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Eren E, Watts NR, Randazzo D, Palmer I, Sackett DL, Wingfield PT. Structural basis of microtubule depolymerization by the kinesin-like activity of HIV-1 Rev. Structure 2023; 31:1233-1246.e5. [PMID: 37572662 PMCID: PMC10592302 DOI: 10.1016/j.str.2023.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 04/07/2023] [Accepted: 07/18/2023] [Indexed: 08/14/2023]
Abstract
HIV-1 Rev is an essential regulatory protein that transports unspliced and partially spliced viral mRNAs from the nucleus to the cytoplasm for the expression of viral structural proteins. During its nucleocytoplasmic shuttling, Rev interacts with several host proteins to use the cellular machinery for the advantage of the virus. Here, we report the 3.5 Å cryo-EM structure of a 4.8 MDa Rev-tubulin ring complex. Our structure shows that Rev's arginine-rich motif (ARM) binds to both the acidic surfaces and the C-terminal tails of α/β-tubulin. The Rev-tubulin interaction is functionally homologous to that of kinesin-13, potently destabilizing microtubules at sub-stoichiometric levels. Expression of Rev in astrocytes and HeLa cells shows that it can modulate the microtubule cytoskeleton within the cellular environment. These results show a previously undefined regulatory role of Rev.
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Affiliation(s)
- Elif Eren
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Norman R Watts
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Davide Randazzo
- Light Imaging Section, Office of Science and Technology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ira Palmer
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dan L Sackett
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul T Wingfield
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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2
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Umaña CA, Henry JL, Saltzman CT, Sackett DL, Jenkins LM, Taylor RE. Linear (-)-Zampanolide: Flexibility in Conformation-Activity Relationships. ChemMedChem 2023; 18:e202300292. [PMID: 37552215 PMCID: PMC10615712 DOI: 10.1002/cmdc.202300292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/20/2023] [Accepted: 08/01/2023] [Indexed: 08/09/2023]
Abstract
Through an understanding of the conformational preferences of the polyketide natural product (-)-zampanolide, and the structural motifs that control these preferences, we developed a linear zampanolide analogue that exhibits potent cytotoxicity against cancer cell lines. This discovery provides a set of three structural handles for further structure-activity relationship (SAR) studies of this potent microtubule-stabilizing agent. Moreover, it provides additional evidence of the complex relationship between ligand preorganization, conformational flexibility, and biological potency. In contrast to medicinal chemistry dogma, these results demonstrate that increased overall conformational flexibility is not necessarily detrimental to protein binding affinity and biological activity.
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Affiliation(s)
- Christian A Umaña
- Department of Chemistry and Biochemistry and the Warren Center for Drug Discovery, University of Notre Dame, Notre Dame, IN 46556-5670, USA
| | - Jeffrey L Henry
- Department of Chemistry and Biochemistry and the Warren Center for Drug Discovery, University of Notre Dame, Notre Dame, IN 46556-5670, USA
| | - Claire T Saltzman
- Department of Chemistry and Biochemistry and the Warren Center for Drug Discovery, University of Notre Dame, Notre Dame, IN 46556-5670, USA
| | - Dan L Sackett
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lisa M Jenkins
- Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Richard E Taylor
- Department of Chemistry and Biochemistry and the Warren Center for Drug Discovery, University of Notre Dame, Notre Dame, IN 46556-5670, USA
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3
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McFadden JR, Tolete CDP, Huang Y, Macnamara E, Sept D, Nesterova G, Gahl WA, Sackett DL, Malicdan MCV. Clinical, genetic, and structural characterization of a novel TUBB4B tubulinopathy. Mol Genet Metab Rep 2023; 36:100990. [PMID: 37448631 PMCID: PMC10336574 DOI: 10.1016/j.ymgmr.2023.100990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 06/25/2023] [Indexed: 07/15/2023] Open
Abstract
Microtubules are cytoskeletal polymers of ⍺/β-tubulin heterodimers essential for a wide range of cellular processes. Pathogenic variations in microtubule-encoding genes (e.g., TUBB4B, which encodes the β-4B tubulin isotype) are responsible for a wide spectrum of cerebral malformations, collectively referred to as "tubulinopathies." The phenotypic manifestation of TUBB4B-associated tubulinopathy is Leber congenital amaurosis with early-onset deafness (LCAEOD), an autosomal dominant syndrome characterized by photoreceptor and cochlear cell loss; all known patients have pathogenic variations in amino acid R391. We present the clinical and molecular genetics findings of a 16-year-old female with a de novo missense variant in exon 1 of TUBB4B, c.32 A > G (p.Gln11Arg; Q11R). In addition to hearing loss and hyperopia without retinal abnormalities, our proband presented with two phenotypes of unknown genetic etiology, i.e., renal tubular Fanconi Syndrome (FS) and hypophosphatemic rickets (HR). The Q11R variant expands the genetic basis of early sensory hearing loss; its consequences with respect to microtubule structure are described. A mechanistic explanation for the FS and rickets, involving microtubule-mediated translocation of transporter proteins to and from the apical membrane of renal proximal tubular cells, is proposed.
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Affiliation(s)
- Jason R. McFadden
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Christina Deanne P. Tolete
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Yan Huang
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Ellen Macnamara
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - David Sept
- Departments of Biomedical Engineering and Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Galina Nesterova
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - William A. Gahl
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
- Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892-1851, USA
| | - Dan L. Sackett
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - May Christine V. Malicdan
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
- Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892-1851, USA
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4
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Penjweini R, Pasut A, Roarke B, Alspaugh G, Sackett DL, Knutson JR. High resolution spatial investigation of intracellular oxygen in muscle cells. bioRxiv 2023:2023.07.18.548845. [PMID: 37781589 PMCID: PMC10541121 DOI: 10.1101/2023.07.18.548845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Molecular oxygen (O 2 ) is one of the most functionally relevant metabolites. O 2 is essential for mito-chondrial aerobic respiration. Changes in O 2 affect muscle metabolism and play a critical role in the maintenance of skeletal muscle mass, with lack of sufficient O 2 resulting in detrimental loss of muscle mass and function. How exactly O 2 is used by muscle cells is less known, mainly due to the lack of tools to address O 2 dynamics at the cellular level. Here we discuss a new imaging method for the real time quantification of intracellular O 2 in muscle cells based on a genetically encoded O 2 -responsive sensor, Myoglobin-mCherry. We show that we can spatially resolve and quantify intracellular O 2 concentration in single muscle cells and that the spatiotemporal O 2 gradient measured by the sensor is linked to, and reflects, functional metabolic changes occurring during the process of muscle differentiation. Highlights Real time quantitation of intracellular oxygen with spatial resolutionIdentification of metabolically active sites in single cellsOxygen metabolism is linked to muscle differentiation.
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5
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Montecinos F, Sackett DL. Structural Changes, Biological Consequences, and Repurposing of Colchicine Site Ligands. Biomolecules 2023; 13:biom13050834. [PMID: 37238704 DOI: 10.3390/biom13050834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/06/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Microtubule-targeting agents (MTAs) bind to one of several distinct sites in the tubulin dimer, the subunit of microtubules. The binding affinities of MTAs may vary by several orders of magnitude, even for MTAs that specifically bind to a particular site. The first drug binding site discovered in tubulin was the colchicine binding site (CBS), which has been known since the discovery of the tubulin protein. Although highly conserved throughout eukaryotic evolution, tubulins show diversity in their sequences between tubulin orthologs (inter-species sequence differences) and paralogs (intraspecies differences, such as tubulin isotypes). The CBS is promiscuous and binds to a broad range of structurally distinct molecules that can vary in size, shape, and affinity. This site remains a popular target for the development of new drugs to treat human diseases (including cancer) and parasitic infections in plants and animals. Despite the rich knowledge about the diversity of tubulin sequences and the structurally distinct molecules that bind to the CBS, a pattern has yet to be found to predict the affinity of new molecules that bind to the CBS. In this commentary, we briefly discuss the literature evidencing the coexistence of the varying binding affinities for drugs that bind to the CBS of tubulins from different species and within species. We also comment on the structural data that aim to explain the experimental differences observed in colchicine binding to the CBS of β-tubulin class VI (TUBB1) compared to other isotypes.
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Affiliation(s)
- Felipe Montecinos
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dan L Sackett
- Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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6
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Lindsay KA, Abdelhamid N, Kahawatte S, Dima RI, Sackett DL, Finegan TM, Ross JL. A Tale of 12 Tails: Katanin Severing Activity Affected by Carboxy-Terminal Tail Sequences. Biomolecules 2023; 13:biom13040620. [PMID: 37189368 DOI: 10.3390/biom13040620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/06/2023] [Accepted: 03/09/2023] [Indexed: 04/01/2023] Open
Abstract
In cells, microtubule location, length, and dynamics are regulated by a host of microtubule-associated proteins and enzymes that read where to bind and act based on the microtubule “tubulin code,” which is predominantly encoded in the tubulin carboxy-terminal tail (CTT). Katanin is a highly conserved AAA ATPase enzyme that binds to the tubulin CTTs to remove dimers and sever microtubules. We have previously demonstrated that short CTT peptides are able to inhibit katanin severing. Here, we examine the effects of CTT sequences on this inhibition activity. Specifically, we examine CTT sequences found in nature, alpha1A (TUBA1A), detyrosinated alpha1A, Δ2 alpha1A, beta5 (TUBB/TUBB5), beta2a (TUBB2A), beta3 (TUBB3), and beta4b (TUBB4b). We find that these natural CTTs have distinct abilities to inhibit, most noticeably beta3 CTT cannot inhibit katanin. Two non-native CTT tail constructs are also unable to inhibit, despite having 94% sequence identity with alpha1 or beta5 sequences. Surprisingly, we demonstrate that poly-E and poly-D peptides are capable of inhibiting katanin significantly. An analysis of the hydrophobicity of the CTT constructs indicates that more hydrophobic polypeptides are less inhibitory than more polar polypeptides. These experiments not only demonstrate inhibition, but also likely interaction and targeting of katanin to these various CTTs when they are part of a polymerized microtubule filament.
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7
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Penjweini R, Link KA, Qazi S, Sackett DL, Knutson JR. Fluorescence lifetime imaging insight into the effects of Taxol on cell metabolism. Biophys J 2023; 122:277a. [PMID: 36783370 DOI: 10.1016/j.bpj.2022.11.1578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Rozhin Penjweini
- Laboratory of Advanced Microscopy and Biophotonics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Katie A Link
- Laboratory of Advanced Microscopy and Biophotonics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shureed Qazi
- Laboratory of Advanced Microscopy and Biophotonics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dan L Sackett
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Jay R Knutson
- Laboratory of Advanced Microscopy and Biophotonics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
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Park S, Veluvolu V, Martin WS, Nguyen T, Park J, Sackett DL, Boccara C, Gandjbakhche A. Label-free, non-invasive, and repeatable cell viability bioassay using dynamic full-field optical coherence microscopy and supervised machine learning. Biomed Opt Express 2022; 13:3187-3194. [PMID: 35781969 PMCID: PMC9208588 DOI: 10.1364/boe.452471] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 03/09/2022] [Accepted: 04/05/2022] [Indexed: 06/15/2023]
Abstract
We present a novel method that can assay cellular viability in real-time using supervised machine learning and intracellular dynamic activity data that is acquired in a label-free, non-invasive, and non-destructive manner. Cell viability can be an indicator for cytology, treatment, and diagnosis of diseases. We applied four supervised machine learning models on the observed data and compared the results with a trypan blue assay. The cell death assay performance by the four supervised models had a balanced accuracy of 93.92 ± 0.86%. Unlike staining techniques, where criteria for determining viability of cells is unclear, cell viability assessment using machine learning could be clearly quantified.
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Affiliation(s)
- Soongho Park
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 49 Convent Dr., Bethesda, MD 20814, USA
| | - Vinay Veluvolu
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 49 Convent Dr., Bethesda, MD 20814, USA
| | - William S. Martin
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 49 Convent Dr., Bethesda, MD 20814, USA
| | - Thien Nguyen
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 49 Convent Dr., Bethesda, MD 20814, USA
| | - Jinho Park
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 49 Convent Dr., Bethesda, MD 20814, USA
| | - Dan L. Sackett
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 49 Convent Dr., Bethesda, MD 20814, USA
| | - Claude Boccara
- Institut Langevin, ESPCI Paris, CNRS, PSL University, 1 rue Jussieu, 75005 Paris, France
| | - Amir Gandjbakhche
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 49 Convent Dr., Bethesda, MD 20814, USA
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Montecinos F, Loew M, Chio TI, Bane SL, Sackett DL. Interaction of Colchicine-Site Ligands With the Blood Cell-Specific Isotype of β-Tubulin—Notable Affinity for Benzimidazoles. Front Cell Dev Biol 2022; 10:884287. [PMID: 35712668 PMCID: PMC9194530 DOI: 10.3389/fcell.2022.884287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
Tubulin, the main component of microtubules, is an α-β heterodimer that contains one of multiple isotypes of each monomer. Although the isotypes of each monomer are very similar, the beta tubulin isotype found in blood cells is significantly divergent in amino acid sequence compared to other beta tubulins. This isotype, beta class VI, coded by human gene TUBB1, is found in hematologic cells and is recognized as playing a role in platelet biogenesis and function. Tubulin from the erythrocytes of the chicken Gallus gallus contains almost exclusively βVI tubulin. This form of tubulin has been reported to differ from brain tubulin in binding of colchicine-site ligands, previously thought to be a ubiquitous characteristic of tubulin from higher eukaryotes. In this study, we sought to gain a better understanding of the structure-activity relationship of the colchicine site of this divergent isotype, using chicken erythrocyte tubulin (CeTb) as the model. We developed a fluorescence-based assay to detect binding of drugs to the colchicine site and used it to study the interaction of 53 colchicine-site ligands with CeTb. Among the ligands known to bind at this site, most colchicine derivatives had lower affinity for CeTb compared to brain tubulin. Remarkably, many of the benzimidazole class of ligands shows increased affinity for CeTb compared to brain tubulin. Because the colchicine site of human βVI tubulin is very similar to that of chicken βVI tubulin, these results may have relevance to the effect of anti-cancer agents on hematologic tissues in humans.
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Affiliation(s)
- Felipe Montecinos
- Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Maura Loew
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, NY, United States
| | - Tak I. Chio
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, NY, United States
| | - Susan L. Bane
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, NY, United States
- *Correspondence: Susan L. Bane, ; Dan L. Sackett,
| | - Dan L. Sackett
- Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
- *Correspondence: Susan L. Bane, ; Dan L. Sackett,
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10
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Basseville A, Violet PC, Safari M, Sourbier C, Linehan WM, Robey RW, Levine M, Sackett DL, Bates SE. A Histone Deacetylase Inhibitor Induces Acetyl-CoA Depletion Leading to Lethal Metabolic Stress in RAS-Pathway Activated Cells. Cancers (Basel) 2022; 14:2643. [PMID: 35681624 PMCID: PMC9179484 DOI: 10.3390/cancers14112643] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The mechanism of action of romidepsin and other histone deacetylase inhibitors is still not fully explained. Our goal was to gain a mechanistic understanding of the RAS-linked phenotype associated with romidepsin sensitivity. METHODS The NCI60 dataset was screened for molecular clues to romidepsin sensitivity. Histone acetylation, DNA damage, ROS production, metabolic state (real-time measurement and metabolomics), and gene expression alterations (transcriptomics) were determined in KRAS-WT versus KRAS-mutant cell groups. The search for biomarkers in response to HDACi was implemented by supervised machine learning analysis on a 608-cell transcriptomic dataset and validated in a clinical dataset. RESULTS Romidepsin treatment induced depletion in acetyl-CoA in all tested cell lines, which led to oxidative stress, metabolic stress, and increased death-particularly in KRAS-mutant cell lines. Romidepsin-induced stresses and death were rescued by acetyl-CoA replenishment. Two acetyl-CoA gene expression signatures associated with HDACi sensitivity were derived from machine learning analysis in the CCLE (Cancer Cell Line Encyclopedia) cell panel. Signatures were then validated in the training cohort for seven HDACi, and in an independent 13-patient cohort treated with belinostat. CONCLUSIONS Our study reveals the importance of acetyl-CoA metabolism in HDAC sensitivity, and it highlights acetyl-CoA generation pathways as potential targets to combine with HDACi.
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Affiliation(s)
- Agnes Basseville
- Developmental Therapeutics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA;
- Omics Data Science Unit, Institut de Cancérologie de l’Ouest, 49055 Angers, France
| | - Pierre-Christian Violet
- Molecular and Clinical Nutrition Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (P.-C.V.); (M.L.)
| | - Maryam Safari
- Division of Hematology/Oncology, Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA;
| | - Carole Sourbier
- Urology Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (C.S.); (W.M.L.)
- Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20903, USA
| | - W. Marston Linehan
- Urology Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (C.S.); (W.M.L.)
| | - Robert W. Robey
- Developmental Therapeutics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA;
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark Levine
- Molecular and Clinical Nutrition Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (P.-C.V.); (M.L.)
| | - Dan L. Sackett
- Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Susan E. Bates
- Developmental Therapeutics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA;
- Division of Hematology/Oncology, Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA;
- Hematology/Oncology Research Department, James J. Peters Department of Veterans Affairs Medical Center, New York, NY 10468, USA
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11
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Penjweini R, Roarke B, Alspaugh G, Link KA, Andreoni A, Mori MP, Hwang PM, Sackett DL, Knutson JR. Intracellular imaging of metmyoglobin and oxygen using new dual purpose probe EYFP-Myoglobin-mCherry. J Biophotonics 2022; 15:e202100166. [PMID: 34689421 PMCID: PMC8901566 DOI: 10.1002/jbio.202100166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 10/04/2021] [Accepted: 10/13/2021] [Indexed: 06/13/2023]
Abstract
The biological relevance of nitric oxide (NO) and reactive oxygen species (ROS) in signaling, metabolic regulation, and disease treatment has become abundantly clear. The dramatic change in NO/ROS processing that accompanies a changing oxygen landscape calls for new imaging tools that can provide cellular details about both [O2 ] and the production of reactive species. Myoglobin oxidation to the met state by NO/ROS is a known sensor with absorbance changes in the visible range. We previously employed Förster resonance energy transfer to read out the deoxygenation/oxygenation of myoglobin, creating the subcellular [O2 ] sensor Myoglobin-mCherry. We now add the fluorescent protein EYFP to this sensor to create a novel probe that senses both met formation, a proxy for ROS/NO exposure, and [O2 ]. Since both proteins are present in the construct, it can also relieve users from the need to measure fluorescence lifetime, making [O2 ] sensing available to a wider group of laboratories.
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Affiliation(s)
- Rozhin Penjweini
- Laboratory of Advanced Microscopy and Biophotonics, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892-1412
| | - Branden Roarke
- Laboratory of Advanced Microscopy and Biophotonics, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892-1412
| | - Greg Alspaugh
- Laboratory of Advanced Microscopy and Biophotonics, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892-1412
| | - Katie A. Link
- Laboratory of Advanced Microscopy and Biophotonics, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892-1412
| | - Alessio Andreoni
- Laboratory of Advanced Microscopy and Biophotonics, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892-1412
- Laboratory of Optical Neurophysiology, Department of Biochemistry and Molecular Medicine, University of California Davis, Tupper Hall, Davis, CA 95616
| | - Mateus P. Mori
- Laboratory of Cardiovascular and Cancer Genetics, NHLBI, NIH, Bethesda, MD 20892-1412
| | - Paul M. Hwang
- Laboratory of Cardiovascular and Cancer Genetics, NHLBI, NIH, Bethesda, MD 20892-1412
| | - Dan L. Sackett
- Cytoskeletal Dynamics Group, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda MD, 20892-0924
| | - Jay R. Knutson
- Laboratory of Advanced Microscopy and Biophotonics, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892-1412
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12
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Leigh White A, Sackett DL. Alpha tubulin posttranslational modification by taurine is very unevenly distributed in different tissues and different cells. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.2151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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13
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Penjweini R, Mori MP, Hwang PM, Sackett DL, Knutson JR. Fluorescence lifetime imaging of metMyoglobin formation due to nitric oxide stress. Proc SPIE Int Soc Opt Eng 2022; 11965:119650H. [PMID: 35463920 PMCID: PMC9022600 DOI: 10.1117/12.2608888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Myoglobin is a protein that is expressed quite unevenly among different cell types. Nevertheless, it has been widely acknowledged that the Fe3+ state of myoglobin, metmyoglobin (metMb) has a broad functional role in metabolism, oxidative/nitrative regulation and gene networks. Accordingly, real-time monitoring of oxygenated, deoxygenated and metMb proportions- or, more broadly, of the mechanisms by which metMb is formed, presents a promising line of research. We had previously introduced a Förster resonance energy transfer (FRET) method to read out the deoxygenation/oxygenation states of myoglobin, by creating the targetable oxygen (O2) sensor Myoglobin-mCherry. In this sensor, changes in myoglobin absorbance features that occur with lost O2 occupancy -or upon metMb production- control the FRET rate from the fluorescent protein to myoglobin. When O2 is bound, mCherry fluorescence is only slightly quenched, but if either O2 is released or met is produced, FRET will increase- and this rate competing with emission reduces both emission yield and lifetime. Nitric oxide (NO) is an important signal (but also a toxic molecule) that can oxidize myoglobin to metMb with absorbance increases in the red visible range. mCherry thus senses both met and deoxygenated myoglobin, which cannot be easily separated at hypoxia. In order to dissect this, we treat cells with NO and investigate how the Myoglobin-mCherry lifetime is affected by generating metMb. More discriminatory power is then achieved when the fluorescent protein EYFP is added to Myoglobin-mCherry, creating a sandwich probe whose lifetime can selectively respond to metMb while being indifferent to O2 occupancy.
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Affiliation(s)
- Rozhin Penjweini
- Laboratory of Advanced Microscopy and Biophotonics, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Building 10, Room 5D14, Bethesda, MD 20892-1412
| | - Mateus P Mori
- Laboratory of Cardiovascular and Cancer Genetics, NHLBI, NIH, Bethesda, MD 20892-1412
| | - Paul M Hwang
- Laboratory of Cardiovascular and Cancer Genetics, NHLBI, NIH, Bethesda, MD 20892-1412
| | - Dan L Sackett
- Cytoskeletal Dynamics Group, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Building 9, Room 1E129, Bethesda MD, 20892-0924
| | - Jay R Knutson
- Laboratory of Advanced Microscopy and Biophotonics, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Building 10, Room 5D14, Bethesda, MD 20892-1412
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14
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Park S, Nguyen T, Benoit E, Sackett DL, Garmendia-Cedillos M, Pursley R, Boccara C, Gandjbakhche A. Quantitative evaluation of the dynamic activity of HeLa cells in different viability states using dynamic full-field optical coherence microscopy. Biomed Opt Express 2021; 12:6431-6441. [PMID: 34745747 PMCID: PMC8548024 DOI: 10.1364/boe.436330] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/13/2021] [Accepted: 08/13/2021] [Indexed: 05/30/2023]
Abstract
Dynamic full-field optical coherence microscopy (DFFOCM) was used to characterize the intracellular dynamic activities and cytoskeleton of HeLa cells in different viability states. HeLa cell samples were continuously monitored for 24 hours and compared with histological examination to confirm the cell viability states. The averaged mean frequency and magnitude observed in healthy cells were 4.79±0.5 Hz and 2.44±1.06, respectively. In dead cells, the averaged mean frequency was shifted to 8.57±0.71 Hz, whereas the magnitude was significantly decreased to 0.53±0.25. This cell dynamic activity analysis using DFFOCM is expected to replace conventional time-consuming and biopsies-required histological or biochemical methods.
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Affiliation(s)
- Soongho Park
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 49 Convent Dr., Bethesda 20814, USA
| | - Thien Nguyen
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 49 Convent Dr., Bethesda 20814, USA
| | - Emilie Benoit
- LLTech SAS-Aquyre Biosciences, 58 Rue du Dessous des Berges, 75013 Paris, France
| | - Dan L. Sackett
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 49 Convent Dr., Bethesda 20814, USA
| | - Marcial Garmendia-Cedillos
- The Signal Processing and Instrumentation Section, Center for Information Technology, National Institutes of Health, 49 Convent Dr., Bethesda 20814, USA
| | - Randall Pursley
- The Signal Processing and Instrumentation Section, Center for Information Technology, National Institutes of Health, 49 Convent Dr., Bethesda 20814, USA
| | - Claude Boccara
- LLTech SAS-Aquyre Biosciences, 58 Rue du Dessous des Berges, 75013 Paris, France
- Institut Langevin, ESPCI Paris, CNRS, PSL University, 1 rue Jussieu, 75005 Paris, France
| | - Amir Gandjbakhche
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 49 Convent Dr., Bethesda 20814, USA
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15
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Eren E, Watts NR, Sackett DL, Wingfield PT. Conformational changes in tubulin upon binding cryptophycin-52 reveal its mechanism of action. J Biol Chem 2021; 297:101138. [PMID: 34461087 PMCID: PMC8456064 DOI: 10.1016/j.jbc.2021.101138] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 11/25/2022] Open
Abstract
Cryptophycin-52 (Cp-52) is potentially the most potent anticancer drug known, with IC50 values in the low picomolar range, but its binding site on tubulin and mechanism of action are unknown. Here, we have determined the binding site of Cp-52, and its parent compound, cryptophycin-1, on HeLa tubulin, to a resolution of 3.3 Å and 3.4 Å, respectively, by cryo-EM and characterized this binding further by molecular dynamics simulations. The binding site was determined to be located at the tubulin interdimer interface and partially overlap that of maytansine, another cytotoxic tubulin inhibitor. Binding induces curvature both within and between tubulin dimers that is incompatible with the microtubule lattice. Conformational changes occur in both α-tubulin and β-tubulin, particularly in helices H8 and H10, with distinct differences between α and β monomers and between Cp-52-bound and cryptophycin-1-bound tubulin. From these results, we have determined: (i) the mechanism of action of inhibition of both microtubule polymerization and depolymerization, (ii) how the affinity of Cp-52 for tubulin may be enhanced, and (iii) where linkers for targeted delivery can be optimally attached to this molecule.
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Affiliation(s)
- Elif Eren
- Protein Expression Laboratory, NIAMS, National Institutes of Health, Bethesda, Maryland, USA
| | - Norman R Watts
- Protein Expression Laboratory, NIAMS, National Institutes of Health, Bethesda, Maryland, USA
| | - Dan L Sackett
- Division of Basic and Translational Biophysics, NICHD, National Institutes of Health, Bethesda, Maryland, USA
| | - Paul T Wingfield
- Protein Expression Laboratory, NIAMS, National Institutes of Health, Bethesda, Maryland, USA.
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16
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Mukherjee K, Chio TI, Gu H, Sackett DL, Bane SL, Sever S. A Novel Fluorogenic Assay for the Detection of Nephrotoxin-Induced Oxidative Stress in Live Cells and Renal Tissue. ACS Sens 2021; 6:2523-2528. [PMID: 34214393 PMCID: PMC8314269 DOI: 10.1021/acssensors.1c00422] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Drug-induced kidney
injury frequently leads to aborted clinical
trials and drug withdrawals. Sufficiently sensitive sensors capable
of detecting mild signs of chemical insult in cell-based screening
assays are critical to identifying and eliminating potential toxins
in the preclinical stage. Oxidative stress is a common early manifestation
of chemical toxicity, and biomolecule carbonylation is an irreversible
repercussion of oxidative stress. Here, we present a novel fluorogenic
assay using a sensor, TFCH, that responds to biomolecule carbonylation
and efficiently detects modest forms of renal injury with much greater
sensitivity than standard assays for nephrotoxins. We demonstrate
that this sensor can be deployed in live kidney cells and in renal
tissue. Our robust assay may help inform preclinical decisions to
recall unsafe drug candidates. The application of this sensor in identifying
and analyzing diverse pathologies is envisioned.
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Affiliation(s)
- Kamalika Mukherjee
- Division of Nephrology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Tak Ian Chio
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
| | - Han Gu
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
| | - Dan L. Sackett
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Susan L. Bane
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
| | - Sanja Sever
- Division of Nephrology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, United States
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17
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Penjweini R, Roarke B, Andreoni A, Alspaugh GR, Link KA, Sackett DL, Knutson JR. Intracellular Imaging of Oxygen and Reactive Oxygen Species using Fluorescence Lifetime Imaging of EYFP-Myo-Mcherry. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.2246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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18
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Kowalczyk JT, Wan X, Hernandez ER, Luo R, Lyons GC, Wilson KM, Gallardo DC, Isanogle KA, Robinson CM, Mendoza A, Heske CM, Chen JQ, Luo X, Kelly AE, Difilippantinio S, Robey RW, Thomas CJ, Sackett DL, Morrison DK, Randazzo PA, Jenkins LMM, Yohe ME. Rigosertib Induces Mitotic Arrest and Apoptosis in RAS-Mutated Rhabdomyosarcoma and Neuroblastoma. Mol Cancer Ther 2020; 20:307-319. [PMID: 33158997 DOI: 10.1158/1535-7163.mct-20-0525] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 09/16/2020] [Accepted: 10/30/2020] [Indexed: 11/16/2022]
Abstract
Relapsed pediatric rhabdomyosarcomas (RMS) and neuroblastomas (NBs) have a poor prognosis despite multimodality therapy. In addition, the current standard of care for these cancers includes vinca alkaloids that have severe toxicity profiles, further underscoring the need for novel therapies for these malignancies. Here, we show that the small-molecule rigosertib inhibits the growth of RMS and NB cell lines by arresting cells in mitosis, which leads to cell death. Our data indicate that rigosertib, like the vinca alkaloids, exerts its effects mainly by interfering with mitotic spindle assembly. Although rigosertib has the ability to inhibit oncogenic RAS signaling, we provide evidence that rigosertib does not induce cell death through inhibition of the RAS pathway in RAS-mutated RMS and NB cells. However, the combination of rigosertib and the MEK inhibitor trametinib, which has efficacy in RAS-mutated tumors, synergistically inhibits the growth of an RMS cell line, suggesting a new avenue for combination therapy. Importantly, rigosertib treatment delays tumor growth and prolongs survival in a xenograft model of RMS. In conclusion, rigosertib, through its impact on the mitotic spindle, represents a potential therapeutic for RMS.
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Affiliation(s)
| | - Xiaolin Wan
- National Cancer Institute, Bethesda, Maryland
| | | | - Ruibai Luo
- National Cancer Institute, Bethesda, Maryland
| | | | - Kelli M Wilson
- National Center for Advancing Translational Sciences, Rockville, Maryland
| | | | - Kristine A Isanogle
- Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Christina M Robinson
- Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | | | | | | | | | | | - Simone Difilippantinio
- Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | | | - Craig J Thomas
- National Center for Advancing Translational Sciences, Rockville, Maryland
| | - Dan L Sackett
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland
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19
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Penjweini R, Roarke B, Alspaugh G, Gevorgyan A, Andreoni A, Pasut A, Sackett DL, Knutson JR. Single cell-based fluorescence lifetime imaging of intracellular oxygenation and metabolism. Redox Biol 2020; 34:101549. [PMID: 32403080 PMCID: PMC7217996 DOI: 10.1016/j.redox.2020.101549] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/15/2020] [Accepted: 04/20/2020] [Indexed: 12/02/2022] Open
Abstract
Oxidation-reduction chemistry is fundamental to the metabolism of all living organisms, and hence quantifying the principal redox players is important for a comprehensive understanding of cell metabolism in normal and pathological states. In mammalian cells, this is accomplished by measuring oxygen partial pressure (pO2) in parallel with free and enzyme-bound reduced nicotinamide adenine dinucleotide (phosphate) [H] (NAD(P)H) and flavin adenine dinucleotide (FAD, a proxy for NAD+). Previous optical methods for these measurements had accompanying problems of cytotoxicity, slow speed, population averaging, and inability to measure all redox parameters simultaneously. Herein we present a Förster resonance energy transfer (FRET)-based oxygen sensor, Myoglobin-mCherry, compatible with fluorescence lifetime imaging (FLIM)-based measurement of nicotinamide coenzyme state. This offers a contemporaneous reading of metabolic activity through real-time, non-invasive, cell-by-cell intracellular pO2 and coenzyme status monitoring in living cells. Additionally, this method reveals intracellular spatial heterogeneity and cell-to-cell variation in oxygenation and coenzyme states.
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Affiliation(s)
- Rozhin Penjweini
- Laboratory of Advanced Microscopy and Biophotonics, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Building 10, Room 5D14, Bethesda, MD, 20892-1412, USA
| | - Branden Roarke
- Laboratory of Advanced Microscopy and Biophotonics, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Building 10, Room 5D14, Bethesda, MD, 20892-1412, USA
| | - Greg Alspaugh
- Laboratory of Advanced Microscopy and Biophotonics, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Building 10, Room 5D14, Bethesda, MD, 20892-1412, USA
| | - Anahit Gevorgyan
- Laboratory of Advanced Microscopy and Biophotonics, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Building 10, Room 5D14, Bethesda, MD, 20892-1412, USA
| | - Alessio Andreoni
- Laboratory of Advanced Microscopy and Biophotonics, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Building 10, Room 5D14, Bethesda, MD, 20892-1412, USA; Laboratory of Optical Neurophysiology, Department of Biochemistry and Molecular Medicine, University of California Davis, Tupper Hall, Davis, CA, 95616, USA
| | - Alessandra Pasut
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Leuven Cancer Institute, KU Leuven, Leuven, 3000, Belgium
| | - Dan L Sackett
- Cytoskeletal Dynamics Group, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Building 9, Room 1E129, Bethesda, MD, 20892-0924, USA
| | - Jay R Knutson
- Laboratory of Advanced Microscopy and Biophotonics, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Building 10, Room 5D14, Bethesda, MD, 20892-1412, USA.
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20
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Abstract
Taurine is the most abundant free amino acid in the human body. It is found in relatively high concentrations (1-10 mM) in many animal tissues but not in plants. It has been studied since the early 1800s but has not been found to be covalently incorporated into proteins in any animal tissue. Taurine has been found in only one macromolecular complex as a post-transcriptional modification to mitochondrial tRNA. Tubulin is the subunit of microtubules found in all eukaryotic species and almost all eukaryotic cells and subject to numerous post-translational modifications (PTMs). An important PTM on α-tubulin is the removal and re-ligation of the final carboxyl residue, tyrosine. We here demonstrate that taurine can be covalently incorporated at the C-terminal end of alpha-tubulin in avian erythrocytes in a reaction that requires the de-tyrosination PTM and prevents the re-tyrosination PTM. Further, this is, to our knowledge, the first instance of taurine incorporation into a large protein.
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Affiliation(s)
- Matthew T Olson
- Biomedical Mass Spectrometry Facility, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892-0001, United States
| | - Alfred L Yergey
- Biomedical Mass Spectrometry Facility, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892-0001, United States
| | - Kamalika Mukherjee
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
| | - Melissa R Pergande
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Susan L Bane
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
| | - Stephanie M Cologna
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Dan L Sackett
- Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development National Institutes of Health, Bethesda, Maryland 20892, United States
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21
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Braun R, Anthuber L, Hirsch D, Wangsa D, Lack J, McNeil NE, Heselmeyer-Haddad K, Torres I, Wangsa D, Brown MA, Tubbs A, Auslander N, Gertz EM, Brauer PR, Cam MC, Sackett DL, Habermann JK, Nussenzweig A, Ruppin E, Zhang Z, Rosenberg DW, Ried T. Single-Cell-Derived Primary Rectal Carcinoma Cell Lines Reflect Intratumor Heterogeneity Associated with Treatment Response. Clin Cancer Res 2020; 26:3468-3480. [PMID: 32253233 DOI: 10.1158/1078-0432.ccr-19-1984] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 01/22/2020] [Accepted: 04/01/2020] [Indexed: 12/24/2022]
Abstract
PURPOSE The standard treatment of patients with locally advanced rectal cancer consists of preoperative chemoradiotherapy (CRT) followed by surgery. However, the response of individual tumors to CRT is extremely diverse, presenting a clinical dilemma. This broad variability in treatment response is likely attributable to intratumor heterogeneity (ITH). EXPERIMENTAL DESIGN We addressed the impact of ITH on response to CRT by establishing single-cell-derived cell lines (SCDCL) from a treatment-naïve rectal cancer biopsy after xenografting. RESULTS Individual SCDCLs derived from the same tumor responded profoundly different to CRT in vitro. Clonal reconstruction of the tumor and derived cell lines based on whole-exome sequencing revealed nine separate clusters with distinct proportions in the SCDCLs. Missense mutations in SV2A and ZWINT were clonal in the resistant SCDCL, but not detected in the sensitive SCDCL. Single-cell genetic analysis by multiplex FISH revealed the expansion of a clone with a loss of PIK3CA in the resistant SCDCL. Gene expression profiling by tRNA-sequencing identified the activation of the Wnt, Akt, and Hedgehog signaling pathways in the resistant SCDCLs. Wnt pathway activation in the resistant SCDCLs was confirmed using a reporter assay. CONCLUSIONS Our model system of patient-derived SCDCLs provides evidence for the critical role of ITH for treatment response in patients with rectal cancer and shows that distinct genetic aberration profiles are associated with treatment response. We identified specific pathways as the molecular basis of treatment response of individual clones, which could be targeted in resistant subclones of a heterogenous tumor.
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Affiliation(s)
- Rüdiger Braun
- Section of Cancer Genomics, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Lena Anthuber
- Section of Cancer Genomics, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Daniela Hirsch
- Section of Cancer Genomics, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Darawalee Wangsa
- Section of Cancer Genomics, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Justin Lack
- NIAID Collaborative Bioinformatics Resource (NCBR), National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland.,Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Nicole E McNeil
- Section of Cancer Genomics, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | | | - Irianna Torres
- Section of Cancer Genomics, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Danny Wangsa
- Section of Cancer Genomics, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Markus A Brown
- Section of Cancer Genomics, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Anthony Tubbs
- Laboratory of Genome Integrity, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Noam Auslander
- Cancer Data Science Laboratory, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - E Michael Gertz
- Cancer Data Science Laboratory, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Philip R Brauer
- Section of Cancer Genomics, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Margaret C Cam
- Office of Science and Technology Resources, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Dan L Sackett
- Eunice Kennedy Shriver National Institute of Child Health & Human Development, NIH, Bethesda, Maryland
| | - Jens K Habermann
- Section of Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, Campus Lübeck, Germany
| | - Andre Nussenzweig
- Laboratory of Genome Integrity, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Zhongqiu Zhang
- Department of Surgery, Waterbury Hospital, University of Connecticut School of Medicine, Waterbury, Connecticut
| | - Daniel W Rosenberg
- Center for Molecular Oncology, University of Connecticut Health, Farmington, Waterbury, Connecticut
| | - Thomas Ried
- Section of Cancer Genomics, Center for Cancer Research, NCI, NIH, Bethesda, Maryland.
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22
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Montecinos-Franjola FA, Chaturvedi SK, Schuck P, Sackett DL. All Tubulins are not Alike: Heterodimer Dissociation Differs Among Different Biological Sources: Comparison with Dimer Association. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.3230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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23
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Montecinos-Franjola F, Chaturvedi SK, Schuck P, Sackett DL. All tubulins are not alike: Heterodimer dissociation differs among different biological sources. J Biol Chem 2019; 294:10315-10324. [PMID: 31110044 DOI: 10.1074/jbc.ra119.007973] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 05/10/2019] [Indexed: 12/27/2022] Open
Abstract
Tubulin, the subunit of microtubules, is a noncovalent heterodimer composed of one α- and one β-tubulin monomer. Both tubulins are encoded by multiple genes or composed of different isotypes, which are differentially expressed in different tissues and in development. Tubulin αβ dimers are found throughout the eukaryotes and, although very similar, are known to differ among organisms. We seek to investigate tubulins from different tissues and different organisms for a basic physical characteristic: heterodimer stability and monomer exchange between heterodimers. We previously showed that mammalian brain tubulin heterodimers reversibly dissociate, following the mass action law. Dissociation yields native monomers that can exchange with added tubulin to form new heterodimers. Here, we compared the dissociation of tubulins from multiple sources, including mammalian (rat) brain, cultured human cells (HeLa cells), chicken brain, chicken erythrocytes, and the protozoan Leishmania We used fluorescence-detected analytical ultracentrifugation to measure tubulin dissociation over a >1000-fold range in concentration and found that tubulin heterodimers from different biological sources differ in Kd by as much as 150-fold under the same conditions. Furthermore, when fluorescent tracer tubulins from various sources were titrated with unlabeled tubulin from a single source (rat brain tubulin), heterologous dimerization occurred, exhibiting similar affinities, in some cases binding even more strongly than with autologous tubulin. These results provide additional insight into the regulation of heterodimer formation of tubulin from different biological sources, revealing that monomer exchange appears to contribute to the sorting of α- and β-tubulin monomers that associate following tubulin folding.
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Affiliation(s)
| | - Sumit K Chaturvedi
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, NIBIB, National Institutes of Health, Bethesda, Maryland 20892
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, NIBIB, National Institutes of Health, Bethesda, Maryland 20892
| | - Dan L Sackett
- From the Division of Basic and Translational Biophysics, NICHD, and
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24
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Henry JL, Wilson MR, Mulligan MP, Quinn TR, Sackett DL, Taylor RE. Synthesis, conformational preferences, and biological activity of conformational analogues of the microtubule-stabilizing agents, (-)-zampanolide and (-)-dactylolide. Medchemcomm 2019; 10:800-805. [PMID: 31191870 PMCID: PMC6540953 DOI: 10.1039/c9md00164f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 04/08/2019] [Indexed: 01/07/2023]
Abstract
Zampanolide and dactylolide are microtubule-stabilizing polyketides possessing potent cytotoxicity towards a variety of cancer cell lines. Using our understanding of the conformational preferences of the macrolide core in both natural products, we hypothesized that analogues lacking the C17-methyl group would maintain the necessary conformation for bioactivity while reducing the number of synthetic manipulations necessary for their synthesis. Analogues 3, 4 and 5 were prepared via total synthesis, and their conformational preferences were determined through computational and high-field NMR studies. While no observable activities were present in dactylolide analogues 3 and 4, zampanolide analogue 5 exhibited sub-micromolar cytotoxicity. Herein, we describe these efforts towards understanding the structure- and conformation-activity relationships of dactylolide and zampanolide.
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Affiliation(s)
- Jeffrey L Henry
- The Warren Family Research Center for Drug Discovery and Development and the Department of Chemistry & Biochemistry , University of Notre Dame , Notre Dame , IN 46556-5670 , USA .
| | - Matthew R Wilson
- Vertex Pharmaceuticals , 50 Northern Ave , Boston , MA 02210 , USA
| | - Michael P Mulligan
- The Warren Family Research Center for Drug Discovery and Development and the Department of Chemistry & Biochemistry , University of Notre Dame , Notre Dame , IN 46556-5670 , USA .
| | - Taylor R Quinn
- The Warren Family Research Center for Drug Discovery and Development and the Department of Chemistry & Biochemistry , University of Notre Dame , Notre Dame , IN 46556-5670 , USA .
| | - Dan L Sackett
- Eunice Kennedy Shriver National Institute of Child Health and Human Development , National Institutes of Health , Bethesda , MD 20892 , USA
| | - Richard E Taylor
- The Warren Family Research Center for Drug Discovery and Development and the Department of Chemistry & Biochemistry , University of Notre Dame , Notre Dame , IN 46556-5670 , USA .
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25
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Combs CA, Sackett DL, Knutson JR. A simple empirical algorithm for optimising depletion power and resolution for dye and system specific STED imaging. J Microsc 2019; 274:168-176. [PMID: 31012103 DOI: 10.1111/jmi.12795] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 04/16/2019] [Accepted: 04/17/2019] [Indexed: 11/28/2022]
Abstract
Here we show an easy method for determining an effective dye saturation factor ('PSTED ') for STED (Stimulated Emission Depletion) microscopy. We define PSTED to be a combined microscope system plus dye factor (analogous to the traditional ground truth Is measurement, which is microscope independent) that is functionally defined as the power in the depletion beam that provides a resolution enhancement of 41% compared to confocal, according to the modified Abbe's formula for STED resolution enhancement. We show that the determination of PSTED provides insight not only into the suitability of a particular dye and the best imaging parameters to be used for an experiment, but also sets the critical value for correctly determining the point spread function (PSF) used in deconvolution of STED images. PSTED can be a function of many experimental variables, both microscope and sample related. Here we show the utility of doing PSTED determinations by (1) exploiting the simple relationship between width and a threshold-defined area provided by a Gaussian PSF, for either linear or spherical objects and (2) linearising the normally inverse hyperbolic function of resolution versus power that can determine PSTED . We show that this rearrangement allows us to determine PSTED using only a few measurements: either at a few relatively low depletion powers, on traditional bead size measurements or by finding the total area of a naturally occurring sub-limit sized biological feature (in this case, microtubules). We show the derivation of these equations and methods and the utility of its use by characterising several dyes and a local imaging parameter relevant to STED microscopy. This information is used to predict the enhancement of resolution of the point spread function necessary for post-processing deconvolution. LAY DESCRIPTION: Stimulated Emission Depletion (STED) microscopy is a fluorescence imaging superresolution technique that achieves tens of nanometres resolution. This is done by utilising a depletion laser to effectively quench (deplete) fluorescence in a donut shape overlapping the normally excited fluorescence spot. The size of the remaining (undepleted) central fluorescence spot is power dependent allowing 'tunable' resolution with the power of the STED depletion laser. This depletion power versus resolution relationship is dye and instrument dependent. We have developed a method for quickly measuring this relationship to optimise experiments based on individual dyes and microscope specific parameters. This allows for quickly optimising microscope settings and for correctly postprocessing images.
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Affiliation(s)
- Christian A Combs
- NHLBI Light Microscopy Facility, National Institutes of Health, Bethesda, Maryland, U.S.A
| | - Dan L Sackett
- NICHD Division of Basic and Translational Biophysics, National Institutes of Health, Bethesda, Maryland, U.S.A
| | - Jay R Knutson
- NHLBI Laboratory for Advanced Microscopy and Biophotonics, National Institutes of Health, Bethesda, Maryland, U.S.A
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26
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Andreoni A, Penjweini R, Roarke B, Strub MP, Sackett DL, Knutson JR. Genetically encoded FRET probes for direct mapping and quantification of intracellular oxygenation level via fluorescence lifetime imaging. Proc SPIE Int Soc Opt Eng 2019; 10882:108820O. [PMID: 35046616 PMCID: PMC8765217 DOI: 10.1117/12.2510646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Molecular oxygen is an important reporter of metabolic and physiological status at the cellular and tissue level and its concentration is used for the evaluation of many diseases (e.g.: cancer, coronary artery disease). The development of accurate and quantitative methods to measure O2 concentration ([O2]) in living cells, tissues and organisms is challenging and is subject of intense research. We developed a protein-based, fluorescent oxygen sensor that can be expressed directly in cells to monitor [O2] in the intracellular environment. We fused Myoglobin (Myo), a physiological oxygen carrier, with mCherry, a fluorescent protein, to build a fluorescence resonance energy transfer (FRET) pair, Myo-mCherry. The changes in the spectral properties of Myoglobin upon oxygen binding result in changes of the FRET-depleted emission intensity of mCherry, and this effect is detected by monitoring the fluorescence lifetime of the probe. We present here the preparation and characterization of a series of Myo-mCherry variants and mutants that show the versatility of our protein-based approach: the dynamic range of the sensor is tunable and adaptable to different [O2] ranges, as they occur in vitro in different cell lines, the probe is also easily targeted to subcellular compartments. The use of fluorescence overcomes the most common issues of data collection speed and spatial resolution encountered by currently available methods for O2-monitoring. By using Fluorescence Lifetime Imaging Microscopy (FLIM), we show that we can map the oxygenation level of cells in vitro, providing a quantitative assessment of [O2].
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Affiliation(s)
| | | | | | - Marie-Paule Strub
- Laboratory of Structural Biophysics, Biochemistry and Biophysics Center, National Heart Lung and Blood Institute (NIH)
| | - Dan L Sackett
- Cell Biophysics, National Institute of Child Health and Human Development (NIH)
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27
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McDonald AJ, Curt KM, Patel RP, Kozlowski H, Sackett DL, Robey RW, Gottesman MM, Bates SE. Targeting mitochondrial hexokinases increases efficacy of histone deacetylase inhibitors in solid tumor models. Exp Cell Res 2018; 375:106-112. [PMID: 30579954 DOI: 10.1016/j.yexcr.2018.12.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 12/12/2018] [Accepted: 12/15/2018] [Indexed: 02/06/2023]
Abstract
Hexokinase 1 and 2 have been shown to inhibit Bak- and Bax-mediated apoptosis, leading us to combine the histone deacetylase inhibitor romidepsin with clotrimazole or bifonazole, two compounds that reportedly decrease mitochondrial localization of hexokinases. Cancer cell lines derived from breast, kidney, lung, colon or ovarian cancers were treated with a short-term exposure to 25 ng/ml romidepsin combined with either clotrimazole or bifonazole. The combination of romidepsin with 25 µM clotrimazole or bifonazole resulted in increased annexin staining compared to cells treated with any of the drugs alone. Cell death was caspase-mediated, as the pan-caspase inhibitor Q-VD-OPh was found to inhibit apoptosis induced by the combination. A549 lung cancer cells or HCT-116 cells deficient in Bak and Bax were also resistant to apoptosis with the combination implicating the intrinsic apoptotic pathway. We found that a 24 h treatment with clotrimazole or bifonazole decreased total hexokinase 2 expression, resulting in a 76% or 60% decrease, respectively, of mitochondrial expression of hexokinase 2. Mitochondrial hexokinase 1 levels increased 2-fold or less. Our work suggests that the combination of a short-term romidepsin treatment with bifonazole or clotrimazole leads to increased apoptosis, most likely due to decreased mitochondrial expression of hexokinase 2.
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Affiliation(s)
- Andrew J McDonald
- Developmental Therapeutics Branch, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, United States
| | - Katherine M Curt
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, United States
| | - Ruchi P Patel
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, United States
| | - Hanna Kozlowski
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, United States
| | - Dan L Sackett
- Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, United States
| | - Robert W Robey
- Developmental Therapeutics Branch, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, United States; Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, United States
| | - Michael M Gottesman
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, United States
| | - Susan E Bates
- Developmental Therapeutics Branch, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, United States; Columbia University Medical Center, Division of Hematology/Oncology, New York, NY 10032, United States.
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28
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Suen LM, Tekle-Smith MA, Williamson KS, Infantine JR, Reznik SK, Tanis PS, Casselman TD, Sackett DL, Leighton JL. Design and 22-step synthesis of highly potent D-ring modified and linker-equipped analogs of spongistatin 1. Nat Commun 2018; 9:4710. [PMID: 30413713 PMCID: PMC6226463 DOI: 10.1038/s41467-018-07259-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 10/24/2018] [Indexed: 12/03/2022] Open
Abstract
Spongistatin 1 is among the most potent anti-proliferative agents ever discovered rendering it an attractive candidate for development as a payload for antibody-drug conjugates and other targeted delivery approaches. Unfortunately, it is unavailable from natural sources and its size and complex stereostructure render chemical synthesis highly time- and resource-intensive. As a result, the design and synthesis of more acid-stable and linker functional group-equipped analogs that retain the low picomolar potency of the parent natural product requires more efficient and step-economical synthetic access. Using uniquely enabling direct complex fragment coupling crotyl- and alkallylsilylation reactions, we report a 22-step synthesis of a rationally designed D-ring modified analog of spongistatin 1 that is characterized by GI50 values in the low picomolar range, and a proof-of-concept result that the C(15) acetate may be replaced with linker functional group-bearing esters with only minimal reductions in potency.
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Affiliation(s)
- Linda M Suen
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | | | | | | | - Samuel K Reznik
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Paul S Tanis
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Tyler D Casselman
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Dan L Sackett
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - James L Leighton
- Department of Chemistry, Columbia University, New York, NY, 10027, USA.
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29
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Penjweini R, Andreoni A, Rosales T, Kim J, Brenner MD, Sackett DL, Chung JH, Knutson JR. Intracellular oxygen mapping using a myoglobin-mCherry probe with fluorescence lifetime imaging. J Biomed Opt 2018; 23:1-14. [PMID: 30298706 PMCID: PMC6210794 DOI: 10.1117/1.jbo.23.10.107001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 09/04/2018] [Indexed: 05/05/2023]
Abstract
Oxygen (O2) is one of the most important biometabolites. In abundance, it serves as the limiting terminus of aerobic respiratory chains in the mitochondria of higher organisms; in deficit, it is a potent determinant of development and regulation of other physiological and therapeutic processes. Most knowledge on intracellular and interstitial concentration ([O2]) is derived from mitochondria isolated from cells or tissue biopsies, providing detailed but nonnative insight into respiratory chain function. The possible loss of essential metabolites during isolation and disruption of the normal interactions of the organelle with the cytoskeleton may cause these data to misrepresent intact cells. Several optical methodologies were also developed, but they are often unable to detect heterogeneity of metabolic characteristics among different individual cells in the same culture, and most cannot detect heterogeneous consumption within different areas of a single cell. Here, we propose a noninvasive and highly sensitive fluorescence lifetime microscopy probe, myoglobin-mCherry, appropriate to intracellular targeting. Using our probe, we monitor mitochondrial contributions to O2 consumption in A549 nonsmall cell lung cancer cells and we reveal heterogeneous [O2] within the intracellular environments. The mitochondrial [O2] at a single-cell level is also mapped by adding a peptide to target the probe to the mitochondria.
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Affiliation(s)
- Rozhin Penjweini
- National Heart, Lung, and Blood Institute, National Institutes of Health, Laboratory of Advanced Microscopy and Biophotonics, Bethesda, Maryland, United States
| | - Alessio Andreoni
- National Heart, Lung, and Blood Institute, National Institutes of Health, Laboratory of Advanced Microscopy and Biophotonics, Bethesda, Maryland, United States
| | - Tilman Rosales
- National Heart, Lung, and Blood Institute, National Institutes of Health, Laboratory of Advanced Microscopy and Biophotonics, Bethesda, Maryland, United States
| | - Jeonghan Kim
- National Heart, Lung, and Blood Institute, National Institutes of Health, Laboratory of Obesity and Aging Research, Bethesda, Maryland, United States
| | - Michael D. Brenner
- National Heart, Lung, and Blood Institute, National Institutes of Health, Laboratory of Advanced Microscopy and Biophotonics, Bethesda, Maryland, United States
| | - Dan L. Sackett
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Cytoskeletal Dynamics Group, Division of Basic and Translational Biophysics, Bethesda, Maryland, United States
| | - Jay H. Chung
- National Heart, Lung, and Blood Institute, National Institutes of Health, Laboratory of Obesity and Aging Research, Bethesda, Maryland, United States
| | - Jay R. Knutson
- National Heart, Lung, and Blood Institute, National Institutes of Health, Laboratory of Advanced Microscopy and Biophotonics, Bethesda, Maryland, United States
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30
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Ardeshirpour Y, Sackett DL, Knutson JR, Gandjbakhche AH. Using in vivo fluorescence lifetime imaging to detect HER2-positive tumors. EJNMMI Res 2018; 8:26. [PMID: 29619584 PMCID: PMC5884746 DOI: 10.1186/s13550-018-0384-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 03/26/2018] [Indexed: 12/03/2022] Open
Abstract
Background Assessment of the status of tumor biomarkers in individual patients would facilitate personalizing treatment strategy, and continuous monitoring of those biomarkers and their binding process to the therapeutic drugs would provide a means for early evaluation of the efficacy of therapeutic intervention. Fluorescent probes can accumulate inside the tumor region due to the leakiness of its vascularization and this can make it difficult to distinguish if the measured fluorescence intensity is from probes bound to target receptors or just accumulated unbound probes inside the tumor. In this paper, we have studied the fluorescence lifetime as a means to distinguish bound HER2 specific affibody probes to HER2 receptors. Our imaging system is a time-resolved fluorescence system using a Ti-Sapphire femtosecond pulse laser as source and Time correlated Single photon Counting (TCSPC) system as detector for calculating the lifetime of the contrast agent. HER2-specific Affibody (His6-ZHER2:GS-Cys) (Affibody, Stockholm, Sweden) conjugated with a Dylight750 fluorescent probe (Thermo-Fisher-Scientific, Waltham, Massachusetts) was used as contrast agent and six human cancer cell lines, BT-474, SKOV-3, NCI-N87, MDA-MB-361, MCF-7, and MDA-MB-468, known to express different levels of HER2/neu, are used in athymic mice xenografts. Results By comparing the lifetime of unbound contrast agent (at the contralateral site) to the fluorescence lifetime at the tumor site, our results show that the fluorescence lifetime decreases as HER2 specific Affibody probes bind to the tumor receptors. A decrease of ~15% (100ps) in tumor fluorescence lifetime was observed in tumors with mid to high HER2 expression. Smaller decreases were observed in tumors with low-level of HER2 receptors and no change was observed in the non-HER2-expressing tumors. Conclusions Using HER2-specific Affibody conjugated with the Dylight750 fluorescent probe as contrast agent, we demonstrated in live animals that change in fluorescence lifetime of the bound contrast agent can be used to assess the high to mid-level expression of HER2 expressing tumors in-vivo in only one measurement. The rationale is that the fluorescence lifetime of our specific probe is sensitive to affinity to, and specific interaction with, other molecules.
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Affiliation(s)
- Yasaman Ardeshirpour
- Section on Analytical and Functional Biophotonics, NICHD, NIH, Building 49, Room 5A82, Bethesda, MD, 20892, USA
| | - Dan L Sackett
- Division of Basic and Translational Biophysics, NICHD, NIH, Building 9, Room 1E129, Bethesda, MD, 20892, USA
| | - Jay R Knutson
- Laboratory of Advanced Microscopy and Biophotonics, NHLBI, Building 10, Room 5D14, Bethesda, MD, 20892, USA
| | - Amir H Gandjbakhche
- Section on Analytical and Functional Biophotonics, NICHD, NIH, Building 49, Room 5A82, Bethesda, MD, 20892, USA.
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31
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Abstract
Colchicine is a treatment for gout that has been used for more than a millennium. It is the treatment of choice for familial Mediterranean fever and its associated complication, amyloidosis. The 2009 U.S. Food and Drug Administration approval of colchicine as a new drug had research consequences. Recent investigations with large cohorts of patients with gout who have been taking colchicine for years have demonstrated novel applications within oncology, immunology, cardiology and dermatology. Some emerging dermatological uses include the treatment of epidermolysis bullosa acquisita, leucocytoclastic vasculitis, aphthous stomatitis and others. In this work we relate the history and the new horizon of this ancient medicine.
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Affiliation(s)
- B Dasgeb
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, PA, U.S.A
- Section of Analytical and Functional Biophotonics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, U.S.A
| | - D Kornreich
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, PA, U.S.A
| | - K McGuinn
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, PA, U.S.A
| | - L Okon
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, PA, U.S.A
| | - I Brownell
- Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, U.S.A
| | - D L Sackett
- Dermatology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, U.S.A
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32
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Montecinos-Franjola F, Chaturvedi S, Schuck P, Sackett DL. All Tubulins are Not Alike: Dimer Dissociation and Monomer Exchange Differ Depending on the Biological Source of Tubulin. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.2753] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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33
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Foley CN, Chen LA, Sackett DL, Leighton JL. Synthesis and Evaluation of a Linkable Functional Group-Equipped Analogue of the Epothilones. ACS Med Chem Lett 2017; 8:701-704. [PMID: 28740601 DOI: 10.1021/acsmedchemlett.7b00131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 05/01/2017] [Indexed: 11/28/2022] Open
Abstract
An approach to the validation of a linker strategy for the epothilone family of microtubule-stabilizing agents is reported. An analogue of epothilone B in which the C(6) methyl group has been replaced with a 4-azidobutyl group has been prepared by total chemical synthesis, and amides derived from the azido group have been shown to retain the activity of the parent compound. These results set the stage for an evaluation of the potential of the epothilones to serve as the drug component of antibody-drug conjugates and other selective tumor cell-targeting conjugates.
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Affiliation(s)
- Corinne N. Foley
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Liang-An Chen
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Dan L. Sackett
- Eunice Kennedy
Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - James L. Leighton
- Department of Chemistry, Columbia University, New York, New York 10027, United States
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34
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Woods LM, Arico JW, Frein JD, Sackett DL, Taylor RE. Synthesis and Biological Evaluation of 7-Deoxy-Epothilone Analogues. Int J Mol Sci 2017; 18:E648. [PMID: 28304361 PMCID: PMC5372660 DOI: 10.3390/ijms18030648] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/06/2017] [Accepted: 02/22/2017] [Indexed: 01/27/2023] Open
Abstract
The synthesis of two deoxygenated analogues of potent epothilones is reported in an effort to analyze the relative importance of molecular conformation and ligand-target interactions to biological activity. 7-deoxy-epothilone D and 7-deoxy-(S)-14-methoxy-epothilone D were prepared through total synthesis and shown to maintain the conformational preferences of their biologically active parent congeners through computer modeling and nuclear magnetic resonance (NMR) studies. The significant decrease in observed potency for each compound suggests that a hydrogen bond between the C7-hydroxyl group and the tubulin binding site plays a critical role in the energetics of binding in the epothilone class of polyketides.
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Affiliation(s)
- Laura M Woods
- Department of Chemistry and Biochemistry, the Harper Cancer Research Institute, and the Warren Family Research Center for Drug Discovery & Development, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Joseph W Arico
- Department of Chemistry and Biochemistry, the Harper Cancer Research Institute, and the Warren Family Research Center for Drug Discovery & Development, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Jeffrey D Frein
- Department of Chemistry and Biochemistry, the Harper Cancer Research Institute, and the Warren Family Research Center for Drug Discovery & Development, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Dan L Sackett
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Richard E Taylor
- Department of Chemistry and Biochemistry, the Harper Cancer Research Institute, and the Warren Family Research Center for Drug Discovery & Development, University of Notre Dame, Notre Dame, IN 46556, USA.
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35
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Hester AM, Valencia CC, Marianchuk TL, Sackett DL, Hawkins TL. Microtubule Mechanics in the Presence of Trimethylamine N-Oxide. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.3049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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36
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Kalenkiewicz A, Cruz P, Dolan M, Sackett DL. Targeting Microtubules in Leishmania using a Combined Computational & Experimental Approach. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.2678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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37
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Mukherjee K, Chio TI, Gu H, Banerjee A, Sorrentino AM, Sackett DL, Bane SL. Benzocoumarin Hydrazine: A Large Stokes Shift Fluorogenic Sensor for Detecting Carbonyls in Isolated Biomolecules and in Live Cells. ACS Sens 2017; 2:128-134. [PMID: 28722432 DOI: 10.1021/acssensors.6b00616] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Detection and quantification of biomolecule carbonylation, a critical manifestation of oxidative stress, allows better understanding of associated disease states. Existing approaches for such analyses require further processing of cells and tissues, which leads to loss of both spatial and temporal information about carbonylated biomolecules in cells. Live cell detection of these species requires sensors that are nontoxic, sufficiently reactive with the biocarbonyl in the intracellular milieu, and detectable with commonly available instrumentation. Presented here is a new fluorescent sensor for biomolecule carbonyl detection: a hydrazine derivative of a benzocoumarin, 7-hydrazinyl-4-methyl-2H-benzo[h]chromen-2-one (BzCH), which meets these requirements. This probe is especially well suited for live cell studies. It can be excited by a laser line common to many fluorescence microscopes. The emission maximum of BzCH undergoes a substantial red shift upon hydrazone formation (from ∼430 to ∼550 nm), which is the result of fluorophore disaggregation. Additionally, the hydrazone exhibits an exceptionally large Stokes shift (∼195 nm). The latter properties eliminate self-quenching of the probe and the need to remove unreacted fluorophore for reliable carbonyl detection. Thus, biomolecule carbonylation can be detected and quantified in cells and in cell extracts in a one-step procedure using this probe.
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Affiliation(s)
- Kamalika Mukherjee
- Department
of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
| | - Tak Ian Chio
- Department
of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
| | - Han Gu
- Department
of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
| | - Abhijit Banerjee
- Department
of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
| | - Anthony M. Sorrentino
- Department
of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
| | - Dan L. Sackett
- Eunice
Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Susan L. Bane
- Department
of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
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38
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Bailey ME, Sackett DL, Ross JL. Katanin Severing and Binding Microtubules Are Inhibited by Tubulin Carboxy Tails. Biophys J 2016; 109:2546-2561. [PMID: 26682813 DOI: 10.1016/j.bpj.2015.11.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 10/30/2015] [Accepted: 11/04/2015] [Indexed: 10/22/2022] Open
Abstract
Microtubule dynamics in cells are regulated by associated proteins that can be either stabilizers or destabilizers. A class of destabilizers that is important in a large number of cellular activities is the microtubule-severing enzymes, yet little is known about how they function. Katanin p60 was the first ATPase associated with microtubule severing. Here, we investigate the activity of katanin severing using a GFP-labeled human version. We quantify the effect of katanin concentration on katanin binding and severing activity. We find that free tubulin can inhibit severing activity by interfering with katanin binding to microtubules. The inhibition is mediated by the sequence of the tubulin and specifically depends on the carboxy-terminal tails. We directly investigate the inhibition effect of tubulin carboxy-terminal tails using peptide sequences of α-, β-, or detyrosinated α-tubulin tails that have been covalently linked to bovine serum albumin. Our results show that β-tubulin tails are the most effective at inhibiting severing, and that detyrosinated α-tubulin tails are the least effective. These results are distinct from those for other severing enzymes and suggest a scheme for regulation of katanin activity in cells dependent on free tubulin concentration and the modification state of the tubulin.
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Affiliation(s)
- Megan E Bailey
- Molecular and Cellular Biology Graduate Program, University of Massachusetts-Amherst, Amherst, Massachusetts; Department of Physics, University of Massachusetts-Amherst, Amherst, Massachusetts
| | - Dan L Sackett
- Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Jennifer L Ross
- Department of Physics, University of Massachusetts-Amherst, Amherst, Massachusetts.
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Montecinos-Franjola F, Schuck P, Sackett DL. Tubulin Dimer Reversible Dissociation: AFFINITY, KINETICS, AND DEMONSTRATION OF A STABLE MONOMER. J Biol Chem 2016; 291:9281-94. [PMID: 26934918 DOI: 10.1074/jbc.m115.699728] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Indexed: 11/06/2022] Open
Abstract
Tubulins are evolutionarily conserved proteins that reversibly polymerize and direct intracellular traffic. Of the tubulin family only αβ-tubulin forms stable dimers. We investigated the monomer-dimer equilibrium of rat brain αβ-tubulin using analytical ultracentrifugation and fluorescence anisotropy, observing tubulin in virtually fully monomeric and dimeric states. Monomeric tubulin was stable for a few hours and exchanged into preformed dimers, demonstrating reversibility of dimer dissociation. Global analysis combining sedimentation velocity and fluorescence anisotropy yielded Kd = 84 (54-123) nm Dimer dissociation kinetics were measured by analyzing the shape of the sedimentation boundary and by the relaxation of fluorescence anisotropy following rapid dilution of labeled tubulin, yielding koff in the range 10(-3)-10(-2) s(-1) Thus, tubulin dimers reversibly dissociate with moderately fast kinetics. Monomer-monomer association is much less sensitive than dimer-dimer association to solution changes (GTP/GDP, urea, and trimethylamine oxide).
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Affiliation(s)
| | - Peter Schuck
- the Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering (NHBLI), National Institutes of Health, Bethesda, Maryland 20892
| | - Dan L Sackett
- From the Program in Physical Biology, Eunice Kennedy Shriver NICHD and
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Sackett DL. Tubulin Tails are Intrinsically Disordered Polyanions that Regulate Binding to other Proteins by Sequence as Well as Charge. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.2167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Ho S, Sackett DL, Leighton JL. A "methyl extension" strategy for polyketide natural product linker site validation and its application to dictyostatin. J Am Chem Soc 2015; 137:14047-50. [PMID: 26522184 DOI: 10.1021/jacs.5b09869] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An approach to the validation of linker strategies for polyketide natural products with few or no obvious handles for linker attachment, and its application to dictyostatin, are described. Analogues in which the C(6)- and C(12)-methyl groups were replaced by 4-azidobutyl groups were prepared and shown to retain the low nanomolar potency of dictyostatin. Further, conjugation of the C(6) analogue with a cyclooctyne resulted in only minor attenuations in potency. Together, these results shed light on the binding of dictyostatin to β-tubulin, establish a validated linker strategy for dictyostatin, and set the stage for the synthesis and study of dictyostatin conjugates.
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Affiliation(s)
- Stephen Ho
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| | - Dan L Sackett
- Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - James L Leighton
- Department of Chemistry, Columbia University , New York, New York 10027, United States
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Sheldon KL, Gurnev PA, Bezrukov SM, Sackett DL. Tubulin tail sequences and post-translational modifications regulate closure of mitochondrial voltage-dependent anion channel (VDAC). J Biol Chem 2015; 290:26784-9. [PMID: 26306046 DOI: 10.1074/jbc.m115.678854] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Indexed: 11/06/2022] Open
Abstract
It was previously shown that tubulin dimer interaction with the mitochondrial outer membrane protein voltage-dependent anion channel (VDAC) blocks traffic through the channel and reduces oxidative metabolism and that this requires the unstructured anionic C-terminal tail peptides found on both α- and β-tubulin subunits. It was unclear whether the α- and β-tubulin tails contribute equally to VDAC blockade and what effects might be due to sequence variations in these tail peptides or to tubulin post-translational modifications, which mostly occur on the tails. The nature of the contribution of the tubulin body beyond acting as an anchor for the tails had not been clarified either. Here we present peptide-protein chimeras to address these questions. These constructs allow us to easily combine a tail peptide with different proteins or combine different tail peptides with a particular protein. The results show that a single tail grafted to an inert protein is sufficient to produce channel closure similar to that observed with tubulin. We show that the β-tail is more than an order of magnitude more potent than the α-tail and that the lower α-tail activity is largely due to the presence of a terminal tyrosine. Detyrosination activates the α-tail, and activation is reversed by the removal of the glutamic acid penultimate to the tyrosine. Nitration of tyrosine reverses the tyrosine inhibition of binding and even induces prolonged VDAC closures. Our results demonstrate that small changes in sequence or post-translational modification of the unstructured tails of tubulin result in substantial changes in VDAC closure.
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Affiliation(s)
- Kely L Sheldon
- From the Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - Philip A Gurnev
- From the Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - Sergey M Bezrukov
- From the Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - Dan L Sackett
- From the Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
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Sheldon KL, Sackett DL. Abstract 3044: The ability of tubulin to close mitochondrial VDAC pores depends on beta tubulin isotype. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-3044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Tubulin heterodimers can contain any of a number of beta-tubulin isotypes, and differential beta isotype expression has been found to have prognostic significance in human cancer and in chemotherapy response. We have shown that tubulin dimers can bind to and close the pore of the mitochondrial outer membrane protein VDAC (Voltage Dependent Anion Channel). VDAC acts as the “Gatekeeper” of metabolite flux into or out of the mitochondria, including all movement of ADP and ATP (and hence is a regulator of oxidative phosphorylation), and is also involved in early steps of apoptosis. We wished to test if all beta isotypes are equivalent in their ability to close VDAC, or if there are differences which may correlate to isotype expression in patient tumors. We previously showed that tubulin closure of VDAC blocks channel traffic and reduces oxidative metabolism, and that this requires the unstructured anionic tail peptides found on both the alpha- and beta-tubulin subunits. These intrinsically disordered tails contain only ∼3% of the mass but ∼40% of the net charge on the tubulin heterodimer. While all of the tails share some features, there are significant differences in length and sequence between alpha- and beta-tubulin tails, and between beta tubulin isotypes. Our earlier studies left unclear if the alpha- and beta-tails contribute equally to VDAC blockade, whether tails from different beta isotypes are all equivalent, and the role, if any, of tubulin posttranslational modifications (PTM), which mostly occur on the tails.
Here we use single molecule binding studies to show that channel closure is due to the tails alone, and not the tubulin body, since grafting the tails to albumin gives the same VDAC closure extent as tubulin. The method involves electrophysiological recording from single VDAC molecules inserted in lipid bilayers and exposed to controlled concentrations of tubulin or BSA-tail constructs. We show that the beta-I tail is ∼100-fold more potent than the alpha-tail, and that this difference is largely due to the presence or absence of a terminal tyrosine on alpha. The activation of the alpha-tail by detyrosination is reversed by subsequent removal of the next residue. We also show that BSA-tail constructs from different beta isotypes differ widely in their VDAC closure activity. In particular, beta-I tails are the most potent of those tested, while beta-III is at least 100-fold less active, although the sequence differences between the two isotypes are not great. Other beta isotypes show intermediate levels of closure activity.
Our results demonstrate that small changes in sequence or PTM of the disordered tails of tubulin result in substantial changes in VDAC binding and closure. Sequence differences between beta tubulin isotypes have major consequences on VDAC closure activity. In particular switching from the common epithelial beta-I to the beta-III isotype results in at least 100-fold reduction of VDAC closure.
Citation Format: Kely L. Sheldon, Dan L. Sackett. The ability of tubulin to close mitochondrial VDAC pores depends on beta tubulin isotype. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3044. doi:10.1158/1538-7445.AM2015-3044
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Basseville A, Sourbier C, Robey RW, Sackett DL, Linehan WM, Bates SE. Abstract 1771: Metabolic reprogramming in KRAS mutant cancer cells may cause sensitivity to the histone deacetylase (HDAC) inhibitor romidepsin. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-1771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Ras pathway mutations are very common in cancer, with the highest prevalence for RAS itself, found in about 30% of tumors. Despite multiple efforts, targeting the RAS pathway has not yet been amenable to therapeutic intervention. Taking a different approach, our laboratory has focused on combination treatment with romidepsin, an HDAC inhibitor approved by the FDA to treat T-cell lymphoma. Our group indeed demonstrated perturbation of RAS downstream pathways after romidepsin treatment, by analyzing gene expression in samples obtained from patients treated with romidepsin for T-cell lymphoma (Chakraborty et al, Blood 2013, 121: 4115).
The NCI-60 panel was screened with romidepsin plus or minus RAS pathway downstream inhibitors (MEK and/or Akt inhibitors). We found that mutations in RTK/RAS/BRAF correlated with romidepsin sensitivity (R = 0.472), with cell death ranging from 40% to 95% after 48h (assayed by annexin V labeling). Three KRAS mutant and three KRAS WT cell lines were then chosen to investigate the mechanism of this selectivity. Romidepsin induced histone acetylation and DNA damage from 30min treatment, and an increase in reactive oxygen species (ROS) after 10h exposure, independent of KRAS status. Only KRAS mutant cells showed mitochondrial membrane depolarization, cytochrome c release, and apoptosis, all starting about 24h after the beginning of treatment. Interestingly, cytoplasmic - but not mitochondrial - ROS scavengers rescued KRAS mutant cells from death, suggesting that ROS is required but not sufficient for romidepsin-induced apoptosis. Since Son et al (Nature 2013, 496: 101) reported that glutamine metabolism was reprogrammed by oncogenic KRAS to maintain redox balance, we explored this pathway using the Seahorse XF96 analyzer. We observed that, while all cell lines utilized glutamine for oxidative phosphorylation (OXPHOS) before drug exposure, romidepsin impaired the ability of only KRAS mutant cells to use glutamine for OXPHOS. Metabolomic analysis confirmed reduced glutamine use in KRAS mutant cells after drug treatment, as well as an inability to replenish their reduced glutathione stock. Moreover, this analysis also highlighted a romidepsin-induced drop in nucleotide synthesis in KRAS mutant cells, potentially leading to impaired DNA repair. Accordingly, adding back nucleosides to media blunted the effect of romidepsin on cell growth in KRAS mutant, but not in KRAS WT cells.
From these results, we conclude that romidepsin causes cell damage through DNA damage and subsequent ROS release. And while KRAS WT cells are able to scavenge ROS and repair DNA breaks, KRAS mutant cells cannot. We hypothesize that the reprogramming of glutamine metabolism, which supports redox maintenance and may support nucleoside synthesis, makes KRAS mutant cells particularly sensitive to romidepsin treatment.
Citation Format: Agnes Basseville, Carole Sourbier, Robert W. Robey, Dan L. Sackett, W. Marston Linehan, Susan E. Bates. Metabolic reprogramming in KRAS mutant cancer cells may cause sensitivity to the histone deacetylase (HDAC) inhibitor romidepsin. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1771. doi:10.1158/1538-7445.AM2015-1771
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Mukherjee K, Chio TI, Sackett DL, Bane SL. Detection of oxidative stress-induced carbonylation in live mammalian cells. Free Radic Biol Med 2015; 84:11-21. [PMID: 25801292 PMCID: PMC4457688 DOI: 10.1016/j.freeradbiomed.2015.03.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 03/11/2015] [Accepted: 03/12/2015] [Indexed: 12/11/2022]
Abstract
Oxidative stress is often associated with etiology and/or progression of disease conditions, such as cancer, neurodegenerative diseases, and diabetes. At the cellular level, oxidative stress induces carbonylation of biomolecules such as lipids, proteins, and DNA. The presence of carbonyl-containing biomolecules as a hallmark of these diseases provides a suitable target for diagnostic detection. Here, a simple, robust method for detecting cellular aldehydes and ketones in live cells using a fluorophore is presented. A hydrazine-functionalized synthetic fluorophore serves as an efficient nucleophile that rapidly reacts with reactive carbonyls in the cellular milieu. The product thus formed exhibits a wavelength shift in the emission maximum accompanied by an increase in emission intensity. The photochemical characteristics of the fluorophore enable the identification of the fluorophore-conjugated cellular biomolecules in the presence of unreacted dye, eliminating the need for removal of excess fluorophore. Moreover, this fluorophore is found to be nontoxic and is thus appropriate for live cell analysis. Utility of the probe is demonstrated in two cell lines, PC3 and A549. Carbonylation resulting from serum starvation and hydrogen peroxide-induced stress is detected in both cell lines using fluorescence microscopy and a fluorescence plate reader. The fluorescent signal originates from carbonylated proteins and lipids but not from oxidized DNA, and the majority of the fluorescence signal (>60%) is attributed to fluorophore-conjugated lipid oxidation products. This method should be useful for detecting cellular carbonylation in a high-content assay or high-throughput assay format.
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Affiliation(s)
- Kamalika Mukherjee
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, NY 13902, USA
| | - Tak Ian Chio
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, NY 13902, USA
| | - Dan L Sackett
- Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Susan L Bane
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, NY 13902, USA.
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Ismalaj T, Sackett DL. An inexpensive replacement for dry ice in the laboratory. Anal Biochem 2015; 474:38-9. [PMID: 25617823 DOI: 10.1016/j.ab.2015.01.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 01/12/2015] [Accepted: 01/13/2015] [Indexed: 11/16/2022]
Abstract
A reusable inexpensive replacement for dry ice in laboratory use is presented. Commercially available small pellets of stone or metal can be stored in a -80 °C freezer and used for quickly freezing small samples with a freezing rate that is actually somewhat faster than with dry ice itself. Following use, the material is returned to the freezer to re-chill until the next usage.
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Affiliation(s)
- Tony Ismalaj
- Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Dan L Sackett
- Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, MD 20892, USA.
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Rosales T, Sackett DL, Xu J, Shi ZD, Xu B, Li H, Kaur G, Frohart E, Shenoy N, Cheal SM, Wu H, Dulcey AE, Hu Y, Li C, Lane K, Griffiths GL, Knutson JR. STAQ: A route toward low power, multicolor nanoscopy. Microsc Res Tech 2015; 78:343-55. [PMID: 25762506 DOI: 10.1002/jemt.22478] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 02/01/2015] [Indexed: 11/11/2022]
Abstract
Nanoscopy has now become a real procedure in fluorescence microscopy of living cells. The STED/RESOLFT family of nanoscopy approaches has the best prospects for delivering high speed imaging, but the history of STED includes a continuing struggle to reduce the deactivation power applied, along with difficulties in achieving simultaneous multicolor images. In this manuscript, we present a concept for a similar real-time nanoscopy, using a new class of bipartite probes that separate the luminescent and quenching functions into two coupled molecules. In particular, the STAQ (Superresolution via Transiently Activated Quencher) example we show herein employs the excited state absorbance (not ground state) of the partner to accept energy from and quench the luminescent dye. The result is that much less deactivation power is needed for superresolved (∼50 nm) imaging. Moreover, the TAQ partner excited by the "donut" beam is shown to quench several different visible dyes via the same mechanism, opening the door to easier multicolor imaging. We demonstrate three dyes sharing the same deactivation and show examples of superresolved multicolor images. We suggest STAQ will facilitate the growth of real-time nanoscopy by reducing confounding photodamage within living cells while expanding the nanoscopist's palette.
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Affiliation(s)
- Tilman Rosales
- Optical Spectroscopy Section, Laboratory of Molecular Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Marylad, 20892-1412
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Dasgeb B, Smirnov AV, Ardeshirpour Y, Sackett DL, Knutson JR, Mehregan D, Gandjbakhche A, Halpern AC. Multiscale BerEp4 molecular imaging of microtumor phantoms: toward theranostics for basal cell carcinoma. Mol Imaging 2015; 13. [PMID: 25022347 DOI: 10.2310/7290.2014.00016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Basal cell carcinoma (BCC), the most common cancer in humans, appears macroscopically and microscopically similar to many other skin lesions, which makes differential diagnosis difficult. We are developing an approach for quantitative molecular imaging of BerEP4, a transmembrane biomarker for BCC, with the goal of increasing the precision and accuracy of diagnosis. This pilot study was conducted to assess the affinity and selectivity of BerEp4 antibody and assess its possible use in designing theranostic probes for BCC. We provide evidence that our photon-counting fluorescence macrodetection system can recover specific signal increases from a film/pellet phantom. Additionally, we show that a two-photon excited fluorescence /backscatter confocal microscopy system can image BerEP4 antibody/antigen complex on the surface of BerEP4-expressing cancer cells in three dimensions. Based on the initial results, BerEP4 seems to be a promising biomarker for molecular imaging of BCC. To prepare BerEP4 for eventual theranostic use, we examined the feasibility of a combined macro-/micro-optical approach to imaging BCC with various histologies. These optical methods, endowed with the ability to monitor treatment in real time, may open an opportunity for noninvasive diagnosis, treatments, and follow-up.
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Zustiak S, Nossal R, Sackett DL. Multiwell stiffness assay for the study of cell responsiveness to cytotoxic drugs. Biotechnol Bioeng 2014; 111:396-403. [PMID: 24018833 PMCID: PMC3933463 DOI: 10.1002/bit.25097] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 08/12/2013] [Accepted: 08/13/2013] [Indexed: 12/14/2022]
Abstract
It is now well understood that the cell microenvironment, including the surrounding matrix, profoundly affects cell fate. This is especially true for solid tumors where, for example, matrix stiffness is believed to be an important factor in tumorogenesis. Our hypothesis is that since matrix stiffness affects cell fate, it may also be important in drug resistance. To test this hypothesis, we designed and built a multiwell polyacrylamide (PA) gel-based stiffness assay, in which the gels were coated with collagen in order to facilitate cell attachment and proliferation. This PA-based assay was used to examine the effect of stiffness on cultured cell responsiveness to cytotoxic drugs. In particular, we tested multiple cancer cell lines and their susceptibility to paclitaxel, a microtubule-targeting agent. By assessing cell proliferation, morphology, and the IC50 of the drug, we were able to establish that the stiffness affects responsiveness to cytotoxic drugs in a cell-dependent manner.
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Affiliation(s)
- Silviya Zustiak
- Program on Physical Biology (PPB), Eunice Kennedy Shriver National Institute of Child Health & Human Development, National Institutes of Health, 9000 Rockville Pike, Bldg. 9, Bethesda, Maryland, 20892.
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50
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Montecinos-Franjola F, Sackett DL, Schuck P. Tubulin Heterodimers Reversibly Dissociate with Moderate Kinetics as Demonstrated using Sedimentation Velocity Analytical Ultracentrifugation. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.1995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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