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Williams NB, Batool S, Zumrut HE, Patel R, Sosa G, Jamal M, Mallikaratchy P. An In Vitro Selection Platform to Identify Multiple Aptamers against Multiple Cell-Surface Markers Using Ligand-Guided Selection. Biochemistry 2022; 61:1600-1613. [PMID: 35829681 PMCID: PMC10117398 DOI: 10.1021/acs.biochem.2c00105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aptamer ligand discovery against multiple molecules expressed on whole cells is an essential component in molecular tool development. However, owing to their intrinsic structural characteristics, cell-surface receptors have proven to be challenging targets in ligand discovery. Several variants to systematic evolution of ligands by exponential enrichment (SELEX) have been introduced to address the ″target problem″ for aptamer screening. To this end, we introduced a variant of SELEX, termed ligand-guided selection (LIGS), to identify highly specific aptamers against complex cell-surface markers in their native state. So far, the application of LIGS has been aimed at identifying aptamers against the most dominant receptors on the cell surface. Here, we report that LIGS can be expanded to identify two receptors on the same cell surface, paving the way to generate a multiplexed ligand discovery platform based on SELEX-targeting membrane receptors in their native functional state. Using CD19 and CD20 expressed on Toledo cells as a model system, multiple aptamer families were evolved against Toledo cells. We then utilized two monoclonal antibodies (mAbs) against CD20 and CD19 to selectively partition specific aptamers against CD19 and CD20. Following biochemical characterization, we introduce two specific aptamers against CD19 and two specific aptamers against CD20 with high affinity. Multi-target LIGS, as reported here, demonstrates a successful combinatorial approach for nucleic acid library screening to generate multiple artificial nucleic acid ligands against multiple receptors expressed on a single cell.
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Affiliation(s)
- Nicole B Williams
- Ph.D. Program in Molecular, Cellular and Developmental Biology, CUNY Graduate Center, The City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
| | - Sana Batool
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Blvd., West Bronx, New York, New York 10468, United States
| | - Hasan E Zumrut
- Ph.D. Programs in Chemistry and Biochemistry, CUNY Graduate Center, The City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
| | - Rutika Patel
- Ph.D. Programs in Chemistry and Biochemistry, CUNY Graduate Center, The City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
| | - German Sosa
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Blvd., West Bronx, New York, New York 10468, United States
| | - Mohammad Jamal
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Blvd., West Bronx, New York, New York 10468, United States
| | - Prabodhika Mallikaratchy
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Blvd., West Bronx, New York, New York 10468, United States
- Ph.D. Programs in Chemistry and Biochemistry, CUNY Graduate Center, The City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
- Ph.D. Program in Molecular, Cellular and Developmental Biology, CUNY Graduate Center, The City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
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Liu N, Huang Y, Zhang H, Wang T, Tao C, Zhang A, Chen B, Yin Y, Song M, Qu G, Liang Y, Shi J, He B, Hu L, Jiang G. Unified Probability Distribution and Dynamics of Lead Contents in Human Erythrocytes Revealed by Single-Cell Analysis. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:3819-3826. [PMID: 33660988 DOI: 10.1021/acs.est.0c05989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Understanding the presence and dynamics of chemical pollutants in individual cells is fundamentally important for their trafficking, fate, and toxicity in humans. The presence of molecular components (i.e., proteins and mRNA) in individual cells of higher organisms is considered a stochastic event. The characteristics of chemical pollutants, as extrinsic compounds, in subpopulation of human cells on single-cell basis have not been explored yet. Here, we demonstrated the lead (Pb) content in individual mature erythrocytes (m-erythrocytes) of Pb-intoxicated patients, and healthy subjects exhibited a unified pattern in probability distribution (gamma distribution) and dynamics, despite being highly heterogeneous. The Pb content in individual m-erythrocytes decreased with the lifetime of m-erythrocytes. Meanwhile, the distribution and dynamics were found to be highly related to the Pb content in m-erythrocytes and was independent of patients and their status. This is the first study to analyze the distribution pattern of chemical pollutants at a single-cell level in higher organisms. This study sheds light on the molecular mechanism of Pb trafficking and fate in humans and the search for an efficient strategy to improve Pb excretion during Pb treatment.
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Affiliation(s)
- Nian Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongshun Huang
- Department of Occupational Medicine, Guangdong Province Hospital for Occupational Disease Prevention and Treatment, Guangzhou, Guangdong 510300, China
| | - Huazhou Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ting Wang
- Huizhou City Occupational Disease Prevention and Control Hospital, Huizhou, Guangdong 516008, China
| | - Chen Tao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Aiqian Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baowei Chen
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yongguang Yin
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Maoyong Song
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guangbo Qu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong Liang
- Institute of Environment and Health, Jianghan University, Wuhan 430056, China
| | - Jianbo Shi
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bin He
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ligang Hu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Environment and Health, Jianghan University, Wuhan 430056, China
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310000, China
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Environment and Health, Jianghan University, Wuhan 430056, China
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310000, China
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Live-cell lipid biochemistry reveals a role of diacylglycerol side-chain composition for cellular lipid dynamics and protein affinities. Proc Natl Acad Sci U S A 2020; 117:7729-7738. [PMID: 32213584 PMCID: PMC7149225 DOI: 10.1073/pnas.1912684117] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Every cell produces thousands of lipid species, but studying the function of individual lipids in living cells is almost impossible with existing methodologies. Addressing this experimental bottleneck, we developed a strategy to quantify dissociation constants for lipid–protein interactions and transmembrane flip-flop rates of native lipids in live-cell experiments. Using a combination of plasma membrane-specific photochemical probes and mathematical modeling, we demonstrate that, for diacylglycerols as a model lipid class, the inherent lipid structural diversity caused by variations in acyl chain composition determines lipid protein affinities and transbilayer kinetics. In fact, subtle chemical differences change these values by orders of magnitude. Our approach represents a generally applicable method for elucidating the biological function of single lipid species on subcellular scales. Every cell produces thousands of distinct lipid species, but insight into how lipid chemical diversity contributes to biological signaling is lacking, particularly because of a scarcity of methods for quantitatively studying lipid function in living cells. Using the example of diacylglycerols, prominent second messengers, we here investigate whether lipid chemical diversity can provide a basis for cellular signal specification. We generated photo-caged lipid probes, which allow acute manipulation of distinct diacylglycerol species in the plasma membrane. Combining uncaging experiments with mathematical modeling, we were able to determine binding constants for diacylglycerol–protein interactions, and kinetic parameters for diacylglycerol transbilayer movement and turnover in quantitative live-cell experiments. Strikingly, we find that affinities and kinetics vary by orders of magnitude due to diacylglycerol side-chain composition. These differences are sufficient to explain differential recruitment of diacylglycerol binding proteins and, thus, differing downstream phosphorylation patterns. Our approach represents a generally applicable method for elucidating the biological function of single lipid species on subcellular scales in quantitative live-cell experiments.
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Saavedra E, González-Chávez Z, Moreno-Sánchez R, Michels PA. Drug Target Selection for Trypanosoma cruzi Metabolism by Metabolic Control Analysis and Kinetic Modeling. Curr Med Chem 2019; 26:6652-6671. [DOI: 10.2174/0929867325666180917104242] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 08/17/2018] [Accepted: 08/17/2018] [Indexed: 11/22/2022]
Abstract
In the search for therapeutic targets in the intermediary metabolism of trypanosomatids
the gene essentiality criterion as determined by using knock-out and knock-down genetic
strategies is commonly applied. As most of the evaluated enzymes/transporters have
turned out to be essential for parasite survival, additional criteria and approaches are clearly
required for suitable drug target prioritization. The fundamentals of Metabolic Control
Analysis (MCA; an approach in the study of control and regulation of metabolism) and kinetic
modeling of metabolic pathways (a bottom-up systems biology approach) allow quantification
of the degree of control that each enzyme exerts on the pathway flux (flux control coefficient)
and metabolic intermediate concentrations (concentration control coefficient). MCA
studies have demonstrated that metabolic pathways usually have two or three enzymes with
the highest control of flux; their inhibition has more negative effects on the pathway function
than inhibition of enzymes exerting low flux control. Therefore, the enzymes with the highest
pathway control are the most convenient targets for therapeutic intervention. In this review,
the fundamentals of MCA as well as experimental strategies to determine the flux control coefficients
and metabolic modeling are analyzed. MCA and kinetic modeling have been applied
to trypanothione metabolism in Trypanosoma cruzi and the model predictions subsequently
validated in vivo. The results showed that three out of ten enzyme reactions analyzed
in the T. cruzi anti-oxidant metabolism were the most controlling enzymes. Hence, MCA and
metabolic modeling allow a further step in target prioritization for drug development against
trypanosomatids and other parasites.
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Affiliation(s)
- Emma Saavedra
- Departamento de Bioquimica, Instituto Nacional de Cardiologia Ignacio Chavez. Mexico City, Mexico
| | - Zabdi González-Chávez
- Departamento de Bioquimica, Instituto Nacional de Cardiologia Ignacio Chavez. Mexico City, Mexico
| | - Rafael Moreno-Sánchez
- Departamento de Bioquimica, Instituto Nacional de Cardiologia Ignacio Chavez. Mexico City, Mexico
| | - Paul A.M. Michels
- Centre for Immunity, Infection and Evolution (CIIE) and Centre for Translational and Chemical Biology (CTCB), School of Biological Sciences, The University of Edinburgh, Edinburgh, Scotland
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Wagner N, Schuhmacher M, Lohmann A, Nadler A. A Coumarin Triflate Reagent Enables One-Step Synthesis of Photo-Caged Lipid Metabolites for Studying Cell Signaling. Chemistry 2019; 25:15483-15487. [PMID: 31461184 PMCID: PMC6916161 DOI: 10.1002/chem.201903909] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Indexed: 12/31/2022]
Abstract
Photorelease of caged compounds is among the most powerful experimental approaches for studying cellular functions on fast timescales. However, its full potential has yet to be exploited, as the number of caged small molecules available for cell biological studies has been limited by synthetic challenges. Addressing this problem, a straightforward, one-step procedure for efficiently synthesizing caged compounds was developed. An in situ generated benzylic coumarin triflate reagent was used to specifically functionalize carboxylate and phosphate moieties in the presence of free hydroxy groups, generating various caged lipid metabolites, including a number of GPCR ligands. By combining the photo-caged ligands with the respective receptors, an easily implementable experimental platform for the optical control and analysis of GPCR-mediated signal transduction in living cells was developed. Ultimately, the described synthetic strategy allows rapid generation of photo-caged small molecules and thus greatly facilitates the analysis of their biological roles in live cell microscopy assays.
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Affiliation(s)
- Nicolai Wagner
- Max Planck Institute of Molecular Cell Biology and GeneticsPfotenhauerstraße 10801307DresdenGermany
| | - Milena Schuhmacher
- Max Planck Institute of Molecular Cell Biology and GeneticsPfotenhauerstraße 10801307DresdenGermany
| | - Annett Lohmann
- Max Planck Institute of Molecular Cell Biology and GeneticsPfotenhauerstraße 10801307DresdenGermany
| | - André Nadler
- Max Planck Institute of Molecular Cell Biology and GeneticsPfotenhauerstraße 10801307DresdenGermany
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Kol M, Williams B, Toombs-Ruane H, Franquelim HG, Korneev S, Schroeer C, Schwille P, Trauner D, Holthuis JC, Frank JA. Optical manipulation of sphingolipid biosynthesis using photoswitchable ceramides. eLife 2019; 8:43230. [PMID: 30720434 PMCID: PMC6386522 DOI: 10.7554/elife.43230] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 02/02/2019] [Indexed: 12/31/2022] Open
Abstract
Ceramides are central intermediates of sphingolipid metabolism that also function as potent messengers in stress signaling and apoptosis. Progress in understanding how ceramides execute their biological roles is hampered by a lack of methods to manipulate their cellular levels and metabolic fate with appropriate spatiotemporal precision. Here, we report on clickable, azobenzene-containing ceramides, caCers, as photoswitchable metabolic substrates to exert optical control over sphingolipid production in cells. Combining atomic force microscopy on model bilayers with metabolic tracing studies in cells, we demonstrate that light-induced alterations in the lateral packing of caCers lead to marked differences in their metabolic conversion by sphingomyelin synthase and glucosylceramide synthase. These changes in metabolic rates are instant and reversible over several cycles of photoswitching. Our findings disclose new opportunities to probe the causal roles of ceramides and their metabolic derivatives in a wide array of sphingolipid-dependent cellular processes with the spatiotemporal precision of light.
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Affiliation(s)
- Matthijs Kol
- Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
| | - Ben Williams
- Department of Chemistry, Ludwig Maximilians University Munich, Munich, Germany
| | - Henry Toombs-Ruane
- Department of Chemistry, Ludwig Maximilians University Munich, Munich, Germany
| | - Henri G Franquelim
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sergei Korneev
- Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
| | - Christian Schroeer
- Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Dirk Trauner
- Department of Chemistry, New York University, New York, United States
| | - Joost Cm Holthuis
- Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
| | - James A Frank
- The Vollum Institute, Oregon Health and Science University, Portland, United States
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