certain mRNAs have IDR chaperone activity as they control IDR conformations. In addition to post-translational modifications, we found a novel mode of protein activity regulation. Since RNA-IDR interactions are prevalent, we suggest that mRNA-dependent control of protein functional states is widespread.
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Affiliation(s)
- Yang Luo
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Supriya Pratihar
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Ellen H. Horste
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, NY 10065, USA
| | - Sibylle Mitschka
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
| | | | - Hashim M. Al-Hashimi
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Christine Mayr
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, NY 10065, USA
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14
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Yang Q, Bariani MV, Falahati A, Khosh A, Lastra RR, Siblini H, Boyer TG, Al-Hendy A. The Functional Role and Regulatory Mechanism of Bromodomain-Containing Protein 9 in Human Uterine Leiomyosarcoma. Cells 2022; 11:2160. [PMID: 35883603 PMCID: PMC9323884 DOI: 10.3390/cells11142160] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/01/2022] [Accepted: 07/04/2022] [Indexed: 12/22/2022] Open
Abstract
Uterine leiomyosarcoma (uLMS) is the most common type of uterine sarcoma associated with poor prognosis, high rates of recurrence, and metastasis. There is currently limited information about uLMS molecular mechanisms of origin and development. Bromodomain (BRD)-containing proteins are involved in many biological processes, most notably epigenetic regulation of transcription, and BRD protein dysfunction has been linked to many diseases including tumorigenesis. However, the role of BRD proteins in the pathogenesis of uLMS is unknown. Here, we show for the first time that BRD9 is aberrantly overexpressed in uLMS tissues compared to adjacent myometrium. BRD9 expression is also upregulated in uLMS cell lines compared to benign uterine fibroid and myometrium cell lines. Inhibition of BRD9 using the specific inhibitor (TP-472) suppressed uLMS cell proliferation via inducing apoptosis and cell cycle arrest. To further characterize the mechanistic basis for TP-472 inhibition of uLMS cell growth, we performed a comparative RNA-seq analysis of vehicle-treated and TP-472-treated uLMS cells (n = 4 each). Bioinformatics analysis revealed that TP-472 treatment distinctly altered the uLMS cell transcriptome. Gene set enrichment analysis identified critical pathways altered by BRD9 inhibition, including interferon-alpha response, KRAS signaling, MYC targets, TNF-a signaling via NFkB, and MTORC1 signaling. Parsimonious gene correlation network analysis identified nine enriched modules, including cell cycle and apoptosis modules. Moreover, the ENCODE Histone Modifications gene set and TargetScan microRNA analysis in Enrichr suggested that TP-472-induced BRD9 inhibition may alter the uLMS cell transcriptome by reprograming the oncogenic epigenome and inducing miRNA-mediated gene regulation. Therefore, BRD9 constitutes a specific vulnerability in malignant uLMS, and targeting non-BET BRD proteins in uLMS may provide a promising and novel strategy for treating patients with this aggressive uterine cancer.
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Affiliation(s)
- Qiwei Yang
- Department of Obstetrics and Gynecology, University of Chicago, Chicago, IL 60637, USA; (M.V.B.); (H.S.); (A.A.-H.)
| | - Maria Victoria Bariani
- Department of Obstetrics and Gynecology, University of Chicago, Chicago, IL 60637, USA; (M.V.B.); (H.S.); (A.A.-H.)
| | - Ali Falahati
- Department of Biology, Yazd University, Yazd 8915818411, Iran; (A.F.); (A.K.)
| | - Azad Khosh
- Department of Biology, Yazd University, Yazd 8915818411, Iran; (A.F.); (A.K.)
| | - Ricardo R. Lastra
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA;
| | - Hiba Siblini
- Department of Obstetrics and Gynecology, University of Chicago, Chicago, IL 60637, USA; (M.V.B.); (H.S.); (A.A.-H.)
| | - Thomas G. Boyer
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA;
| | - Ayman Al-Hendy
- Department of Obstetrics and Gynecology, University of Chicago, Chicago, IL 60637, USA; (M.V.B.); (H.S.); (A.A.-H.)
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15
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Johansson-Åkhe I, Wallner B. InterPepScore: A Deep Learning Score for Improving the FlexPepDock Refinement Protocol. Bioinformatics 2022; 38:3209-3215. [PMID: 35575349 PMCID: PMC9191208 DOI: 10.1093/bioinformatics/btac325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 04/29/2022] [Accepted: 05/10/2022] [Indexed: 11/15/2022] Open
Abstract
Motivation Interactions between peptide fragments and protein receptors are vital to cell function yet difficult to experimentally determine in structural details of. As such, many computational methods have been developed to aid in peptide–protein docking or structure prediction. One such method is Rosetta FlexPepDock which consistently refines coarse peptide–protein models into sub-Ångström precision using Monte-Carlo simulations and statistical potentials. Deep learning has recently seen increased use in protein structure prediction, with graph neural networks used for protein model quality assessment. Results Here, we introduce a graph neural network, InterPepScore, as an additional scoring term to complement and improve the Rosetta FlexPepDock refinement protocol. InterPepScore is trained on simulation trajectories from FlexPepDock refinement starting from thousands of peptide–protein complexes generated by a wide variety of docking schemes. The addition of InterPepScore into the refinement protocol consistently improves the quality of models created, and on an independent benchmark on 109 peptide–protein complexes its inclusion results in an increase in the number of complexes for which the top-scoring model had a DockQ-score of 0.49 (Medium quality) or better from 14.8% to 26.1%. Availability and implementation InterPepScore is available online at http://wallnerlab.org/InterPepScore. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Isak Johansson-Åkhe
- Division of Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, Linköping, SE-581 83, Sweden
| | - Björn Wallner
- Division of Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, Linköping, SE-581 83, Sweden
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16
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Mullen PJ, Christofk HR. The Metabolic Relationship Between Viral Infection and Cancer. ANNUAL REVIEW OF CANCER BIOLOGY 2022. [DOI: 10.1146/annurev-cancerbio-070120-090423] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Viruses are fundamental tools in cancer research. They were used to discover the first oncogenes in the 1970s, and they are now being modified for use as antitumor therapeutics. Key to both of these oncogenic and oncolytic properties is the ability of viruses to rewire host cell metabolism. In this review, we describe how viral oncogenes alter metabolism to increase the synthesis of macromolecules necessary for both viral replication and tumor growth. We then describe how understanding the specific metabolic requirements of virus-infected cells can help guide strategies to improve the efficacy of oncolytic viruses, and we highlight immunometabolism and tumor microenvironment research that could also increase the therapeutic benefits of oncolytic viruses. We also describe how studies describing the therapeutic effects of dietary nutrient restriction in cancer can suggest new avenues for research into antiviral therapeutics.
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Affiliation(s)
- Peter J. Mullen
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Heather R. Christofk
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, USA
- Jonsson Comprehensive Cancer Center and Eli and Edythe Broad Stem Cell Research Center, University of California, Los Angeles, California, USA
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17
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Wei Y, Redel C, Ahlner A, Lemak A, Johansson-Åkhe I, Houliston S, Kenney TMG, Tamachi A, Morad V, Duan S, Andrews DW, Wallner B, Sunnerhagen M, Arrowsmith CH, Penn LZ. The MYC oncoprotein directly interacts with its chromatin cofactor PNUTS to recruit PP1 phosphatase. Nucleic Acids Res 2022; 50:3505-3522. [PMID: 35244724 PMCID: PMC8989513 DOI: 10.1093/nar/gkac138] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 01/11/2022] [Accepted: 02/28/2022] [Indexed: 02/07/2023] Open
Abstract
Despite MYC dysregulation in most human cancers, strategies to target this potent oncogenic driver remain an urgent unmet need. Recent evidence shows the PP1 phosphatase and its regulatory subunit PNUTS control MYC phosphorylation, chromatin occupancy, and stability, however the molecular basis remains unclear. Here we demonstrate that MYC interacts directly with PNUTS through the MYC homology Box 0 (MB0), a highly conserved region recently shown to be important for MYC oncogenic activity. By NMR we identified a distinct peptide motif within MB0 that interacts with PNUTS residues 1–148, a functional unit, here termed PNUTS amino-terminal domain (PAD). Using NMR spectroscopy we determined the solution structure of PAD, and characterised its MYC-binding patch. Point mutations of residues at the MYC-PNUTS interface significantly weaken their interaction both in vitro and in vivo, leading to elevated MYC phosphorylation. These data demonstrate that the MB0 region of MYC directly interacts with the PAD of PNUTS, which provides new insight into the control mechanisms of MYC as a regulator of gene transcription and a pervasive cancer driver.
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Affiliation(s)
- Yong Wei
- Princess Margaret Cancer Centre, University Health Network, 101 College St, Toronto, ON M5G 0A3, Canada.,Structural Genomics Consortium (SGC), University of Toronto, 101 College St., Suite 700, Toronto, ON, M5G 1L7, Canada.,Sunnybrook Research Institute, 2075 Bayview Ave. Toronto, ON, M4N 3M5, Canada
| | - Cornelia Redel
- Princess Margaret Cancer Centre, University Health Network, 101 College St, Toronto, ON M5G 0A3, Canada.,Department of Medical Biophysics, University of Toronto, 101 College St, Toronto, ON M5G 1L7, Canada
| | - Alexandra Ahlner
- Department of Physics, Chemistry, and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Alexander Lemak
- Princess Margaret Cancer Centre, University Health Network, 101 College St, Toronto, ON M5G 0A3, Canada.,Structural Genomics Consortium (SGC), University of Toronto, 101 College St., Suite 700, Toronto, ON, M5G 1L7, Canada
| | - Isak Johansson-Åkhe
- Department of Physics, Chemistry, and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Scott Houliston
- Princess Margaret Cancer Centre, University Health Network, 101 College St, Toronto, ON M5G 0A3, Canada.,Structural Genomics Consortium (SGC), University of Toronto, 101 College St., Suite 700, Toronto, ON, M5G 1L7, Canada
| | - Tristan M G Kenney
- Princess Margaret Cancer Centre, University Health Network, 101 College St, Toronto, ON M5G 0A3, Canada.,Department of Medical Biophysics, University of Toronto, 101 College St, Toronto, ON M5G 1L7, Canada
| | - Aaliya Tamachi
- Princess Margaret Cancer Centre, University Health Network, 101 College St, Toronto, ON M5G 0A3, Canada
| | - Vivian Morad
- Department of Physics, Chemistry, and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | | | - David W Andrews
- Sunnybrook Research Institute, 2075 Bayview Ave. Toronto, ON, M4N 3M5, Canada.,Department of Medical Biophysics, University of Toronto, 101 College St, Toronto, ON M5G 1L7, Canada
| | - Björn Wallner
- Department of Physics, Chemistry, and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Maria Sunnerhagen
- Department of Physics, Chemistry, and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Cheryl H Arrowsmith
- Princess Margaret Cancer Centre, University Health Network, 101 College St, Toronto, ON M5G 0A3, Canada.,Structural Genomics Consortium (SGC), University of Toronto, 101 College St., Suite 700, Toronto, ON, M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, 101 College St, Toronto, ON M5G 1L7, Canada
| | - Linda Z Penn
- Princess Margaret Cancer Centre, University Health Network, 101 College St, Toronto, ON M5G 0A3, Canada.,Department of Medical Biophysics, University of Toronto, 101 College St, Toronto, ON M5G 1L7, Canada
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18
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Llombart V, Mansour MR. Therapeutic targeting of "undruggable" MYC. EBioMedicine 2022; 75:103756. [PMID: 34942444 PMCID: PMC8713111 DOI: 10.1016/j.ebiom.2021.103756] [Citation(s) in RCA: 161] [Impact Index Per Article: 80.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 11/23/2021] [Accepted: 12/01/2021] [Indexed: 12/13/2022] Open
Abstract
c-MYC controls global gene expression and regulates cell proliferation, cell differentiation, cell cycle, metabolism and apoptosis. According to some estimates, MYC is dysregulated in ≈70% of human cancers and strong evidence implicates aberrantly expressed MYC in both tumor initiation and maintenance. In vivo studies show that MYC inhibition elicits a prominent anti-proliferative effect and sustained tumor regression while any alteration on healthy tissue remains reversible. This opens an exploitable window for treatment that makes MYC one of the most appealing therapeutic targets for cancer drug development. This review describes the main functional and structural features of the protein structure of MYC and provides a general overview of the most relevant or recently identified interactors that modulate MYC oncogenic activity. This review also summarizes the different approaches aiming to abrogate MYC oncogenic function, with a particular focus on the prototype inhibitors designed for the direct and indirect targeting of MYC.
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Affiliation(s)
- Victor Llombart
- UCL Cancer Institute, University College London, Department of Haematology, London WC1E 6DD, UK
| | - Marc R Mansour
- UCL Cancer Institute, University College London, Department of Haematology, London WC1E 6DD, UK; UCL Great Ormond Street Institute of Child Health, Developmental Biology and Cancer, London, UK.
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19
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Differential Transcriptional Reprogramming by Wild Type and Lymphoma-Associated Mutant MYC Proteins as B-Cells Convert to a Lymphoma Phenotype. Cancers (Basel) 2021; 13:cancers13236093. [PMID: 34885204 PMCID: PMC8657136 DOI: 10.3390/cancers13236093] [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: 10/27/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 11/16/2022] Open
Abstract
The MYC transcription factor regulates a vast number of genes and is implicated in many human malignancies. In some hematological malignancies, MYC is frequently subject to missense mutations that enhance its transformation activity. Here, we use a novel murine cell system to (i) characterize the transcriptional effects of progressively increasing MYC levels as normal primary B-cells transform to lymphoma cells and (ii) determine how this gene regulation program is modified by lymphoma-associated MYC mutations (T58A and T58I) that enhance its transformation activity. Unlike many previous studies, the cell system exploits primary B-cells that are transduced to allow regulated MYC expression under circumstances where apoptosis and senescence pathways are abrogated by the over-expression of the Bcl-xL and BMI1 proteins. In such cells, transition from a normal to a lymphoma phenotype is directly dependent on the MYC expression level, without a requirement for secondary events that are normally required during MYC-driven oncogenic transformation. A generalized linear model approach allowed an integrated analysis of RNA sequencing data to identify regulated genes in relation to both progressively increasing MYC level and wild type or mutant status. Using this design, a total of 7569 regulated genes were identified, of which the majority (n = 7263) were regulated in response to progressively increased levels of wild type MYC, while a smaller number of genes (n = 917) were differentially regulated, compared to wild type MYC, in T58A MYC- and/or T58I MYC-expressing cells. Unlike most genes that are similarly regulated by both wild type and mutant MYC genes, the set of 917 genes did not significantly overlap with known lipopolysaccharide regulated genes, which represent genes regulated by MYC in normal B cells. The genes that were differently regulated in cells expressing mutant MYC proteins were significantly enriched in DNA replication and G2 phase to mitosis transition genes. Thus, mutants affecting MYC proteins may augment quantitative oncogenic effects on the expression of normal MYC-target genes with qualitative oncogenic effects, by which sets of cell cycle genes are abnormally targeted by MYC as B cells transition into lymphoma cells. The T58A and T58I mutations augment MYC-driven transformation by distinct mechanisms.
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20
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Medina JR, Tian X, Li WH, Suarez D, Mack JF, LaFrance L, Martyr C, Brackley J, Di Marco C, Rivero R, Heerding DA, McHugh C, Minthorn E, Bhaskar A, Rubin J, Butticello M, Carpenter C, Nartey EN, Berrodin TJ, Kallal LA, Mangatt B. Cell-Based Drug Discovery: Identification and Optimization of Small Molecules that Reduce c-MYC Protein Levels in Cells. J Med Chem 2021; 64:16056-16087. [PMID: 34669409 DOI: 10.1021/acs.jmedchem.1c01416] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Elevated expression of the c-MYC oncogene is one of the most common abnormalities in human cancers. Unfortunately, efforts to identify pharmacological inhibitors that directly target MYC have not yet yielded a drug-like molecule due to the lack of any known small molecule binding pocket in the protein, which could be exploited to disrupt MYC function. We have recently described a strategy to target MYC indirectly, where a screening effort designed to identify compounds that can rapidly decrease endogenous c-MYC protein levels in a MYC-amplified cell line led to the discovery of a compound series that phenocopies c-MYC knockdown by siRNA. Herein, we describe our medicinal chemistry program that led to the discovery of potent, orally bioavailable c-MYC-reducing compounds. The development of a minimum pharmacophore model based on empirical structure activity relationship as well as the property-based approach used to modulate pharmacokinetics properties will be highlighted.
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Affiliation(s)
- Jesús R Medina
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Xinrong Tian
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - William H Li
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Dominic Suarez
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - James F Mack
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Louis LaFrance
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Cuthbert Martyr
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - James Brackley
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Christina Di Marco
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Ralph Rivero
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Dirk A Heerding
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Charles McHugh
- Oncology Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Elisabeth Minthorn
- Oncology Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Aishwarya Bhaskar
- Oncology Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Jacob Rubin
- Oncology Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Michael Butticello
- Oncology Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | | | - Eldridge N Nartey
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Thomas J Berrodin
- Oncology Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Lorena A Kallal
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Biju Mangatt
- Oncology Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
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21
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Johansson-Åkhe I, Mirabello C, Wallner B. InterPepRank: Assessment of Docked Peptide Conformations by a Deep Graph Network. FRONTIERS IN BIOINFORMATICS 2021; 1:763102. [PMID: 36303778 PMCID: PMC9581042 DOI: 10.3389/fbinf.2021.763102] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 10/05/2021] [Indexed: 11/13/2022] Open
Abstract
Peptide-protein interactions between a smaller or disordered peptide stretch and a folded receptor make up a large part of all protein-protein interactions. A common approach for modeling such interactions is to exhaustively sample the conformational space by fast-Fourier-transform docking, and then refine a top percentage of decoys. Commonly, methods capable of ranking the decoys for selection fast enough for larger scale studies rely on first-principle energy terms such as electrostatics, Van der Waals forces, or on pre-calculated statistical potentials. We present InterPepRank for peptide-protein complex scoring and ranking. InterPepRank is a machine learning-based method which encodes the structure of the complex as a graph; with physical pairwise interactions as edges and evolutionary and sequence features as nodes. The graph network is trained to predict the LRMSD of decoys by using edge-conditioned graph convolutions on a large set of peptide-protein complex decoys. InterPepRank is tested on a massive independent test set with no targets sharing CATH annotation nor 30% sequence identity with any target in training or validation data. On this set, InterPepRank has a median AUC of 0.86 for finding coarse peptide-protein complexes with LRMSD < 4Å. This is an improvement compared to other state-of-the-art ranking methods that have a median AUC between 0.65 and 0.79. When included as a selection-method for selecting decoys for refinement in a previously established peptide docking pipeline, InterPepRank improves the number of medium and high quality models produced by 80% and 40%, respectively. The InterPepRank program as well as all scripts for reproducing and retraining it are available from: http://wallnerlab.org/InterPepRank.
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22
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Jiménez Martín O, Schlosser A, Furtwängler R, Wegert J, Gessler M. MYCN and MAX alterations in Wilms tumor and identification of novel N-MYC interaction partners as biomarker candidates. Cancer Cell Int 2021; 21:555. [PMID: 34689785 PMCID: PMC8543820 DOI: 10.1186/s12935-021-02259-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 10/12/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Wilms tumor (WT) is the most common renal tumor in childhood. Among others, MYCN copy number gain and MYCN P44L and MAX R60Q mutations have been identified in WT. MYCN encodes a transcription factor that requires dimerization with MAX to activate transcription of numerous target genes. MYCN gain has been associated with adverse prognosis in different childhood tumors including WT. The MYCN P44L and MAX R60Q mutations, located in either the transactivating or basic helix-loop-helix domain, respectively, are predicted to be damaging by different pathogenicity prediction tools, but the functional consequences remain to be characterized. METHODS We screened a large cohort of unselected WTs for MYCN and MAX alterations. Wild-type and mutant protein function were characterized biochemically, and we analyzed the N-MYC protein interactome by mass spectrometric analysis of N-MYC containing protein complexes. RESULTS Mutation screening revealed mutation frequencies of 3% for MYCN P44L and 0.9% for MAX R60Q that are associated with a higher risk of relapse. Biochemical characterization identified a reduced transcriptional activation potential for MAX R60Q, while the MYCN P44L mutation did not change activation potential or protein stability. The protein interactome of N-MYC-P44L was likewise not altered as shown by mass spectrometric analyses of purified N-MYC complexes. Nevertheless, we could identify a number of novel N-MYC partner proteins, e.g. PEG10, YEATS2, FOXK1, CBLL1 and MCRS1, whose expression is correlated with MYCN in WT samples and several of these are known for their own oncogenic potential. CONCLUSIONS The strongly elevated risk of relapse associated with mutant MYCN and MAX or elevated MYCN expression corroborates their role in WT oncogenesis. Together with the newly identified co-expressed interactors they expand the range of potential biomarkers for WT stratification and targeting, especially for high-risk WT.
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Affiliation(s)
- Ovidio Jiménez Martín
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, Wuerzburg University, 97074, Wuerzburg, Germany
| | - Andreas Schlosser
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, Wuerzburg University, 97078, Wuerzburg, Germany
| | - Rhoikos Furtwängler
- Department of Pediatric Oncology Und Hematology, Saarland University Hospital, 66421, Homburg, Saar, Germany
| | - Jenny Wegert
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, Wuerzburg University, 97074, Wuerzburg, Germany
| | - Manfred Gessler
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, Wuerzburg University, 97074, Wuerzburg, Germany. .,Comprehensive Cancer Center Mainfranken, Wuerzburg University, 97078, Wuerzburg, Germany.
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23
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Zhou Y, Gao X, Yuan M, Yang B, He Q, Cao J. Targeting Myc Interacting Proteins as a Winding Path in Cancer Therapy. Front Pharmacol 2021; 12:748852. [PMID: 34658888 PMCID: PMC8511624 DOI: 10.3389/fphar.2021.748852] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/10/2021] [Indexed: 12/26/2022] Open
Abstract
MYC, as a well-known oncogene, plays essential roles in promoting tumor occurrence, development, invasion and metastasis in many kinds of solid tumors and hematologic neoplasms. In tumors, the low expression and the short half-life of Myc are reversed, cause tumorigenesis. And proteins that directly interact with different Myc domains have exerted a significant impact in the process of Myc-driven carcinogenesis. Apart from affecting the transcription of Myc target genes, Myc interaction proteins also regulate the stability of Myc through acetylation, methylation, phosphorylation and other post-translational modifications, as well as competitive combination with Myc. In this review, we summarize a series of Myc interacting proteins and recent advances in the related inhibitors, hoping that can provide new opportunities for Myc-driven cancer treatment.
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Affiliation(s)
- Yihui Zhou
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Xiaomeng Gao
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Meng Yuan
- Cancer Center of Zhejiang University, Hangzhou, China
| | - Bo Yang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,The Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, China
| | - Qiaojun He
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,Cancer Center of Zhejiang University, Hangzhou, China.,The Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, China
| | - Ji Cao
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,Cancer Center of Zhejiang University, Hangzhou, China.,The Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, China
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24
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Lourenco C, Resetca D, Redel C, Lin P, MacDonald AS, Ciaccio R, Kenney TMG, Wei Y, Andrews DW, Sunnerhagen M, Arrowsmith CH, Raught B, Penn LZ. MYC protein interactors in gene transcription and cancer. Nat Rev Cancer 2021; 21:579-591. [PMID: 34188192 DOI: 10.1038/s41568-021-00367-9] [Citation(s) in RCA: 130] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/04/2021] [Indexed: 02/07/2023]
Abstract
The transcription factor and oncoprotein MYC is a potent driver of many human cancers and can regulate numerous biological activities that contribute to tumorigenesis. How a single transcription factor can regulate such a diverse set of biological programmes is central to the understanding of MYC function in cancer. In this Perspective, we highlight how multiple proteins that interact with MYC enable MYC to regulate several central control points of gene transcription. These include promoter binding, epigenetic modifications, initiation, elongation and post-transcriptional processes. Evidence shows that a combination of multiple protein interactions enables MYC to function as a potent oncoprotein, working together in a 'coalition model', as presented here. Moreover, as MYC depends on its protein interactome for function, we discuss recent research that emphasizes an unprecedented opportunity to target protein interactors to directly impede MYC oncogenesis.
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Affiliation(s)
| | - Diana Resetca
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Cornelia Redel
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Peter Lin
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Alannah S MacDonald
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Roberto Ciaccio
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Tristan M G Kenney
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Yong Wei
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Biological Sciences, Sunnybrook Research Institute, Toronto, ON, Canada
| | - David W Andrews
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Biological Sciences, Sunnybrook Research Institute, Toronto, ON, Canada
| | - Maria Sunnerhagen
- Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Cheryl H Arrowsmith
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Structural Genomics Consortium, Toronto, ON, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Linda Z Penn
- Princess Margaret Cancer Centre, Toronto, ON, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
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25
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Gonzalez-Pecchi V, Kwan AK, Doyle S, Ivanov AA, Du Y, Fu H. NSD3S stabilizes MYC through hindering its interaction with FBXW7. J Mol Cell Biol 2021; 12:438-447. [PMID: 31638140 PMCID: PMC7333476 DOI: 10.1093/jmcb/mjz098] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 06/08/2019] [Accepted: 09/15/2019] [Indexed: 01/16/2023] Open
Abstract
The MYC transcription factor plays a key role in cell growth control. Enhanced MYC protein stability has been found to promote tumorigenesis. Thus, understanding how MYC stability is controlled may have significant implications for revealing MYC-driven growth regulatory mechanisms in physiological and pathological processes. Our previous work identified the histone lysine methyltransferase nuclear receptor binding SET domain protein 3 (NSD3) as a MYC modulator. NSD3S, a noncatalytic isoform of NSD3 with oncogenic activity, appears to bind, stabilize, and activate the transcriptional activity of MYC. However, the mechanism by which NSD3S stabilizes MYC remains to be elucidated. To uncover the nature of the interaction and the underlying mechanism of MYC regulation by NSD3S, we characterized the binding interface between both proteins by narrowing the interface to a 15-amino acid region in NSD3S that is partially required for MYC regulation. Mechanistically, NSD3S binds to MYC and reduces the association of F-box and WD repeat domain containing 7 (FBXW7) with MYC, which results in suppression of FBXW7-mediated proteasomal degradation of MYC and an increase in MYC protein half-life. These results support a critical role for NSD3S in the regulation of MYC function and provide a novel mechanism for NSD3S oncogenic function through inhibition of FBXW7-mediated degradation of MYC.
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Affiliation(s)
- Valentina Gonzalez-Pecchi
- Graduate Program in Cancer Biology, Emory University, Atlanta, GA, USA.,Department of Pharmacology and Chemical Biology, Emory Chemical Biology Discovery Center, Emory University, Atlanta, GA, USA
| | - Albert K Kwan
- Department of Pharmacology and Chemical Biology, Emory Chemical Biology Discovery Center, Emory University, Atlanta, GA, USA
| | - Sean Doyle
- Department of Pharmacology and Chemical Biology, Emory Chemical Biology Discovery Center, Emory University, Atlanta, GA, USA
| | - Andrey A Ivanov
- Department of Pharmacology and Chemical Biology, Emory Chemical Biology Discovery Center, Emory University, Atlanta, GA, USA.,Winship Cancer Institute, Emory University, Atlanta, GA, USA.,Department of Hematology & Medical Oncology, Emory University, Atlanta, GA, USA
| | - Yuhong Du
- Department of Pharmacology and Chemical Biology, Emory Chemical Biology Discovery Center, Emory University, Atlanta, GA, USA.,Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Haian Fu
- Department of Pharmacology and Chemical Biology, Emory Chemical Biology Discovery Center, Emory University, Atlanta, GA, USA.,Winship Cancer Institute, Emory University, Atlanta, GA, USA.,Department of Hematology & Medical Oncology, Emory University, Atlanta, GA, USA
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26
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Han Y, He F, Chen Y, Qin W, Yu H, Xu D. Quality Assessment of Protein Docking Models Based on Graph Neural Network. FRONTIERS IN BIOINFORMATICS 2021; 1:693211. [PMID: 36303780 PMCID: PMC9581034 DOI: 10.3389/fbinf.2021.693211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 08/02/2021] [Indexed: 11/24/2022] Open
Abstract
Protein docking provides a structural basis for the design of drugs and vaccines. Among the processes of protein docking, quality assessment (QA) is utilized to pick near-native models from numerous protein docking candidate conformations, and it directly determines the final docking results. Although extensive efforts have been made to improve QA accuracy, it is still the bottleneck of current protein docking systems. In this paper, we presented a Deep Graph Attention Neural Network (DGANN) to evaluate and rank protein docking candidate models. DGANN learns inter-residue physio-chemical properties and structural fitness across the two protein monomers in a docking model and generates their probabilities of near-native models. On the ZDOCK decoy benchmark, our DGANN outperformed the ranking provided by ZDOCK in terms of ranking good models into the top selections. Furthermore, we conducted comparative experiments on an independent testing dataset, and the results also demonstrated the superiority and generalization of our proposed method.
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Affiliation(s)
- Ye Han
- School of Information Technology, Jilin Agricultural University, Changchun, China
- Department of Electrical Engineering and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Fei He
- Department of Electrical Engineering and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
- School of Information Science and Technology, Northeast Normal University, Changchun, China
| | - Yongbing Chen
- School of Information Science and Technology, Northeast Normal University, Changchun, China
| | - Wenyuan Qin
- School of Information Science and Technology, Northeast Normal University, Changchun, China
| | - Helong Yu
- School of Information Technology, Jilin Agricultural University, Changchun, China
- *Correspondence: Helong Yu, ; Dong Xu,
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
- *Correspondence: Helong Yu, ; Dong Xu,
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27
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Ahmadi SE, Rahimi S, Zarandi B, Chegeni R, Safa M. MYC: a multipurpose oncogene with prognostic and therapeutic implications in blood malignancies. J Hematol Oncol 2021; 14:121. [PMID: 34372899 PMCID: PMC8351444 DOI: 10.1186/s13045-021-01111-4] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/12/2021] [Indexed: 12/17/2022] Open
Abstract
MYC oncogene is a transcription factor with a wide array of functions affecting cellular activities such as cell cycle, apoptosis, DNA damage response, and hematopoiesis. Due to the multi-functionality of MYC, its expression is regulated at multiple levels. Deregulation of this oncogene can give rise to a variety of cancers. In this review, MYC regulation and the mechanisms by which MYC adjusts cellular functions and its implication in hematologic malignancies are summarized. Further, we also discuss potential inhibitors of MYC that could be beneficial for treating hematologic malignancies.
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Affiliation(s)
- Seyed Esmaeil Ahmadi
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Samira Rahimi
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Bahman Zarandi
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Rouzbeh Chegeni
- Medical Laboratory Sciences Program, College of Health and Human Sciences, Northern Illinois University, DeKalb, IL, USA.
| | - Majid Safa
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran.
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran.
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28
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Biophysical and Structural Methods to Study the bHLHZip Region of Human c-MYC. Methods Mol Biol 2021. [PMID: 34019285 DOI: 10.1007/978-1-0716-1476-1_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The C-terminal region of the c-MYC transcription factor consists of approximately 100 amino acids that in its native state does not adopt a stable structure. When this region binds to the obligatory partner MAX via a coupled folding-and-binding mechanism, it forms a basic-helix-loop-helix-leucine zipper (bHLHZip) heterodimeric complex. The C-terminal region of MYC is the target for numerous drug discovery programs for direct MYC inhibition via blocking the dimerization event and/or binding to DNA, and a proper understanding of the partially folded, dynamic nature of the heterodimeric complex is essential to these efforts. The bHLHZip motif also drives protein-protein interactions with cofactors that are crucial for both transcriptional repression and activation of MYC target genes. Targeting these interactions could potentially provide a means of developing alternative approaches to halt MYC functions; however, the molecular mechanism of these regulatory interactions is poorly understood. Herein we provide methods to produce high-quality human c-MYC C-terminal by itself and in complex MAX, and how to study them using Nuclear Magnetic Resonance spectroscopy and X-ray crystallography. Our protein expression and purification protocols have already been used to study interactions with cofactors.
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29
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Sun XX, Li Y, Sears RC, Dai MS. Targeting the MYC Ubiquitination-Proteasome Degradation Pathway for Cancer Therapy. Front Oncol 2021; 11:679445. [PMID: 34178666 PMCID: PMC8226175 DOI: 10.3389/fonc.2021.679445] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/24/2021] [Indexed: 12/23/2022] Open
Abstract
Deregulated MYC overexpression and activation contributes to tumor growth and progression. Given the short half-life and unstable nature of the MYC protein, it is not surprising that the oncoprotein is highly regulated via diverse posttranslational mechanisms. Among them, ubiquitination dynamically controls the levels and activity of MYC during normal cell growth and homeostasis, whereas the disturbance of the ubiquitination/deubiquitination balance enables unwanted MYC stabilization and activation. In addition, MYC is also regulated by SUMOylation which crosstalks with the ubiquitination pathway and controls MYC protein stability and activity. In this mini-review, we will summarize current updates regarding MYC ubiquitination and provide perspectives about these MYC regulators as potential therapeutic targets in cancer.
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Affiliation(s)
- Xiao-Xin Sun
- Department of Molecular & Medical Genetics, School of Medicine and the OHSU Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States
| | - Yanping Li
- Department of Molecular & Medical Genetics, School of Medicine and the OHSU Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States
| | - Rosalie C Sears
- Department of Molecular & Medical Genetics, School of Medicine and the OHSU Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States
| | - Mu-Shui Dai
- Department of Molecular & Medical Genetics, School of Medicine and the OHSU Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States
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30
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Pellanda P, Dalsass M, Filipuzzi M, Loffreda A, Verrecchia A, Castillo Cano V, Thabussot H, Doni M, Morelli MJ, Soucek L, Kress T, Mazza D, Mapelli M, Beaulieu ME, Amati B, Sabò A. Integrated requirement of non-specific and sequence-specific DNA binding in Myc-driven transcription. EMBO J 2021; 40:e105464. [PMID: 33792944 DOI: 10.15252/embj.2020105464] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 02/15/2021] [Accepted: 02/24/2021] [Indexed: 12/17/2022] Open
Abstract
Eukaryotic transcription factors recognize specific DNA sequence motifs, but are also endowed with generic, non-specific DNA-binding activity. How these binding modes are integrated to determine select transcriptional outputs remains unresolved. We addressed this question by site-directed mutagenesis of the Myc transcription factor. Impairment of non-specific DNA backbone contacts caused pervasive loss of genome interactions and gene regulation, associated with increased intra-nuclear mobility of the Myc protein in murine cells. In contrast, a mutant lacking base-specific contacts retained DNA-binding and mobility profiles comparable to those of the wild-type protein, but failed to recognize its consensus binding motif (E-box) and could not activate Myc-target genes. Incidentally, this mutant gained weak affinity for an alternative motif, driving aberrant activation of different genes. Altogether, our data show that non-specific DNA binding is required to engage onto genomic regulatory regions; sequence recognition in turn contributes to transcriptional activation, acting at distinct levels: stabilization and positioning of Myc onto DNA, and-unexpectedly-promotion of its transcriptional activity. Hence, seemingly pervasive genome interaction profiles, as detected by ChIP-seq, actually encompass diverse DNA-binding modalities, driving defined, sequence-dependent transcriptional responses.
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Affiliation(s)
- Paola Pellanda
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy.,Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Mattia Dalsass
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
| | | | - Alessia Loffreda
- Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Virginia Castillo Cano
- Peptomyc S.L., Barcelona, Spain.,Vall d'Hebron Institute of Oncology (VHIO), Edifici Cellex, Barcelona, Spain
| | | | - Mirko Doni
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
| | - Marco J Morelli
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Laura Soucek
- Peptomyc S.L., Barcelona, Spain.,Vall d'Hebron Institute of Oncology (VHIO), Edifici Cellex, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.,Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Theresia Kress
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Davide Mazza
- Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Marina Mapelli
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
| | | | - Bruno Amati
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
| | - Arianna Sabò
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
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31
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Wang C, Zou H, Chen A, Yang H, Yu X, Yu X, Wang Y. C-Myc-activated long non-coding RNA PVT1 enhances the proliferation of cervical cancer cells by sponging miR-486-3p. J Biochem 2021; 167:565-575. [PMID: 31943014 DOI: 10.1093/jb/mvaa005] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/06/2020] [Indexed: 12/18/2022] Open
Abstract
Cervical cancer is one of the most prevalent gynecological malignancies. Although the functions of long non-coding RNA (lncRNA) plasmacytoma variant translocation 1 (PVT1) and c-Myc in tumorigenesis have been acknowledged, the roles of c-Myc and lncRNA-PVT1 in the proliferation of cervical cancer are still unclear. Our study is designed to demonstrate the regulatory network involving c-Myc and lncRNA-PVT1 in cervical cancer. Quantitative real-time PCR and western blot assays were performed in our research to estimate the expression levels of RNA and proteins. CCK8 assays were applied to demonstrate the viability of HeLa and SiHa cells. Immunofluorescence assay was then used to investigate the co-localization of lncRNA-PVT1 and miR-486-3p. Binding of c-Myc to the promoter region of PVT1 was identified by ChIP-assay. Functionally, upregulation of lncRNA-PVT1 enhanced the proliferation and viability of cervical cancer cells. Mechanistically, lncRNA-PVT1 sponged miR-486-3p and released its repression of extracellular matrix protein 1. Besides, c-Myc functioned as an activator of lncRNA-PVT1 and upregulated its expression by binding to the promoter of PVT1 in cervical cancer cells. lncRNA-PVT1 was upregulated by c-Myc and thus enhanced the proliferation of cervical cancer cells by sponging miR-486-3p.
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Affiliation(s)
- Chang Wang
- Department of Gynecology, The Affiliated Hospital of Qingdao University, 16 Jiangsu Road, Shinan District, Qingdao 266000, Shandong, China
| | - Hao Zou
- Department of Hepatopancreatobiliary Surgery, The Affiliated Hospital of Qingdao University, 16 Jiangsu Road, Shinan District, Qingdao 266000, Shandong, China
| | - Aiping Chen
- Department of Gynecology, The Affiliated Hospital of Qingdao University, 16 Jiangsu Road, Shinan District, Qingdao 266000, Shandong, China
| | - Hongjuan Yang
- Department of Gynecology, The Affiliated Hospital of Qingdao University, 16 Jiangsu Road, Shinan District, Qingdao 266000, Shandong, China
| | - Xinping Yu
- Department of Gynecology, The Affiliated Hospital of Qingdao University, 16 Jiangsu Road, Shinan District, Qingdao 266000, Shandong, China
| | - Xiao Yu
- Department of Gynecology, The Affiliated Hospital of Qingdao University, 16 Jiangsu Road, Shinan District, Qingdao 266000, Shandong, China
| | - Yankui Wang
- Department of Gynecology, The Affiliated Hospital of Qingdao University, 16 Jiangsu Road, Shinan District, Qingdao 266000, Shandong, China
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32
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Abstract
To screen and identify ideal leading compounds from a drug library (ZINC15 database) with potential inhibition effect against c-Myc to contribute to medication design and development.A series of computer-aided virtual screening techniques were performed to identify potential inhibitors of c-Myc. LibDock from the software Discovery Studio was used to do a structure-based screening after ADME (absorption, distribution, metabolism, excretion) and toxicity prediction. Molecular docking was utilized to show the binding affinity and potential mechanism between ligands and c-Myc. Stability of the ligand-receptor complex was analyzed by molecular dynamic simulation at the end of the research.Compounds with more interactive energy which are confirmed to be the potential inhibitors for c-Myc were identified from the ZINC15 databases. Additionally, those compounds are also anticipated with fewer ames mutagenicity, rodent carcinogenicity, nondevelopmental toxic potential, and tolerant with cytochrome p450 2D6(CYP2D6). Dynamic simulation analysis also revealed that the very compounds had more favorable potential energy compared with 10058-F4(ZINC12406714). Furthermore, we prove that those compounds are stable and can exist in natural conditions.This study demonstrates that the compounds are potential therapeutic inhibitors for c-Myc. These compounds are safe and stable for drug candidates and may play a critical role in c-Myc inhibitor development.
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Affiliation(s)
- Junan Ren
- Clinical College, Jilin University, Changchun
| | | | - Junliang Ge
- Clinical College, Jilin University, Changchun
| | - Bo Wu
- Clinical College, Jilin University, Changchun
- Department of Orthopedics
| | - Weihang Li
- Department of Orthopaedics, Xijing Hospital, The Fourth Military Medical University, Xian, China
| | - Xinhui Wang
- Clinical College, Jilin University, Changchun
- Department of Oncology, The First Hospital of Jilin University, Changchun
| | - Liyan Zhao
- Department of Clinical Laboratory, The Second Hospital of Jilin University
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33
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Li Y, Sun XX, Qian DZ, Dai MS. Molecular Crosstalk Between MYC and HIF in Cancer. Front Cell Dev Biol 2020; 8:590576. [PMID: 33251216 PMCID: PMC7676913 DOI: 10.3389/fcell.2020.590576] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 10/21/2020] [Indexed: 12/26/2022] Open
Abstract
The transcription factor c-MYC (MYC thereafter) is a global regulator of gene expression. It is overexpressed or deregulated in human cancers of diverse origins and plays a key role in the development of cancers. Hypoxia-inducible factors (HIFs), a central regulator for cells to adapt to low cellular oxygen levels, is also often overexpressed and activated in many human cancers. HIF mediates the primary transcriptional response of a wide range of genes in response to hypoxia. Earlier studies focused on the inhibition of MYC by HIF during hypoxia, when MYC is expressed at physiological level, to help cells survive under low oxygen conditions. Emerging evidence suggests that MYC and HIF also cooperate to promote cancer cell growth and progression. This review will summarize the current understanding of the complex molecular interplay between MYC and HIF.
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Affiliation(s)
- Yanping Li
- Department of Molecular and Medical Genetics, School of Medicine, Portland, OR, United States
| | - Xiao-Xin Sun
- Department of Molecular and Medical Genetics, School of Medicine, Portland, OR, United States
| | - David Z Qian
- The OHSU Knight Cancer Institute, Oregon Health and Science University, Portland, OR, United States
| | - Mu-Shui Dai
- Department of Molecular and Medical Genetics, School of Medicine, Portland, OR, United States.,The OHSU Knight Cancer Institute, Oregon Health and Science University, Portland, OR, United States
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34
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Sicoli G, Kress T, Vezin H, Ledolter K, Kurzbach D. A Switch between Two Intrinsically Disordered Conformational Ensembles Modulates the Active Site of a Basic-Helix-Loop-Helix Transcription Factor. J Phys Chem Lett 2020; 11:8944-8951. [PMID: 33030907 PMCID: PMC7649839 DOI: 10.1021/acs.jpclett.0c02242] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
We report a conformational switch between two distinct intrinsically disordered subensembles within the active site of a transcription factor. This switch highlights an evolutionary benefit conferred by the high plasticity of intrinsically disordered domains, namely, their potential to dynamically sample a heterogeneous conformational space housing multiple states with tailored properties. We focus on proto-oncogenic basic-helix-loop-helix (bHLH)-type transcription factors, as these play key roles in cell regulation and function. Despite intense research efforts, the understanding of structure-function relations of these transcription factors remains incomplete as they feature intrinsically disordered DNA-interaction domains that are difficult to characterize, theoretically as well as experimentally. Here we characterize the structural dynamics of the intrinsically disordered region DNA-binding site of the vital MYC-associated transcription factor X (MAX). Integrating nuclear magnetic resonance (NMR) measurements, molecular dynamics (MD) simulations, and electron paramagnetic resonance (EPR) measurements, we show that, in the absence of DNA, the binding site of the free MAX2 homodimer samples two intrinsically disordered conformational subensembles. These feature distinct structural properties: one subensemble consists of a set of highly flexible and spatially extended conformers, while the second features a set of "hinged" conformations. In this latter ensemble, the disordered N-terminal tails of MAX2 fold back along the dimer, forming transient long-range contacts with the HLH-region and thereby exposing the DNA binding site to the solvent. The features of these divergent substates suggest two mechanisms by which protein conformational dynamics in MAX2 might modulate DNA-complex formation: by enhanced initial recruitment of free DNA ligands, as a result of the wider conformational space sampled by the extended ensemble, and by direct exposure of the binding site and the corresponding strong electrostatic attractions presented while in the hinged conformations.
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Affiliation(s)
- Giuseppe Sicoli
- Laboratoire
Avancé de Spectroscopie pour les Interactions, la Réactivité
et l’Environnement (LASIRE), UMR CNRS 8516, Université de Lille, Avenue Paul Langevin − C4, F-59655 Villeneuve d’Ascq, France
| | - Thomas Kress
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Hervé Vezin
- Laboratoire
Avancé de Spectroscopie pour les Interactions, la Réactivité
et l’Environnement (LASIRE), UMR CNRS 8516, Université de Lille, Avenue Paul Langevin − C4, F-59655 Villeneuve d’Ascq, France
| | - Karin Ledolter
- Department
for Structural and Computational Biology, Max F. Perutz Laboratories, University Vienna, Campus Vienna BioCenter 5, 1030 Vienna, Austria
| | - Dennis Kurzbach
- Faculty
of Chemistry, Institute of Biological Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
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Development and survival of MYC-driven lymphomas require the MYC antagonist MNT to curb MYC-induced apoptosis. Blood 2020; 135:1019-1031. [PMID: 31978211 DOI: 10.1182/blood.2019003014] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 12/23/2019] [Indexed: 01/06/2023] Open
Abstract
Deregulated overexpression of MYC is implicated in the development and malignant progression of most (∼70%) human tumors. MYC drives cell growth and proliferation, but also, at high levels, promotes apoptosis. Here, we report that the proliferative capacity of MYC-driven normal and neoplastic B lymphoid cells depends on MNT, a MYC-related transcriptional repressor. Our genetic data establish that MNT synergizes with MYC by suppressing MYC-driven apoptosis, and that it does so primarily by reducing the level of pro-apoptotic BIM. In Eμ-Myc mice, which model the MYC/IGH chromosome translocation in Burkitt's lymphoma, homozygous Mnt deletion greatly reduced lymphoma incidence by enhancing apoptosis and markedly decreasing premalignant B lymphoid cell populations. Strikingly, by inducing Mnt deletion within transplanted fully malignant Eμ-Myc lymphoma cells, we significantly extended transplant recipient survival. The dependency of lymphomas on MNT for survival suggests that drugs inhibiting MNT could significantly boost therapy of MYC-driven tumors by enhancing intrinsic MYC-driven apoptosis.
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Johansson-Åkhe I, Mirabello C, Wallner B. InterPep2: global peptide-protein docking using interaction surface templates. Bioinformatics 2020; 36:2458-2465. [PMID: 31917413 PMCID: PMC7178396 DOI: 10.1093/bioinformatics/btaa005] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 12/16/2019] [Accepted: 01/03/2020] [Indexed: 12/23/2022] Open
Abstract
Motivation Interactions between proteins and peptides or peptide-like intrinsically disordered regions are involved in many important biological processes, such as gene expression and cell life-cycle regulation. Experimentally determining the structure of such interactions is time-consuming and difficult because of the inherent flexibility of the peptide ligand. Although several prediction-methods exist, most are limited in performance or availability. Results InterPep2 is a freely available method for predicting the structure of peptide–protein interactions. Improved performance is obtained by using templates from both peptide–protein and regular protein–protein interactions, and by a random forest trained to predict the DockQ-score for a given template using sequence and structural features. When tested on 252 bound peptide–protein complexes from structures deposited after the complexes used in the construction of the training and templates sets of InterPep2, InterPep2-Refined correctly positioned 67 peptides within 4.0 Å LRMSD among top10, similar to another state-of-the-art template-based method which positioned 54 peptides correctly. However, InterPep2 displays a superior ability to evaluate the quality of its own predictions. On a previously established set of 27 non-redundant unbound-to-bound peptide–protein complexes, InterPep2 performs on-par with leading methods. The extended InterPep2-Refined protocol managed to correctly model 15 of these complexes within 4.0 Å LRMSD among top10, without using templates from homologs. In addition, combining the template-based predictions from InterPep2 with ab initio predictions from PIPER-FlexPepDock resulted in 22% more near-native predictions compared to the best single method (22 versus 18). Availability and implementation The program is available from: http://wallnerlab.org/InterPep2. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Isak Johansson-Åkhe
- Division of Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Claudio Mirabello
- Division of Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Björn Wallner
- Division of Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
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Górka M, Żerko S, Konrat R, Koźmiński W, Kurzbach D. 1H, 13C and 15N backbone resonance assignment of BRCA1 fragment 219-504. BIOMOLECULAR NMR ASSIGNMENTS 2020; 14:289-293. [PMID: 32583165 PMCID: PMC7462910 DOI: 10.1007/s12104-020-09963-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 06/17/2020] [Indexed: 06/11/2023]
Abstract
The breast cancer susceptibility protein 1 (BRCA1) plays a central role in the suppression of human breast and ovarian cancer. Germ line mutations of the BRCA1 gene are responsible for the hereditary breast and ovarian cancer (HBOC) syndrome. Here were report 1H, 13C, and 15N resonance assignments for the intrinsically disordered BRCA1 fragment 219-504, which contains important interaction sites for the proto-oncogenic transcription factor MYC as well as for p53. A nuclear magnetic resonance assignment was achieved at 18.8 T magnetic field strength using a 5D HN(CA)CONH experiment and its associated 4D H(NCA)CONH and 4D (H)N(CA)CONH experiments. 13Cα and 13Cβ assignments were obtained using a 5D HabCabCONH experiment. With this strategy, 90% of 1H/15N backbone pairs could be assigned. Similarly, 264 C' resonances were assigned corresponding to 86% of the total number of C' atoms. In addition, 252 Cβ resonances (i.e. 85%) were assigned, together with 461 attached Hβ nuclei, as well as 264 (i.e. 86%) Cα resonances, together with 275 attached Hα nuclei.
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Affiliation(s)
- Michał Górka
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Szymon Żerko
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Robert Konrat
- Department for Structural and Computational Biology, University Vienna, Campus Vienna BioCenter 5, 1030, Vienna, Austria
| | - Wiktor Koźmiński
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Dennis Kurzbach
- Faculty of Chemistry, Institute of Biological Chemistry, University Vienna, Währinger Straße 38, 1090, Vienna, Austria.
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Sayyadi M, Safaroghli-Azar A, Safa M, Abolghasemi H, Momeny M, Bashash D. NF-κB-dependent Mechanism of Action of c-Myc Inhibitor 10058-F4: Highlighting a Promising Effect of c-Myc Inhibition in Leukemia Cells, Irrespective of p53 Status. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2020; 19:153-165. [PMID: 32922477 PMCID: PMC7462502 DOI: 10.22037/ijpr.2020.112926.14018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Due to the frequent contribution in the pathogenesis of different human malignancies, c-Myc is among those transcription factors that are believed to be pharmacologically targeted for cancer therapeutic approaches. In the present study, we examined the anti-leukemic effect of a well-known c-Myc inhibitor 10058-F4 on a panel of hematologic malignant cells harboring either mutant or wild-type p53. Notably, we found that the suppression of c-Myc was coupled with the reduction in the survival of all the tested leukemic cells; however, as far as we are aware, this study suggests for the first time that the cytotoxic effect of 10058-F4 was not significantly affected by the molecular status of p53. Delving into the molecular mechanisms of the inhibitor in the most sensitive cell line revealed that 10058-F4 could induce apoptotic cell death in mutant p53-expressing NB4 cells through the suppression of NF-κB pathway coupled with a significant induction of intracellular reactive oxygen species (ROS). In addition, we found that the anti-leukemic effect of 10058-F4 was overshadowed, at least partially, through the compensatory activation of the PI3K signaling pathway; highlighting a plausible attenuating role of this axis on 10058-F4 cytotoxicity. In conclusion, the results of the present study shed light on the favorable anti-leukemic effect of 10058-F4, especially in combination with PI3K inhibitors in acute promyelocytic leukemia; however, further investigations should be accomplished to determine the efficacy of the inhibitor, either as a single agent or in a combined-modal strategy, in leukemia treatment.
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Affiliation(s)
- Mohammad Sayyadi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ava Safaroghli-Azar
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Majid Safa
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Hassan Abolghasemi
- Pediatric Congenital Hematologic Disorders Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Majid Momeny
- Cancer Cell Signaling, Turku Center for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Wu C, Su J, Long W, Qin C, Wang X, Xiao K, Li Y, Xiao Q, Wang J, Pan Y, Liu Q. LINC00470 promotes tumour proliferation and invasion, and attenuates chemosensitivity through the LINC00470/miR-134/Myc/ABCC1 axis in glioma. J Cell Mol Med 2020; 24:12094-12106. [PMID: 32916774 PMCID: PMC7579701 DOI: 10.1111/jcmm.15846] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/30/2020] [Accepted: 08/19/2020] [Indexed: 12/24/2022] Open
Abstract
Glioma is the most common primary malignant tumour in the brain; temozolomide (TMZ) is the most prevalent chemotherapeutic drug currently used to combat this cancer. We reported previously that the long intergenic non‐protein coding RNA 470 (LINC00470) is a novel prognostic biomarker for glioma and promotes the tumour growth in an intracranial transplantation mouse model. However, the effects of LINC00470 on glioma cell proliferation, invasion and TMZ chemosensitivity, as well as its molecular mechanism, remain unclear. In this study, we found elevated expression levels of LINC00470 and MYC in glioma tissues and cells and decreased expression of microRNA‐134 (miR‐134). Functional studies have shown that LINC00470 promotes proliferation and invasion, and attenuates chemosensitivity of glioma cells, while miR‐134 exerts the opposite effect. In the rescue experiments, the tumorigenic effect of LINC00470 was offset by miR‐134. In the mechanism study, we found that LINC00470 was a competitive endogenous RNA (ceRNA) of miR‐134 and that miR‐134 can directly target MYC and negatively regulate its expression. Furthermore, MYC was positively correlated with ATP‐binding cassette subfamily C member 1 (ABCC1) expression in glioma cells and MYC up‐regulated ABCC1 expression. Further studies found that LINC00470 regulated MYC by sponging miR‐134 to regulate the expression of ABCC1. We concluded that LINC00470 promoted the expression of MYC and ABCC1 by suppressing miR‐134, thus promoting glioma cell proliferation and invasion, and attenuating TMZ chemosensitivity. Moreover, the LINC00470/miR‐134/MYC/ABCC1 axis constitutes a potential therapeutic target.
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Affiliation(s)
- Changwu Wu
- Department of Neurosurgery, Xiangya Hospital, Central-South University, Changsha, China.,Institute of Anatomy, University of Leipzig, Leipzig, Germany
| | - Jun Su
- Department of Neurosurgery, Xiangya Hospital, Central-South University, Changsha, China
| | - Wenyong Long
- Department of Neurosurgery, Xiangya Hospital, Central-South University, Changsha, China
| | - Chaoying Qin
- Department of Neurosurgery, Xiangya Hospital, Central-South University, Changsha, China
| | - Xiangyu Wang
- Department of Neurosurgery, Xiangya Hospital, Central-South University, Changsha, China
| | - Kai Xiao
- Department of Neurosurgery, Xiangya Hospital, Central-South University, Changsha, China
| | - Yang Li
- Department of Neurosurgery, Xiangya Hospital, Central-South University, Changsha, China
| | - Qun Xiao
- Department of Neurosurgery, Xiangya Hospital, Central-South University, Changsha, China
| | - Junquan Wang
- Department of Neurosurgery, Xiangya Hospital, Central-South University, Changsha, China
| | - Yimin Pan
- Department of Neurosurgery, Xiangya Hospital, Central-South University, Changsha, China
| | - Qing Liu
- Department of Neurosurgery, Xiangya Hospital, Central-South University, Changsha, China.,Institute of Skull Base Surgery and Neuro-oncology at Hunan, Changsha, China
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In Vitro Evaluation of a Peptide-Mesoporous Silica Nanoparticle Drug Release System against HIV-1. INORGANICS 2020. [DOI: 10.3390/inorganics8070042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
It has been shown that the optimized VIR-576 derivative of the natural HIV-1 entry inhibitor targeting the viral gp41 fusion peptide is safe and effective in infected individuals. However, high doses of this peptide were required, and stability, as well as delivery, must be improved for clinical application. Here, we examined the loading and release of VIR-576 into/from mesoporous silica nanoparticles (MSNs) in vitro. We found that a moderately high peptide loading of 11.5 wt % could be achieved by adsorption from PBS buffer (pH 7.2), i.e., under mild, fully peptide-compatible conditions. The release rate of peptide into the same buffer was slow and the equilibrium concentration as indicated by the adsorption isotherm could not be reached even within 50 h at the particle concentrations studied. However, a faster release was observed at lower particle concentrations, indicating that partial particle dissolution had a positive influence on peptide release. To determine the antiviral activity of VIR-576-loaded MSNs, TZM-bl indicator cells were exposed to HIV-1 and the infection rates were followed as a function of time and VIR-576 concentration. The inhibitory activity observed for VIR-576 released from the MSNs was virtually identical to that of free VIR-576 at the 48 h time point, indicating that (a) VIR-576 was released in an active form from the MSNs, and (b) the release rate in the presence of serum proteins was clearly higher than that observed under protein-free conditions. These observations are discussed based on competitive peptide/protein adsorption, as well as potential influences of serum proteins on the dissolution-reprecipitation of silica under conditions where the total silica concentration is above the saturation level for dissolved silica. Our results highlight the need for studying drug release kinetics in the presence of serum proteins, in order to allow for a better extrapolation of in vitro data to in vivo conditions. Furthermore, due to the high peptide loadings that can be achieved using MSNs as carriers, such a formulation appears promising for local release applications. For systemic administration, however, peptides with a higher potency would be needed, due to their high molar masses limiting the drug loading in terms of moles per gram carrier.
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Huang W, Dong S, Cha Y, Yuan X. SNHG11 promotes cell proliferation in colorectal cancer by forming a positive regulatory loop with c-Myc. Biochem Biophys Res Commun 2020; 527:985-992. [PMID: 32439170 DOI: 10.1016/j.bbrc.2020.05.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/01/2020] [Indexed: 12/24/2022]
Abstract
Dysregulation of long non-coding RNAs (lncRNA) have long been linked to the onset and development of colorectal cancer (CRC), yet the underlying mechanisms remain elusive. Small nucleolar RNA host gene 11 (SNHG11) is a novel lncRNA with few information about its role in development and progression of CRC. Here, we found SNHG11, a highly conserved lncRNA, was commonly overexpressed in various cancer including CRC. High expression of SNHG11 correlated with poor prognosis in patients with CRC. Gain of function and loss-of function experiments showed that SNHG11 visibly promoted proliferation in CRC cells. Mechanistic assays revealed that SNHG11 interacted with Insulin-like growth factor 2 (IGF2) mRNA-binding protein 1 (IGF2BP1), thereby enhancing the interaction between IGF2BP1 and c-Myc mRNA, a well-known target of IGF2BP1. Consequently, c-Myc mRNA expression was stabilized and its downstream targets were significantly upregulated. Further investigation demonstrated that SNHG11 upregulated c-Myc which in turn transcriptionally upregulated SNHG11. Taken together, our findings suggested that reciprocal regulation of SNHG11 and c-Myc promotes cell proliferation in CRC.
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Affiliation(s)
- Weizhen Huang
- Department of Medical Oncology, Huizhou Municipal Central Hospital of Guangdong Province, 41 North Eling Road, Huizhou, Guangdong Province, 516000, PR China
| | - Shaoting Dong
- Department of Medical Oncology, Huizhou Municipal Central Hospital of Guangdong Province, 41 North Eling Road, Huizhou, Guangdong Province, 516000, PR China
| | - Yinlian Cha
- Department of Medical Oncology, Huizhou Municipal Central Hospital of Guangdong Province, 41 North Eling Road, Huizhou, Guangdong Province, 516000, PR China
| | - Xia Yuan
- Department of Medical Oncology, Huizhou Municipal Central Hospital of Guangdong Province, 41 North Eling Road, Huizhou, Guangdong Province, 516000, PR China.
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Beaulieu ME, Castillo F, Soucek L. Structural and Biophysical Insights into the Function of the Intrinsically Disordered Myc Oncoprotein. Cells 2020; 9:E1038. [PMID: 32331235 PMCID: PMC7226237 DOI: 10.3390/cells9041038] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/16/2020] [Accepted: 04/17/2020] [Indexed: 12/13/2022] Open
Abstract
Myc is a transcription factor driving growth and proliferation of cells and involved in the majority of human tumors. Despite a huge body of literature on this critical oncogene, our understanding of the exact molecular determinants and mechanisms that underlie its function is still surprisingly limited. Indubitably though, its crucial and non-redundant role in cancer biology makes it an attractive target. However, achieving successful clinical Myc inhibition has proven challenging so far, as this nuclear protein is an intrinsically disordered polypeptide devoid of any classical ligand binding pockets. Indeed, Myc only adopts a (partially) folded structure in some contexts and upon interacting with some protein partners, for instance when dimerizing with MAX to bind DNA. Here, we review the cumulative knowledge on Myc structure and biophysics and discuss the implications for its biological function and the development of improved Myc inhibitors. We focus this biophysical walkthrough mainly on the basic region helix-loop-helix leucine zipper motif (bHLHLZ), as it has been the principal target for inhibitory approaches so far.
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Affiliation(s)
| | | | - Laura Soucek
- Peptomyc S.L., Edifici Cellex, 08035 Barcelona, Spain; (F.C.); (L.S.)
- Vall d’Hebron Institute of Oncology (VHIO), Edifici Cellex, 08035 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08035 Barcelona, Spain
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08035 Bellaterra, Spain
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Abstract
MYC is a master transcriptional regulator that controls almost all cellular processes. Over the last several decades, researchers have strived to define the context-dependent transcriptional gene programs that are controlled by MYC, as well as the mechanisms that regulate MYC function, in an effort to better understand the contribution of this oncoprotein to cancer progression. There are a wealth of data indicating that deregulation of MYC activity occurs in a large number of cancers and significantly contributes to disease progression, metastatic potential, and therapeutic resistance. Although the therapeutic targeting of MYC in cancer is highly desirable, there remain substantial structural and functional challenges that have impeded direct MYC-targeted drug development and efficacy. While efforts to drug the ‘undruggable’ may seem futile given these challenges and considering the broad reach of MYC, significant strides have been made to identify points of regulation that can be exploited for therapeutic purposes. These include targeting the deregulation of MYC transcription in cancer through small-molecule inhibitors that induce epigenetic silencing or that regulate the G-quadruplex structures within the MYC promoter. Alternatively, compounds that disrupt the DNA-binding activities of MYC have been the long-standing focus of many research groups, since this method would prevent downstream MYC oncogenic activities regardless of upstream alterations. Finally, proteins involved in the post-translational regulation of MYC have been identified as important surrogate targets to reduce MYC activity downstream of aberrant cell stimulatory signals. Given the complex regulation of the MYC signaling pathway, a combination of these approaches may provide the most durable response, but this has yet to be shown. Here, we provide a comprehensive overview of the different therapeutic strategies being employed to target oncogenic MYC function, with a focus on post-translational mechanisms.
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Feris EJ, Hinds JW, Cole MD. Formation of a structurally-stable conformation by the intrinsically disordered MYC:TRRAP complex. PLoS One 2019; 14:e0225784. [PMID: 31790487 PMCID: PMC6886782 DOI: 10.1371/journal.pone.0225784] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/12/2019] [Indexed: 01/08/2023] Open
Abstract
Our primary goal is to therapeutically target the oncogenic transcription factor MYC to stop tumor growth and cancer progression. Here, we report aspects of the biophysical states of the MYC protein and its interaction with one of the best-characterized MYC cofactors, TRansactivation/tRansformation-domain Associated Protein (TRRAP). The MYC:TRRAP interaction is critical for MYC function in promoting cancer. The interaction between MYC and TRRAP occurs at a precise region in the MYC protein, called MYC Homology Box 2 (MB2), which is central to the MYC transactivation domain (TAD). Although the MYC TAD is inherently disordered, this report suggests that MB2 may acquire a defined structure when complexed with TRRAP which could be exploited for the investigation of inhibitors of MYC function by preventing this protein-protein interaction (PPI). The MYC TAD, and in particular the MB2 motif, is unique and invariant in evolution, suggesting that MB2 is an ideal site for inhibiting MYC function.
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Affiliation(s)
- Edmond J. Feris
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth College, Hanover, NH, United States of America
- Norris Cotton Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, NH, United States of America
| | - John W. Hinds
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth College, Hanover, NH, United States of America
- Norris Cotton Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, NH, United States of America
| | - Michael D. Cole
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth College, Hanover, NH, United States of America
- Norris Cotton Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, NH, United States of America
- * E-mail:
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New prognostic markers revealed by RNA-Seq transcriptome analysis after MYC silencing in a metastatic gastric cancer cell line. Oncotarget 2019; 10:5768-5779. [PMID: 31645899 PMCID: PMC6791377 DOI: 10.18632/oncotarget.27208] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 08/27/2019] [Indexed: 02/06/2023] Open
Abstract
MYC overexpression is considered a driver event in gastric cancer (GC), and is frequently correlated with poor prognosis and metastasis. In this study, we evaluated the prognostic value of genes upregulated by MYC in patients with GC. Metastatic GC cells (AGP01) characterized by MYC amplification, were transfected with siRNAs targeting MYC. RNA-seq was performed in silenced and non-silenced AGP01 cells. Among the differentially expressed genes, CIAPIN1, MTA2, and UXT were validated using qRT-PCR, western blot, and immunohistochemistry in gastric tissues of 213 patients with GC; and their expressions were correlated with clinicopathological and survival data. High mRNA and protein levels of CIAPIN1, MTA2, and UXT were strongly associated with advanced GC stages (P < 0.0001). However, only CIAPIN1 and UXT gene expressions were able to predict distant metastases in patients with early-stage GC (P < 0.0001), with high sensitivity (> 92%) and specificity (> 90%). Overall survival rate of patients with overexpressed CIAPIN1 or UXT was significantly lower (P < 0.0001). In conclusion, CIAPIN1 and UXT may serve as potential molecular markers for GC prognosis.
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Zhong S, Wu B, Wang X, Sun D, Liu D, Jiang S, Ge J, Zhang Y, Liu X, Zhou X, Jin R, Chen Y. Identification of driver genes and key pathways of prolactinoma predicts the therapeutic effect of genipin. Mol Med Rep 2019; 20:2712-2724. [PMID: 31322266 PMCID: PMC6691206 DOI: 10.3892/mmr.2019.10505] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 04/11/2019] [Indexed: 11/06/2022] Open
Abstract
The purpose of the present study was to identify the potential targets and markers for diagnosis, therapy and prognosis in patients with prolactinoma at the molecular level and to determine the therapeutic effects of genipin in prolactinoma. The gene expression profiles of GSE2175, GSE26966 and GSE36314 were obtained from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) were identified after comparing between gene expression profiles of the prolactinoma tissues and normal tissues. Then, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and protein‑protein interaction (PPI) network analysis were conducted. In addition, in vitro, scratch assay, colony‑forming assay, Cell Counting Kit 8 (CCK8) assay and flow cytometry were performed to verify the functional effects of genipin. An aggregate of 12,695, 3,847 and 5,310 DEGs were identified from GSE2175, GSE26966 and GSE36314, respectively. The results of GO and KEGG analysis showed that the DEGs significant and important for prolactinoma were mostly involved with 'spindle pole' and 'oocyte meiosis'. A total of 20 genes were selected as hub genes with high degrees after PPI network analysis, including mitogen‑activated protein kinase 1 (MAPK1), MYC, early growth response 1 (EGR1), Bcl2 and calmodulin 1 (CALM1). CCK8 assay, colony‑forming assay and scratch assay were performed to verify the anti‑prolactinoma effect of genipin. The results of flow cytometry showed that apoptosis was increased by genipin. MAPK1, MYC, EGR1, Bcl2 and CALM1 were screened as main hub genes. Genipin upregulated the expression level of EGR1 and p21 (downstream mediator of EGR1) and EGR1, inhibited the proliferation and migration of prolactinoma cells. Genipin is a promising drug for treatment of patients with prolactinoma.
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Affiliation(s)
- Sheng Zhong
- Department of Neurosurgery, The First Hospital of Jilin University, Changchun, Jilin 130012, P.R. China
| | - Bo Wu
- Clinical College, Jilin University, Changchun, Jilin 130012, P.R. China
| | - Xinhui Wang
- Clinical College, Jilin University, Changchun, Jilin 130012, P.R. China
| | - Dandan Sun
- Clinical College, Jilin University, Changchun, Jilin 130012, P.R. China
| | - Daqun Liu
- Clinical College, Jilin University, Changchun, Jilin 130012, P.R. China
| | - Shanshan Jiang
- College of Pharmacy, Jilin University, Changchun, Jilin 130012, P.R. China
| | - Junliang Ge
- Clinical College, Jilin University, Changchun, Jilin 130012, P.R. China
| | - Yuan Zhang
- Clinical College, Jilin University, Changchun, Jilin 130012, P.R. China
| | - Xinrui Liu
- Department of Neurosurgery, The First Hospital of Jilin University, Changchun, Jilin 130012, P.R. China
| | - Xiaoli Zhou
- Department of Cell Biology, Basic Medical College, Jilin University, Changchun, Jilin 130012, P.R. China
| | - Rihua Jin
- Department of Neurosurgery, The First Hospital of Jilin University, Changchun, Jilin 130012, P.R. China
| | - Yong Chen
- Department of Neurosurgery, The First Hospital of Jilin University, Changchun, Jilin 130012, P.R. China
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Sammak S, Hamdani N, Gorrec F, Allen MD, Freund SMV, Bycroft M, Zinzalla G. Crystal Structures and Nuclear Magnetic Resonance Studies of the Apo Form of the c-MYC:MAX bHLHZip Complex Reveal a Helical Basic Region in the Absence of DNA. Biochemistry 2019; 58:3144-3154. [PMID: 31260268 PMCID: PMC6791285 DOI: 10.1021/acs.biochem.9b00296] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
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The c-MYC transcription
factor is a master regulator of cell growth
and proliferation and is an established target for cancer therapy.
This basic helix–loop–helix Zip protein forms a heterodimer
with its obligatory partner MAX, which binds to DNA via the basic
region. Considerable research efforts are focused on targeting the
heterodimerization interface and the interaction of the complex with
DNA. The only available crystal structure is that of a c-MYC:MAX complex
artificially tethered by an engineered disulfide linker and prebound
to DNA. We have carried out a detailed structural analysis of the
apo form of the c-MYC:MAX complex, with no artificial linker, both
in solution using nuclear magnetic resonance (NMR) spectroscopy and
by X-ray crystallography. We have obtained crystal structures in three
different crystal forms, with resolutions between 1.35 and 2.2 Å,
that show extensive helical structure in the basic region. Determination
of the α-helical propensity using NMR chemical shift analysis
shows that the basic region of c-MYC and, to a lesser extent, that
of MAX populate helical conformations. We have also assigned the NMR
spectra of the c-MYC basic helix–loop–helix Zip motif
in the absence of MAX and showed that the basic region has an intrinsic
helical propensity even in the absence of its dimerization partner.
The presence of helical structure in the basic regions in the absence
of DNA suggests that the molecular recognition occurs via a conformational
selection rather than an induced fit. Our work provides both insight
into the mechanism of DNA binding and structural information to aid
in the development of MYC inhibitors.
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Affiliation(s)
- Susan Sammak
- Microbiology, Tumor and Cell Biology (MTC) , Karolinska Institutet , Solnavägen 9 , 171 65 Stockholm , Sweden
| | - Najoua Hamdani
- Microbiology, Tumor and Cell Biology (MTC) , Karolinska Institutet , Solnavägen 9 , 171 65 Stockholm , Sweden
| | - Fabrice Gorrec
- MRC Laboratory of Molecular Biology , Cambridge Biomedical Campus , Francis Crick Avenue , Cambridge CB2 0QH , U.K
| | - Mark D Allen
- MRC Laboratory of Molecular Biology , Cambridge Biomedical Campus , Francis Crick Avenue , Cambridge CB2 0QH , U.K
| | - Stefan M V Freund
- MRC Laboratory of Molecular Biology , Cambridge Biomedical Campus , Francis Crick Avenue , Cambridge CB2 0QH , U.K
| | - Mark Bycroft
- MRC Laboratory of Molecular Biology , Cambridge Biomedical Campus , Francis Crick Avenue , Cambridge CB2 0QH , U.K
| | - Giovanna Zinzalla
- Microbiology, Tumor and Cell Biology (MTC) , Karolinska Institutet , Solnavägen 9 , 171 65 Stockholm , Sweden
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García-Gutiérrez L, Delgado MD, León J. MYC Oncogene Contributions to Release of Cell Cycle Brakes. Genes (Basel) 2019; 10:E244. [PMID: 30909496 PMCID: PMC6470592 DOI: 10.3390/genes10030244] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 03/16/2019] [Accepted: 03/18/2019] [Indexed: 12/12/2022] Open
Abstract
Promotion of the cell cycle is a major oncogenic mechanism of the oncogene c-MYC (MYC). MYC promotes the cell cycle by not only activating or inducing cyclins and CDKs but also through the downregulation or the impairment of the activity of a set of proteins that act as cell-cycle brakes. This review is focused on the role of MYC as a cell-cycle brake releaser i.e., how MYC stimulates the cell cycle mainly through the functional inactivation of cell cycle inhibitors. MYC antagonizes the activities and/or the expression levels of p15, ARF, p21, and p27. The mechanism involved differs for each protein. p15 (encoded by CDKN2B) and p21 (CDKN1A) are repressed by MYC at the transcriptional level. In contrast, MYC activates ARF, which contributes to the apoptosis induced by high MYC levels. At least in some cells types, MYC inhibits the transcription of the p27 gene (CDKN1B) but also enhances p27's degradation through the upregulation of components of ubiquitin ligases complexes. The effect of MYC on cell-cycle brakes also opens the possibility of antitumoral therapies based on synthetic lethal interactions involving MYC and CDKs, for which a series of inhibitors are being developed and tested in clinical trials.
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Affiliation(s)
- Lucía García-Gutiérrez
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC) CSIC-Universidad de Cantabria and Department of Biología Molecular, Universidad de Cantabria, 39011 Santander, Spain.
- Current address: Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland.
| | - María Dolores Delgado
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC) CSIC-Universidad de Cantabria and Department of Biología Molecular, Universidad de Cantabria, 39011 Santander, Spain.
| | - Javier León
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC) CSIC-Universidad de Cantabria and Department of Biología Molecular, Universidad de Cantabria, 39011 Santander, Spain.
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49
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Johansson-Åkhe I, Mirabello C, Wallner B. Predicting protein-peptide interaction sites using distant protein complexes as structural templates. Sci Rep 2019; 9:4267. [PMID: 30862810 PMCID: PMC6414505 DOI: 10.1038/s41598-019-38498-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 12/31/2018] [Indexed: 01/07/2023] Open
Abstract
Protein-peptide interactions play an important role in major cellular processes, and are associated with several human diseases. To understand and potentially regulate these cellular function and diseases it is important to know the molecular details of the interactions. However, because of peptide flexibility and the transient nature of protein-peptide interactions, peptides are difficult to study experimentally. Thus, computational methods for predicting structural information about protein-peptide interactions are needed. Here we present InterPep, a pipeline for predicting protein-peptide interaction sites. It is a novel pipeline that, given a protein structure and a peptide sequence, utilizes structural template matches, sequence information, random forest machine learning, and hierarchical clustering to predict what region of the protein structure the peptide is most likely to bind. When tested on its ability to predict binding sites, InterPep successfully pinpointed 255 of 502 (50.7%) binding sites in experimentally determined structures at rank 1 and 348 of 502 (69.3%) among the top five predictions using only structures with no significant sequence similarity as templates. InterPep is a powerful tool for identifying peptide-binding sites; with a precision of 80% at a recall of 20% it should be an excellent starting point for docking protocols or experiments investigating peptide interactions. The source code for InterPred is available at http://wallnerlab.org/InterPep/ .
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Affiliation(s)
- Isak Johansson-Åkhe
- Division of Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, SE-581 83, Linköping, Sweden
| | - Claudio Mirabello
- Division of Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, SE-581 83, Linköping, Sweden
| | - Björn Wallner
- Division of Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, SE-581 83, Linköping, Sweden.
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Swier LJYM, Dzikiewicz‐Krawczyk A, Winkle M, van den Berg A, Kluiver J. Intricate crosstalk between MYC and non-coding RNAs regulates hallmarks of cancer. Mol Oncol 2019; 13:26-45. [PMID: 30451365 PMCID: PMC6322196 DOI: 10.1002/1878-0261.12409] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/10/2018] [Accepted: 10/23/2018] [Indexed: 01/17/2023] Open
Abstract
Myelocytomatosis viral oncogene homolog (MYC) plays an important role in the regulation of many cellular processes, and its expression is tightly regulated at the level of transcription, translation, protein stability, and activity. Despite this tight regulation, MYC is overexpressed in many cancers and contributes to multiple hallmarks of cancer. In recent years, it has become clear that noncoding RNAs add a crucial additional layer to the regulation of MYC and its downstream effects. So far, twenty-five microRNAs and eighteen long noncoding RNAs that regulate MYC have been identified. Thirty-three miRNAs and nineteen lncRNAs are downstream effectors of MYC that contribute to the broad oncogenic role of MYC, including its effects on diverse hallmarks of cancer. In this review, we give an overview of this extensive, multilayered noncoding RNA network that exists around MYC. Current data clearly show explicit roles of crosstalk between MYC and ncRNAs to allow tumorigenesis.
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Affiliation(s)
- Lotteke J. Y. M. Swier
- Department of Pathology and Medical BiologyUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | | | - Melanie Winkle
- Department of Pathology and Medical BiologyUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - Anke van den Berg
- Department of Pathology and Medical BiologyUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - Joost Kluiver
- Department of Pathology and Medical BiologyUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
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