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Xiang J, Katz L, Winokur PL, Chaudhary A, Digmann B, Bradford R, Rashid S, Ghosh S, Robertson A, Menetski J, Xu M, Gao P, Chen CZ, Lee T, Poelaert B, Eastman RT, Hall MD, Stapleton JT. Establishment of human post-vaccination SARS-CoV-2 standard reference sera. J Immunol Methods 2024; 530:113698. [PMID: 38823574 PMCID: PMC11215511 DOI: 10.1016/j.jim.2024.113698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/03/2024]
Abstract
There is a critical need to understand the effectiveness of serum elicited by different SARS-CoV-2 vaccines against SARS-CoV-2 variants. We describe the generation of reference reagents comprised of post-vaccination sera from recipients of different primary vaccines with or without different vaccine booster regimens in order to allow standardized characterization of SARS-CoV-2 neutralization in vitro. We prepared and pooled serum obtained from donors who received a either primary vaccine series alone, or a vaccination strategy that included primary and boosted immunization using available SARS-CoV-2 mRNA vaccines (BNT162b2, Pfizer and mRNA-1273, Moderna), replication-incompetent adenovirus type 26 vaccine (Ad26.COV2·S, Johnson and Johnson), or recombinant baculovirus-expressed spike protein in a nanoparticle vaccine plus Matrix-M adjuvant (NVX-CoV2373, Novavax). No subjects had a history of clinical SARS-CoV-2 infection, and sera were screened with confirmation that there were no nucleocapsid antibodies detected to suggest natural infection. Twice frozen sera were aliquoted, and serum antibodies were characterized for SARS-CoV-2 spike protein binding (estimated WHO antibody binding units/ml), spike protein competition for ACE-2 binding, and SARS-CoV-2 spike protein pseudotyped lentivirus transduction. These reagents are available for distribution to the research community (BEI Resources), and should allow the direct comparison of antibody neutralization results between different laboratories. Further, these sera are an important tool to evaluate the functional neutralization activity of vaccine-induced antibodies against emerging SARS-CoV-2 variants of concern. IMPORTANCE: The explosion of COVID-19 demonstrated how novel coronaviruses can rapidly spread and evolve following introduction into human hosts. The extent of vaccine- and infection-induced protection against infection and disease severity is reduced over time due to the fall in concentration, and due to emerging variants that have altered antibody binding regions on the viral envelope spike protein. Here, we pooled sera obtained from individuals who were immunized with different SARS-CoV-2 vaccines and who did not have clinical or serologic evidence of prior infection. The sera pools were characterized for direct spike protein binding, blockade of virus-receptor binding, and neutralization of spike protein pseudotyped lentiviruses. These sera pools were aliquoted and are available to allow inter-laboratory comparison of results and to provide a tool to determine the effectiveness of prior vaccines in recognizing and neutralizing emerging variants of concern.
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Affiliation(s)
- Jinhua Xiang
- Iowa City Veterans Administration Healthcare System, 601 Highway 6, Iowa City, IA 52246, USA; The University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, USA
| | - Louis Katz
- Impact Life Blood Services, 5500 Lakeview Parkway, Davenport, IA 52807, USA
| | | | - Ashok Chaudhary
- Iowa City Veterans Administration Healthcare System, 601 Highway 6, Iowa City, IA 52246, USA; The University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, USA
| | - Barbara Digmann
- Impact Life Blood Services, 5500 Lakeview Parkway, Davenport, IA 52807, USA
| | - Rebecca Bradford
- American Type Culture Collection (ATCC), 10801 University Boulevard, Manassas, VA 20110, USA; The Biodefense and Emerging Infections Research Resources Repository (BEI Resources), 10801 University Boulevard, Manassas, VA 20110, USA
| | - Sujatha Rashid
- American Type Culture Collection (ATCC), 10801 University Boulevard, Manassas, VA 20110, USA; The Biodefense and Emerging Infections Research Resources Repository (BEI Resources), 10801 University Boulevard, Manassas, VA 20110, USA
| | - Sudakshina Ghosh
- American Type Culture Collection (ATCC), 10801 University Boulevard, Manassas, VA 20110, USA; The Biodefense and Emerging Infections Research Resources Repository (BEI Resources), 10801 University Boulevard, Manassas, VA 20110, USA
| | - Angela Robertson
- American Type Culture Collection (ATCC), 10801 University Boulevard, Manassas, VA 20110, USA; The Biodefense and Emerging Infections Research Resources Repository (BEI Resources), 10801 University Boulevard, Manassas, VA 20110, USA
| | - Joseph Menetski
- Foundation for the National Institutes of Health, Bethesda, MD 20814, USA
| | - Miao Xu
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Peng Gao
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Catherine Z Chen
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Taylor Lee
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Brittany Poelaert
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Richard T Eastman
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Jack T Stapleton
- Iowa City Veterans Administration Healthcare System, 601 Highway 6, Iowa City, IA 52246, USA; The University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, USA.
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Kelm JM, Ferrer M, Bittner MI, Lal-Nag M. Data standards in drug discovery: A long way to go. Drug Discov Today 2024; 29:103879. [PMID: 38216119 DOI: 10.1016/j.drudis.2024.103879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/31/2023] [Accepted: 01/08/2024] [Indexed: 01/14/2024]
Abstract
Each year, millions to trillions of data points are generated to evaluate the response of chemicals and biologicals to human cells in vitro and in vivo using various technologies and endpoints. Despite the vast amount of data available, the development process has not become significantly more efficient in recent years. Given the increasing use of more complex physiological models, which are time-consuming and significantly more expensive, it is crucial to maximize the value of these valuable data through improved standardization.
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Affiliation(s)
- Jens M Kelm
- Precomb Therapeutics AG, Hombrechtikon, Switzerland.
| | - Marc Ferrer
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Rockville, MD, USA
| | - Martin-Immanuel Bittner
- Arctoris Ltd, Oxford, UK; Young Academy of the German National Academy of Sciences, Berlin, Germany
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3
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Karuppasamy M, English KG, Henry CA, Manzini MC, Parant JM, Wright MA, Ruparelia AA, Currie PD, Gupta VA, Dowling JJ, Maves L, Alexander MS. Standardization of zebrafish drug testing parameters for muscle diseases. Dis Model Mech 2024; 17:dmm050339. [PMID: 38235578 PMCID: PMC10820820 DOI: 10.1242/dmm.050339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 12/06/2023] [Indexed: 01/19/2024] Open
Abstract
Skeletal muscular diseases predominantly affect skeletal and cardiac muscle, resulting in muscle weakness, impaired respiratory function and decreased lifespan. These harmful outcomes lead to poor health-related quality of life and carry a high healthcare economic burden. The absence of promising treatments and new therapies for muscular disorders requires new methods for candidate drug identification and advancement in animal models. Consequently, the rapid screening of drug compounds in an animal model that mimics features of human muscle disease is warranted. Zebrafish are a versatile model in preclinical studies that support developmental biology and drug discovery programs for novel chemical entities and repurposing of established drugs. Due to several advantages, there is an increasing number of applications of the zebrafish model for high-throughput drug screening for human disorders and developmental studies. Consequently, standardization of key drug screening parameters, such as animal husbandry protocols, drug compound administration and outcome measures, is paramount for the continued advancement of the model and field. Here, we seek to summarize and explore critical drug treatment and drug screening parameters in the zebrafish-based modeling of human muscle diseases. Through improved standardization and harmonization of drug screening parameters and protocols, we aim to promote more effective drug discovery programs.
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Affiliation(s)
- Muthukumar Karuppasamy
- Division of Neurology, Department of Pediatrics, University of Alabama at Birmingham and Children's of Alabama, Birmingham, AL 35294, USA
| | - Katherine G. English
- Division of Neurology, Department of Pediatrics, University of Alabama at Birmingham and Children's of Alabama, Birmingham, AL 35294, USA
| | - Clarissa A. Henry
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME 04469, USA
- School of Biology and Ecology, University of Maine, Orono, ME 04469, USA
| | - M. Chiara Manzini
- Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Rutgers, Robert Wood Johnson Medical School, New Brunswick, NJ 08901, USA
| | - John M. Parant
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35294, USA
| | - Melissa A. Wright
- Department of Pediatrics, Section of Child Neurology, University of Colorado at Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Avnika A. Ruparelia
- Department of Anatomy and Physiology, School of Biomedical Sciences, Faculty of Medicine Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria 3010, Australia
- Centre for Muscle Research, Department of Anatomy and Physiology, University of Melbourne, Melbourne, Victoria 3010, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Peter D. Currie
- Centre for Muscle Research, Department of Anatomy and Physiology, University of Melbourne, Melbourne, Victoria 3010, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria 3800, Australia
- EMBL Australia, Victorian Node, Monash University, Clayton, Victoria 3800, Australia
| | - Vandana A. Gupta
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - James J. Dowling
- Division of Neurology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario M5G 1X8, Canada
- Program for Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 0A4, Canada
| | - Lisa Maves
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Matthew S. Alexander
- Division of Neurology, Department of Pediatrics, University of Alabama at Birmingham and Children's of Alabama, Birmingham, AL 35294, USA
- UAB Center for Exercise Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Civitan International Research Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- UAB Center for Neurodegeneration and Experimental Therapeutics (CNET), Birmingham, AL 35294, USA
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4
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Siramshetty VB, Xu X, Shah P. Artificial Intelligence in ADME Property Prediction. Methods Mol Biol 2024; 2714:307-327. [PMID: 37676606 DOI: 10.1007/978-1-0716-3441-7_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Absorption, distribution, metabolism, excretion (ADME) are key properties of a small molecule that govern pharmacokinetic profiles and impact its efficacy and safety. Computational methods such as machine learning and artificial intelligence have gained significant interest in both academic and industrial settings to predict pharmacokinetic properties of small molecules. These methods are applied in drug discovery to optimize chemical libraries, prioritize hits from biological screens, and optimize ADME properties of lead molecules. In the recent years, the drug discovery community witnessed the use of a range of neural network architectures such as deep neural networks, recurrent neural networks, graph neural networks, and transformer neural networks, which marked a paradigm shift in computer-aided drug design and development. This chapter discusses recent developments with an emphasis on their application to predict ADME properties.
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Affiliation(s)
- Vishal B Siramshetty
- National Center for Advancing Translational Sciences, Rockville, MD, USA
- Department of Safety Assessment, Genentech, Inc., South San Francisco, CA, USA
| | - Xin Xu
- National Center for Advancing Translational Sciences, Rockville, MD, USA
| | - Pranav Shah
- National Center for Advancing Translational Sciences, Rockville, MD, USA.
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5
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Duff AF, Chasser KM, McGovern KE, Trombetta M, Bielke LR. Adapted tissue assay for the assessment of ileal granulocyte degranulation following in ovo inoculation with select bacteria or coccidial challenge in chickens. PLoS One 2023; 18:e0286532. [PMID: 37498859 PMCID: PMC10374004 DOI: 10.1371/journal.pone.0286532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 05/17/2023] [Indexed: 07/29/2023] Open
Abstract
A previously described heterophil degranulation assay was adapted for use with ileal mucosal tissue via quantification of β-D-glucuronidase and assay end product 4-methylumbelliferone (4-MU). Three initial experiments evaluated the effect of in ovo inoculations of Citrobacter freundii (CF) or mixed lactic acid bacteria (LAB) on ileal granulocyte degranulation. Inoculations were administered on embryonic d18, body weights (BW) were recorded on day of hatch (DOH) and d10 to calculate body weight gain (BWG), and ileal mucosal scrapings were collected on DOH or d10 for the 4-MU assay. In all experiments, treatments were statistically analyzed relative to control groups. Treatments minimally affected BWG in all in ovo experiments (p > 0.05) relative to respective control groups. Similarly, ileal degranulation in in ovo treatments did not statistically differ (p > 0.05). Based on BWG, in ovo treatments may have induced low-level inflammation unable to elicit detectable changes via the 4-MU assay. Four subsequent experiments were conducted to evaluate effects of Eimeria maxima (EM) on ileal degranulation. Treatments included non-inoculated controls and low, medium, or high EM infection. Across all four experiments, final BW or BWG over the inoculation period were suppressed (p < 0.05) in EM groups relative to respective controls with the exception of EM-low (p = 0.094) and EM-medium (p = 0.096) in one trial. Ileal mucosal scrapings for the 4-MU assay were collected on day of peak lesions. Resulting values were reduced (p < 0.05) for EM treated birds in three experiments with the exception of EM-medium (p = 0.247). No differences were observed in one experiment (p = 0.351), which may have been attributed to a variation in strain of infecting Eimeria. Although refinement for low level inflammation is warranted, results indicate successful adaptation of the 4-MU assay for use with intestinal tissue during significant gastrointestinal inflammation.
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Affiliation(s)
- Audrey F Duff
- Department of Animal Sciences, The Ohio State University, Columbus, OH, United States of America
| | - Kaylin M Chasser
- Department of Animal Sciences, The Ohio State University, Columbus, OH, United States of America
| | - Kate E McGovern
- Department of Animal Sciences, The Ohio State University, Columbus, OH, United States of America
| | - Michael Trombetta
- Department of Animal Sciences, The Ohio State University, Columbus, OH, United States of America
| | - Lisa R Bielke
- Department of Animal Sciences, The Ohio State University, Columbus, OH, United States of America
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6
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Abdulkareem NM, Bhat R, Powell RT, Chikermane S, Yande S, Trinh L, Abdelnasser HY, Tabassum M, Ruiz A, Sobieski M, Nguyen ND, Park JH, Johnson CA, Kaipparettu BA, Bond RA, Johnson M, Stephan C, Trivedi MV. Screening of GPCR drugs for repurposing in breast cancer. Front Pharmacol 2022; 13:1049640. [PMID: 36561339 PMCID: PMC9763283 DOI: 10.3389/fphar.2022.1049640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022] Open
Abstract
Drug repurposing can overcome both substantial costs and the lengthy process of new drug discovery and development in cancer treatment. Some Food and Drug Administration (FDA)-approved drugs have been found to have the potential to be repurposed as anti-cancer drugs. However, the progress is slow due to only a handful of strategies employed to identify drugs with repurposing potential. In this study, we evaluated GPCR-targeting drugs by high throughput screening (HTS) for their repurposing potential in triple-negative breast cancer (TNBC) and drug-resistant human epidermal growth factor receptor-2-positive (HER2+) breast cancer (BC), due to the dire need to discover novel targets and drugs in these subtypes. We assessed the efficacy and potency of drugs/compounds targeting different GPCRs for the growth rate inhibition in the following models: two TNBC cell lines (MDA-MB-231 and MDA-MB-468) and two HER2+ BC cell lines (BT474 and SKBR3), sensitive or resistant to lapatinib + trastuzumab, an effective combination of HER2-targeting therapies. We identified six drugs/compounds as potential hits, of which 4 were FDA-approved drugs. We focused on β-adrenergic receptor-targeting nebivolol as a candidate, primarily because of the potential role of these receptors in BC and its excellent long-term safety profile. The effects of nebivolol were validated in an independent assay in all the cell line models. The effects of nebivolol were independent of its activation of β3 receptors and nitric oxide production. Nebivolol reduced invasion and migration potentials which also suggests its inhibitory role in metastasis. Analysis of the Surveillance, Epidemiology and End Results (SEER)-Medicare dataset found numerically but not statistically significant reduced risk of all-cause mortality in the nebivolol group. In-depth future analyses, including detailed in vivo studies and real-world data analysis with more patients, are needed to further investigate the potential of nebivolol as a repurposed therapy for BC.
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Affiliation(s)
- Noor Mazin Abdulkareem
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston College of Pharmacy, Houston, TX, United states
| | - Raksha Bhat
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, United states
| | - Reid T. Powell
- Institute of Bioscience and Technology, Texas A&M University, Houston, TX, United states
| | - Soumya Chikermane
- Department of Pharmaceutical Health Outcomes and Policy, University of Houston, Houston, TX, United states
| | - Soham Yande
- Department of Pharmaceutical Health Outcomes and Policy, University of Houston, Houston, TX, United states
| | - Lisa Trinh
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, United states
| | - Hala Y. Abdelnasser
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston College of Pharmacy, Houston, TX, United states
| | - Mantasha Tabassum
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston College of Pharmacy, Houston, TX, United states
| | - Alexis Ruiz
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, United states
| | - Mary Sobieski
- Institute of Bioscience and Technology, Texas A&M University, Houston, TX, United states
| | - Nghi D. Nguyen
- Institute of Bioscience and Technology, Texas A&M University, Houston, TX, United states
| | - Jun Hyoung Park
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United states
| | - Camille A. Johnson
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, United states
| | - Benny A. Kaipparettu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United states
| | - Richard A. Bond
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston College of Pharmacy, Houston, TX, United states
| | - Michael Johnson
- Department of Pharmaceutical Health Outcomes and Policy, University of Houston, Houston, TX, United states
| | - Clifford Stephan
- Institute of Bioscience and Technology, Texas A&M University, Houston, TX, United states
| | - Meghana V. Trivedi
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston College of Pharmacy, Houston, TX, United states,Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, United states,*Correspondence: Meghana V. Trivedi,
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7
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The NCATS Assay Guidance Manual programme: advancing the practice and rigour of preclinical translation. Nat Rev Drug Discov 2022; 21:863-864. [PMID: 36253455 DOI: 10.1038/d41573-022-00170-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Browne DJ, Kelly AM, Brady JL, Doolan DL. A high-throughput screening RT-qPCR assay for quantifying surrogate markers of immunity from PBMCs. Front Immunol 2022; 13:962220. [PMID: 36110843 PMCID: PMC9469018 DOI: 10.3389/fimmu.2022.962220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/03/2022] [Indexed: 11/13/2022] Open
Abstract
Immunoassays that quantitate cytokines and other surrogate markers of immunity from peripheral blood mononuclear cells (PBMCs), such as flow cytometry or Enzyme-Linked Immunosorbent Spot (ELIspot), allow highly sensitive measurements of immune effector function. However, those assays consume relatively high numbers of cells and expensive reagents, precluding comprehensive analyses and high-throughput screening (HTS). To address this issue, we developed a sensitive and specific reverse transcription-quantitative PCR (RT-qPCR)-based HTS assay, specifically designed to quantify surrogate markers of immunity from very low numbers of PBMCs. We systematically evaluated the volumes and concentrations of critical reagents within the RT-qPCR protocol, miniaturizing the assay and ultimately reducing the cost by almost 90% compared to current standard practice. We assessed the suitability of this cost-optimized RT-qPCR protocol as an HTS tool and determined the assay exceeds HTS uniformity and signal variance testing standards. Furthermore, we demonstrate this technique can effectively delineate a hierarchy of responses from as little as 50,000 PBMCs stimulated with CD4+ or CD8+ T cell peptide epitopes. Finally, we establish that this HTS-optimized protocol has single-cell analytical sensitivity and a diagnostic sensitivity equivalent to detecting 1:10,000 responding cells (i.e., 100 Spot Forming Cells/106 PBMCs by ELIspot) with over 90% accuracy. We anticipate this assay will have widespread applicability in preclinical and clinical studies, especially when samples are limited, and cost is an important consideration.
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9
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Sowa ST, Galera-Prat A, Wazir S, Alanen HI, Maksimainen MM, Lehtiö L. Preparation of screening assays for ADP-ribosyl readers and erasers using the GAP-tag as a binding probe. STAR Protoc 2022; 3:101147. [PMID: 35141567 PMCID: PMC8810561 DOI: 10.1016/j.xpro.2022.101147] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Here, we describe a protocol to set up a screening assay for ADP-ribosyl binding proteins including proteins that possess O-glycosidase or N-glycosidase activities. The FRET-based assay measures the interaction of any ADP-ribosyl binding protein fused to CFP with a cysteine-ADP-ribosylated GAP-tag fused to YFP. Recombinant PtxS1 and PARP2 are used to mono-ADP-ribosylate and poly-ADP-ribosylate the GAP-tag. The protocol does not require specialized compounds or substrates, making it accessible and easy to adapt in any laboratory or for other proteins of interest. For complete details on the use and execution of this profile, please refer to Sowa et al. (2021). Development of FRET-based assays for ADP-ribosyl binding proteins An ADP-ribosylated GAP-tag is used as non-hydrolyzable binding probe Instructions for protein production, signal validation and inhibitor screening
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10
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Dorjsuren D, Eastman RT, Song MJ, Yasgar A, Chen Y, Bharti K, Zakharov AV, Jadhav A, Ferrer M, Shi PY, Simeonov A. A platform of assays for the discovery of anti-Zika small-molecules with activity in a 3D-bioprinted outer-blood-retina model. PLoS One 2022; 17:e0261821. [PMID: 35041689 PMCID: PMC8765781 DOI: 10.1371/journal.pone.0261821] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 12/10/2021] [Indexed: 01/24/2023] Open
Abstract
The global health emergency posed by the outbreak of Zika virus (ZIKV), an arthropod-borne flavivirus causing severe neonatal neurological conditions, has subsided, but there continues to be transmission of ZIKV in endemic regions. As such, there is still a medical need for discovering and developing therapeutical interventions against ZIKV. To identify small-molecule compounds that inhibit ZIKV disease and transmission, we screened multiple small-molecule collections, mostly derived from natural products, for their ability to inhibit wild-type ZIKV. As a primary high-throughput screen, we used a viral cytopathic effect (CPE) inhibition assay conducted in Vero cells that was optimized and miniaturized to a 1536-well format. Suitably active compounds identified from the primary screen were tested in a panel of orthogonal assays using recombinant Zika viruses, including a ZIKV Renilla luciferase reporter assay and a ZIKV mCherry reporter system. Compounds that were active in the wild-type ZIKV inhibition and ZIKV reporter assays were further evaluated for their inhibitory effects against other flaviviruses. Lastly, we demonstrated that wild-type ZIKV is able to infect a 3D-bioprinted outer-blood-retina barrier tissue model and disrupt its barrier function, as measured by electrical resistance. One of the identified compounds (3-Acetyl-13-deoxyphomenone, NCGC00380955) was able to prevent the pathological effects of the viral infection on this clinically relevant ZIKV infection model.
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Affiliation(s)
- Dorjbal Dorjsuren
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Richard T. Eastman
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Min Jae Song
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Adam Yasgar
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Yuchi Chen
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Kapil Bharti
- Unit on Ocular and Stem Cell Translational Research, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Alexey V. Zakharov
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Ajit Jadhav
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Marc Ferrer
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Pei-Yong Shi
- University of Texas Medical Branch Galveston, Galveston, TX, United States of America
| | - Anton Simeonov
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
- * E-mail:
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11
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Fernández DI, Provenzale I, Cheung HY, van Groningen J, Tullemans BM, Veninga A, Dunster JL, Honarnejad S, van den Hurk H, Kuijpers MJ, Heemskerk JW. Ultra-high-throughput Ca 2+ assay in platelets to distinguish ITAM-linked and G-protein-coupled receptor activation. iScience 2022; 25:103718. [PMID: 35072010 PMCID: PMC8762394 DOI: 10.1016/j.isci.2021.103718] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 11/12/2021] [Accepted: 12/29/2021] [Indexed: 12/30/2022] Open
Abstract
Antiplatelet drugs targeting G-protein-coupled receptors (GPCRs), used for the secondary prevention of arterial thrombosis, coincide with an increased bleeding risk. Targeting ITAM-linked receptors, such as the collagen receptor glycoprotein VI (GPVI), is expected to provide a better antithrombotic-hemostatic profile. Here, we developed and characterized an ultra-high-throughput (UHT) method based on intracellular [Ca2+]i increases to differentiate GPVI and GPCR effects on platelets. In 96-, 384-, or 1,536-well formats, Calcium-6-loaded human platelets displayed a slow-prolonged or fast-transient [Ca2+]i increase when stimulated with the GPVI agonist collagen-related peptide or with thrombin and other GPCR agonists, respectively. Semi-automated curve fitting revealed five parameters describing the Ca2+ responses. Verification of the UHT assay was done with a robustness compound library and clinically relevant platelet inhibitors. Taken together, these results present proof of principle of distinct receptor-type-dependent Ca2+ signaling curves in platelets, which allow identification of new inhibitors in a UHT way.
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Affiliation(s)
- Delia I. Fernández
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229 ER Maastricht, The Netherlands
- Platelet Proteomics Group, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Isabella Provenzale
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229 ER Maastricht, The Netherlands
- Institute for Cardiovascular and Metabolic Research, University of Reading, RG6 6AX Reading, UK
| | - Hilaire Y.F. Cheung
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229 ER Maastricht, The Netherlands
- ISASLeibniz-Institut fur Analytische Wissenschaften-ISAS-e.V., 44227 Dortmund, Germany
- Institute of Cardiovascular Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | | | - Bibian M.E. Tullemans
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Alicia Veninga
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Joanne L. Dunster
- Institute for Cardiovascular and Metabolic Research, University of Reading, RG6 6AX Reading, UK
| | | | | | - Marijke J.E. Kuijpers
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229 ER Maastricht, The Netherlands
- Thrombosis Expertise Centre, Heart and Vascular Centre, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Johan W.M. Heemskerk
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229 ER Maastricht, The Netherlands
- Synapse Research Institute, Kon. Emmaplein 7, 6214 AC, Maastricht, the Netherlands
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12
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Markossian S, Coussens NP, Dahlin JL, Sittampalam GS. Assay Guidance Manual for Drug Discovery: Robust or Go Bust. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2021; 26:1241-1242. [PMID: 34813395 PMCID: PMC9590373 DOI: 10.1177/24725552211054044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Affiliation(s)
- Sarine Markossian
- National Center for Advancing Translational Sciences (NCATS), Rockville, MD, USA
| | - Nathan P. Coussens
- Molecular Pharmacology Laboratories, Applied and Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Jayme L. Dahlin
- National Center for Advancing Translational Sciences (NCATS), Rockville, MD, USA
| | - G. Sitta Sittampalam
- National Center for Advancing Translational Sciences (NCATS), Rockville, MD, USA
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13
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Synthesis, Biological Evaluation of ortho-Carboxamidostilbenes as Potential Inhibitors of Hyperglycemic Enzymes, and Molecular Docking Study. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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14
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Markossian S, Coussens NP, Dahlin JL, Sitta Sittampalam G. Assay Guidance Manual for Drug Discovery: Technologies That Matter. SLAS Technol 2021; 26:553-554. [PMID: 34813399 DOI: 10.1177/24726303211056338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Sarine Markossian
- National Center for Advancing Translational Sciences (NCATS), Rockville, MD, USA
| | - Nathan P Coussens
- Molecular Pharmacology Laboratories, Applied and Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Jayme L Dahlin
- National Center for Advancing Translational Sciences (NCATS), Rockville, MD, USA
| | - G Sitta Sittampalam
- National Center for Advancing Translational Sciences (NCATS), Rockville, MD, USA
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15
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Elder S, Klumpp-Thomas C, Yasgar A, Travers J, Frebert S, Wilson KM, Zakharov AV, Dahlin JL, Kreisbeck C, Sheberla D, Sittampalam GS, Godfrey AG, Simeonov A, Michael S. Cross-Platform Bayesian Optimization System for Autonomous Biological Assay Development. SLAS Technol 2021; 26:579-590. [PMID: 34813400 DOI: 10.1177/24726303211053782] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Current high-throughput screening assay optimization is often a manual and time-consuming process, even when utilizing design-of-experiment approaches. A cross-platform, Cloud-based Bayesian optimization-based algorithm was developed as part of the National Center for Advancing Translational Sciences (NCATS) ASPIRE (A Specialized Platform for Innovative Research Exploration) Initiative to accelerate preclinical drug discovery. A cell-free assay for papain enzymatic activity was used as proof of concept for biological assay development and system operationalization. Compared with a brute-force approach that sequentially tested all 294 assay conditions to find the global optimum, the Bayesian optimization algorithm could find suitable conditions for optimal assay performance by testing 21 assay conditions on average, with up to 20 conditions being tested simultaneously, as confirmed by repeated simulation. The algorithm could achieve a sevenfold reduction in costs for lab supplies and high-throughput experimentation runtime, all while being controlled from a remote site through a secure connection. Based on this proof of concept, this technology is expected to be applied to more complex biological assays and automated chemistry reaction screening at NCATS, and should be transferable to other institutions.
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Affiliation(s)
| | - Carleen Klumpp-Thomas
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Adam Yasgar
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Jameson Travers
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Shayne Frebert
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Kelli M Wilson
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Alexey V Zakharov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Jayme L Dahlin
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | | | | | - Gurusingham S Sittampalam
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Alexander G Godfrey
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Sam Michael
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
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16
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Machine Learning Applied to the Modeling of Pharmacological and ADMET Endpoints. Methods Mol Biol 2021. [PMID: 34731464 DOI: 10.1007/978-1-0716-1787-8_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
The well-known concept of quantitative structure-activity relationships (QSAR) has been gaining significant interest in the recent years. Data, descriptors, and algorithms are the main pillars to build useful models that support more efficient drug discovery processes with in silico methods. Significant advances in all three areas are the reason for the regained interest in these models. In this book chapter we review various machine learning (ML) approaches that make use of measured in vitro/in vivo data of many compounds. We put these in context with other digital drug discovery methods and present some application examples.
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17
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Henderson YC, Mohamed ASR, Maniakas A, Chen Y, Powell RT, Peng S, Cardenas M, Williams MD, Bell D, Zafereo ME, Wang RJ, Scherer SE, Wheeler DA, Cabanillas ME, Hofmann MC, Johnson FM, Stephan CC, Sandulache V, Lai SY. A High-throughput Approach to Identify Effective Systemic Agents for the Treatment of Anaplastic Thyroid Carcinoma. J Clin Endocrinol Metab 2021; 106:2962-2978. [PMID: 34120183 PMCID: PMC8475220 DOI: 10.1210/clinem/dgab424] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Indexed: 11/19/2022]
Abstract
BACKGROUND Despite the use of aggressive multimodality treatment, most anaplastic thyroid carcinoma (ATC) patients die within a year of diagnosis. Although the combination of BRAF and MEK inhibitors has recently been approved for use in BRAF-mutated ATC, they remain effective in a minority of patients who are likely to develop drug resistance. There remains a critical clinical need for effective systemic agents for ATC with a reasonable toxicity profile to allow for rapid translational development. MATERIAL AND METHODS Twelve human thyroid cancer cell lines with comprehensive genomic characterization were used in a high-throughput screening (HTS) of 257 compounds to select agents with maximal growth inhibition. Cell proliferation, colony formation, orthotopic thyroid models, and patient-derived xenograft (PDX) models were used to validate the selected agents. RESULTS Seventeen compounds were effective, and docetaxel, LBH-589, and pralatrexate were selected for additional in vitro and in vivo analysis as they have been previously approved by the US Food and Drug Administration for other cancers. Significant tumor growth inhibition (TGI) was detected in all tested models treated with LBH-589; pralatrexate demonstrated significant TGI in the orthotopic papillary thyroid carcinoma model and 2 PDX models; and docetaxel demonstrated significant TGI only in the context of mutant TP53. CONCLUSIONS HTS identified classes of systemic agents that demonstrate preferential effectiveness against aggressive thyroid cancers, particularly those with mutant TP53. Preclinical validation in both orthotopic and PDX models, which are accurate in vivo models mimicking tumor microenvironment, may support initiation of early-phase clinical trials in non-BRAF mutated or refractory to BRAF/MEK inhibition ATC.
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Affiliation(s)
- Ying C Henderson
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Abdallah S R Mohamed
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Anastasios Maniakas
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Université de Montréal, Hôpital Maisonneuve-Rosemont, Montreal, QB, Canada
| | - Yunyun Chen
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Reid T Powell
- IBT High Throughput Screening Core, Texas A&M Health Science Center, Houston, TX, USA
| | - Shaohua Peng
- Department of Thoracic, Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Maria Cardenas
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Michelle D Williams
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Diana Bell
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mark E Zafereo
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rui Jennifer Wang
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Steve E Scherer
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - David A Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Maria E Cabanillas
- Department of Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Marie-Claude Hofmann
- Department of Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Faye M Johnson
- MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, TX, USA
- Department of Thoracic, Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Clifford C Stephan
- IBT High Throughput Screening Core, Texas A&M Health Science Center, Houston, TX, USA
| | - Vlad Sandulache
- Department of Otolaryngology–Head and Neck Surgery, Baylor College of Medicine, Houston, TX, USA
| | - Stephen Y Lai
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Cellular and Molecular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Correspondence: Stephen Y. Lai, MD PhD FACS, Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Unit 1445, Houston, TX 77030, USA.
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18
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Austin CP. Opportunities and challenges in translational science. Clin Transl Sci 2021; 14:1629-1647. [PMID: 33982407 PMCID: PMC8504824 DOI: 10.1111/cts.13055] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/11/2021] [Accepted: 04/12/2021] [Indexed: 12/31/2022] Open
Abstract
The mission of translational science is to bring predictivity and efficiency to the development and dissemination of interventions that improve human health. Ten years ago this year, the National Center for Advancing Translational Sciences was founded to embody, conduct, and support this new discipline. The Center's first decade has brought substantial progress across a broad range of translational areas, from diagnostic and drug development to clinical trials to implementation science to education. The origins of the translational science and advances to this point are reviewed here and allow the establishment of an ambitious future research agenda for the field.
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Affiliation(s)
- Christopher P. Austin
- National Center for Advancing Translational SciencesNational Institutes of HealthBethesdaMarylandUSA
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19
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Coussens NP, Auld DS, Thielman JR, Wagner BK, Dahlin JL. Addressing Compound Reactivity and Aggregation Assay Interferences: Case Studies of Biochemical High-Throughput Screening Campaigns Benefiting from the National Institutes of Health Assay Guidance Manual Guidelines. SLAS DISCOVERY 2021; 26:1280-1290. [PMID: 34218710 DOI: 10.1177/24725552211026239] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Compound-dependent assay interferences represent a continued burden in drug and chemical probe discovery. The open-source National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS) Assay Guidance Manual (AGM) established an "Assay Artifacts and Interferences" section to address different sources of artifacts and interferences in biological assays. In addition to the frequent introduction of new chapters in this important topic area, older chapters are periodically updated by experts from academia, industry, and government to include new technologies and practices. Section chapters describe many best practices for mitigating and identifying compound-dependent assay interferences. Using two previously reported biochemical high-throughput screening campaigns for small-molecule inhibitors of the epigenetic targets Rtt109 and NSD2, the authors review best practices and direct readers to high-yield resources in the AGM and elsewhere for the mitigation and identification of compound-dependent reactivity and aggregation assay interferences.
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Affiliation(s)
- Nathan P Coussens
- Molecular Pharmacology Laboratories, Division of Cancer Treatment and Diagnosis Laboratory Support, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Douglas S Auld
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Jonathan R Thielman
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA
| | - Bridget K Wagner
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA
| | - Jayme L Dahlin
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
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20
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Petersen EJ, Reipa V, Xia M, Sharma M. Resources for Developing Reliable and Reproducible In Vitro Toxicological Test Methods. Chem Res Toxicol 2021; 34:1367-1369. [PMID: 33899460 PMCID: PMC9867873 DOI: 10.1021/acs.chemrestox.1c00093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A broad range of in vitro test methods have been developed given their numerous potential advantages over in vivo tests. We describe here key resources and tools to increase the reliability and reproducibility of in vitro toxicological test methods.
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Affiliation(s)
- Elijah J. Petersen
- Biosystems and Biomaterials Division, Material Measurement Laboratory, National Institute of Standards and Technology (NIST), 100 Bureau Drive, Gaithersburg, MD 20899,Corresponding author: Elijah Petersen, , Tel: +1 301 975 8142
| | - Vytautas Reipa
- Biosystems and Biomaterials Division, Material Measurement Laboratory, National Institute of Standards and Technology (NIST), 100 Bureau Drive, Gaithersburg, MD 20899
| | - Menghang Xia
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
| | - Monita Sharma
- PETA Science Consortium International e.V., Stuttgart, Germany
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21
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Stanford SM, Diaz MA, Ardecky RJ, Zou J, Roosild T, Holmes ZJ, Nguyen TP, Hedrick MP, Rodiles S, Guan A, Grotegut S, Santelli E, Chung TDY, Jackson MR, Bottini N, Pinkerton AB. Discovery of Orally Bioavailable Purine-Based Inhibitors of the Low-Molecular-Weight Protein Tyrosine Phosphatase. J Med Chem 2021; 64:5645-5653. [PMID: 33914534 DOI: 10.1021/acs.jmedchem.0c02126] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Obesity-associated insulin resistance plays a central role in the pathogenesis of type 2 diabetes. A promising approach to decrease insulin resistance in obesity is to inhibit the protein tyrosine phosphatases that negatively regulate insulin receptor signaling. The low-molecular-weight protein tyrosine phosphatase (LMPTP) acts as a critical promoter of insulin resistance in obesity by inhibiting phosphorylation of the liver insulin receptor activation motif. Here, we report development of a novel purine-based chemical series of LMPTP inhibitors. These compounds inhibit LMPTP with an uncompetitive mechanism and are highly selective for LMPTP over other protein tyrosine phosphatases. We also report the generation of a highly orally bioavailable purine-based analogue that reverses obesity-induced diabetes in mice.
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Affiliation(s)
- Stephanie M Stanford
- Department of Medicine, University of California, San Diego, La Jolla, California 92037, United States
| | - Michael A Diaz
- Department of Medicine, University of California, San Diego, La Jolla, California 92037, United States
| | - Robert J Ardecky
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Jiwen Zou
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Tarmo Roosild
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Zachary J Holmes
- Department of Medicine, University of California, San Diego, La Jolla, California 92037, United States
| | - Tiffany P Nguyen
- Department of Medicine, University of California, San Diego, La Jolla, California 92037, United States
| | - Michael P Hedrick
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Socorro Rodiles
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - April Guan
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Stefan Grotegut
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Eugenio Santelli
- Department of Medicine, University of California, San Diego, La Jolla, California 92037, United States
| | - Thomas D Y Chung
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Michael R Jackson
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Nunzio Bottini
- Department of Medicine, University of California, San Diego, La Jolla, California 92037, United States
| | - Anthony B Pinkerton
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
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22
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Haynes B, Brimacombe K, Hare C, Faupel-Badger J. The National Center for Advancing Translational Sciences' Intramural Training Program and Fellow Career Outcomes. CBE LIFE SCIENCES EDUCATION 2020; 19:ar51. [PMID: 33001768 PMCID: PMC8693946 DOI: 10.1187/cbe.20-03-0048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The National Center for Advancing Translational Sciences (NCATS) defines translational science as "the field of investigation focused on understanding the scientific and operational principles underlying each step of the translational process." A major goal of translational science is to determine commonalities across projects to identify principles for addressing persistent bottlenecks in this process. To meet this goal, translational scientists must be conversant in multiple disciplines, work in teams, and understand the larger translational science ecosystem. The development of these skills through translational science training opportunities, such as the translational science training offered by the NCATS intramural research program, prepares fellows for a variety of career options. The unique structure of the NCATS intramural program and the career outcomes of its alumni are described herein to demonstrate the distinct features of this training environment, the productivity of fellows during their time in training, and how this prepares fellows to be competitive for a variety of science careers. To date, the NCATS intramural research program has trained 213 people, ranging from high school to postdoctoral levels. These alumni have transitioned into a wide array of career functions, types, and sectors.
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Affiliation(s)
- Brittany Haynes
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, MD 20850
- *Address correspondence to: Brittany Haynes ()
| | - Kyle Brimacombe
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, MD 20850
| | - Christy Hare
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, MD 20850
| | - Jessica Faupel-Badger
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, MD 20850
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23
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Mohammadi E, Benfeitas R, Turkez H, Boren J, Nielsen J, Uhlen M, Mardinoglu A. Applications of Genome-Wide Screening and Systems Biology Approaches in Drug Repositioning. Cancers (Basel) 2020; 12:E2694. [PMID: 32967266 PMCID: PMC7563533 DOI: 10.3390/cancers12092694] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/14/2020] [Accepted: 09/16/2020] [Indexed: 12/24/2022] Open
Abstract
Modern drug discovery through de novo drug discovery entails high financial costs, low success rates, and lengthy trial periods. Drug repositioning presents a suitable approach for overcoming these issues by re-evaluating biological targets and modes of action of approved drugs. Coupling high-throughput technologies with genome-wide essentiality screens, network analysis, genome-scale metabolic modeling, and machine learning techniques enables the proposal of new drug-target signatures and uncovers unanticipated modes of action for available drugs. Here, we discuss the current issues associated with drug repositioning in light of curated high-throughput multi-omic databases, genome-wide screening technologies, and their application in systems biology/medicine approaches.
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Affiliation(s)
- Elyas Mohammadi
- Science for Life Laboratory, KTH–Royal Institute of Technology, SE-17121 Stockholm, Sweden; (E.M.); (M.U.)
- Department of Animal Science, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran
| | - Rui Benfeitas
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden;
| | - Hasan Turkez
- Department of Medical Biology, Faculty of Medicine, Atatürk University, 25240 Erzurum, Turkey;
| | - Jan Boren
- Department of Molecular and Clinical Medicine, University of Gothenburg, The Wallenberg Laboratory, Sahlgrenska University Hospital, SE-41345 Gothenburg, Sweden;
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden;
- BioInnovation Institute, DK-2200 Copenhagen N, Denmark
| | - Mathias Uhlen
- Science for Life Laboratory, KTH–Royal Institute of Technology, SE-17121 Stockholm, Sweden; (E.M.); (M.U.)
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH–Royal Institute of Technology, SE-17121 Stockholm, Sweden; (E.M.); (M.U.)
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London SE1 9RT, UK
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24
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Validation of in-vitro bioassay methods: Application in herbal drug research. PROFILES OF DRUG SUBSTANCES, EXCIPIENTS, AND RELATED METHODOLOGY 2020; 46:273-307. [PMID: 33461699 DOI: 10.1016/bs.podrm.2020.07.005] [Citation(s) in RCA: 166] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This present review described the validation method of in-vitro bioassay for its application in herbal drug research. Seven sequencing steps that can be taken for performing a valid bioassay include: literature survey, sample stability evaluation, Biosystem performance testing, Sample performance evaluation, determination of 50% effective concentration or cytotoxic concentrations, selective index evaluation, and determination of accurate relative potency of sample. Detailed methods and acceptance criteria for each step are described herein. Method calculations of the relative potency of sample using European Pharmacopeia 10.0, 5.3 (2020) were recommended instead of using United States Pharmacopeia 42 (2019). For having reliable data and conclusions, all methods (chemical and bioassay) need to be first validated before any data collection. Absence of any validation method may results in incorrect conclusions and bias.
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Wilson BAP, Thornburg CC, Henrich CJ, Grkovic T, O'Keefe BR. Creating and screening natural product libraries. Nat Prod Rep 2020; 37:893-918. [PMID: 32186299 PMCID: PMC8494140 DOI: 10.1039/c9np00068b] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: up to 2020The National Cancer Institute of the United States (NCI) has initiated a Cancer Moonshot program entitled the NCI Program for Natural Product Discovery. As part of this effort, the NCI is producing a library of 1 000 000 partially purified natural product fractions which are being plated into 384-well plates and provided to the research community free of charge. As the first 326 000 of these fractions have now been made available, this review seeks to describe the general methods used to collect organisms, extract those organisms, and create a prefractionated library. Importantly, this review also details both cell-based and cell-free bioassay methods and the adaptations necessary to those methods to productively screen natural product libraries. Finally, this review briefly describes post-screen dereplication and compound purification and scale up procedures which can efficiently identify active compounds and produce sufficient quantities of natural products for further pre-clinical development.
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Affiliation(s)
- Brice A P Wilson
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702-1201, USA.
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Zhao W, Wang Y, Liang FS. Chemical and Light Inducible Epigenome Editing. Int J Mol Sci 2020; 21:ijms21030998. [PMID: 32028669 PMCID: PMC7037166 DOI: 10.3390/ijms21030998] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 01/30/2020] [Accepted: 01/30/2020] [Indexed: 12/22/2022] Open
Abstract
The epigenome defines the unique gene expression patterns and resulting cellular behaviors in different cell types. Epigenome dysregulation has been directly linked to various human diseases. Epigenome editing enabling genome locus-specific targeting of epigenome modifiers to directly alter specific local epigenome modifications offers a revolutionary tool for mechanistic studies in epigenome regulation as well as the development of novel epigenome therapies. Inducible and reversible epigenome editing provides unique temporal control critical for understanding the dynamics and kinetics of epigenome regulation. This review summarizes the progress in the development of spatiotemporal-specific tools using small molecules or light as inducers to achieve the conditional control of epigenome editing and their applications in epigenetic research.
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Using design of experiment to optimize enzyme activity assays. CHEMTEXTS 2019. [DOI: 10.1007/s40828-019-0095-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Ardakani AA, Ghader A, Asgari H, Keshavarz M, Tazehmahalleh FE, Majles Ara MH, Malekzadeh M, Ghaznavi H, Shakeri-Zadeh A. The capability of nonlinear optical characteristics as a predictor for cellular uptake of nanoparticles and cell damage. Photodiagnosis Photodyn Ther 2019; 27:442-448. [PMID: 31362112 DOI: 10.1016/j.pdpdt.2019.07.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/21/2019] [Accepted: 07/26/2019] [Indexed: 11/19/2022]
Abstract
Current methods for determining the cellular effects of a treatment modality need expensive materials and much time to provide a researcher with results. The aim of this study was to evaluate the potential of nonlinear optical characteristics of cancer cells using Z-scan technique to monitor the level of cellular uptake and cell damage caused by a nanotechnology based treatment modality. Two nanocomplexes were synthesized and characterized. The first one was made of alginate hydrogel co-loaded with cisplatin and gold nanoparticles (AuNPs) named as ACA nanocomplex. The second one, named as AA nanocomplex, was the same as ACA, but without cisplatin and this AA nanocomplex was considered as the control for ACA. Different groups of CT26 mouse colon cancer cell line received various treatments of cisplatin, ACA, and AA nanocomplexes and then the samples were prepared for Z-scan studies. The MTT assay was used to evaluate the cytotoxicity induced by different treatment modalities. Transmission electron microscopy (TEM) and inductively coupled plasma-mass spectrometry (ICP-MS) were used for qualitative and quantitative assessments of the level of AuNPs cellular uptake. The trend of nonlinear optical properties changes for treated cells was in agreement with MTT, TEM and ICP-MS results. Z-scan technique was able to successfully indicate the occurrence of cell damage. It was also capable to determine the intensity of cell damage induced by ACA nanocomplex in comparison to free cisplatin. Furthermore, Z-scan results showed that it was able to discriminate the differences of optical properties of the cells incubated with ACA nanocomplex for various incubation times. Nonlinear optical characteristics of a cell may be considered as a reliable indicator to predict the level of cellular effects induced by a nanotechnology based treatment modality. The protocol suggested in this article does not waste materials, not take much time to provide the results, and it is inexpensive technique.
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Affiliation(s)
- Ali Abbasian Ardakani
- Finetech in Medicine Research Center, Iran University of Medical Sciences (IUMS), Tehran, Iran; Medical Physics Department, School of Medicine, Iran University of Medical Sciences (IUMS), Tehran, Iran
| | - Alireza Ghader
- Finetech in Medicine Research Center, Iran University of Medical Sciences (IUMS), Tehran, Iran; Medical Physics Department, School of Medicine, Iran University of Medical Sciences (IUMS), Tehran, Iran
| | - Hamid Asgari
- Finetech in Medicine Research Center, Iran University of Medical Sciences (IUMS), Tehran, Iran
| | - Marzieh Keshavarz
- Department of Medical Physics, School of Medicine, Shiraz University of Medical Sciences, Tehran, Iran
| | | | - Mohammad Hosein Majles Ara
- Department of Physics, Biophotonics Lab, Applied Science Research Center (ASRC), Kharazmi University, Karaj, Iran
| | - Malekeh Malekzadeh
- Medical Physics Department, School of Medicine, Iran University of Medical Sciences (IUMS), Tehran, Iran
| | - Habib Ghaznavi
- Zahedan University of Medical Sciences (ZaUMS), Zahedan, Iran.
| | - Ali Shakeri-Zadeh
- Finetech in Medicine Research Center, Iran University of Medical Sciences (IUMS), Tehran, Iran; Medical Physics Department, School of Medicine, Iran University of Medical Sciences (IUMS), Tehran, Iran.
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Berg A, Hallowell S, Tibbetts M, Beasley C, Brown-Phillips T, Healy A, Pustilnik L, Doyonnas R, Pregel M. High-Throughput Surface Liquid Absorption and Secretion Assays to Identify F508del CFTR Correctors Using Patient Primary Airway Epithelial Cultures. SLAS DISCOVERY 2019; 24:724-737. [PMID: 31107611 DOI: 10.1177/2472555219849375] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
High-throughput screening for drug discovery is increasingly utilizing cellular systems of high physiological relevance, such as patient primary cells and organoid cultures. We used 3D-cultured cystic fibrosis patient bronchial epithelial cells to screen for new small-molecule correctors of the disease-causing F508del mutation in CFTR. Impaired mucociliary clearance due to insufficient airway hydration is a hallmark of cystic fibrosis and we used a simple measure of surface liquid levels to quantify F508del CFTR correction in cultured bronchial epithelial cells. Two robust assay formats were configured and used to screen more than 100,000 compounds as mixtures or individual compounds in 96-well format. The corrector discovery success rate, as measured by the number of hits confirmed by an electrophysiology assay on patient primary bronchial epithelial cells, was superior to screens in cell lines expressing recombinant F508del CFTR. Several novel corrector scaffolds were discovered that when combined with the clinical corrector VX-809 delivered combination responses greater than double that of VX-809 alone. This work exemplifies the advantages of a disease-relevant readout and 3D-cultured patient primary cells for the discovery of new drug candidates.
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Affiliation(s)
- Allison Berg
- 1 Rare Disease Research, Pfizer Inc., Cambridge, MA, USA
| | - Shawn Hallowell
- 2 Primary Pharmacology Group, Medicine Design, Pfizer Inc., Groton, CT, USA
| | - Mark Tibbetts
- 2 Primary Pharmacology Group, Medicine Design, Pfizer Inc., Groton, CT, USA
| | - Chad Beasley
- 2 Primary Pharmacology Group, Medicine Design, Pfizer Inc., Groton, CT, USA
| | | | - Anita Healy
- 2 Primary Pharmacology Group, Medicine Design, Pfizer Inc., Groton, CT, USA
| | - Leslie Pustilnik
- 2 Primary Pharmacology Group, Medicine Design, Pfizer Inc., Groton, CT, USA
| | - Regis Doyonnas
- 2 Primary Pharmacology Group, Medicine Design, Pfizer Inc., Groton, CT, USA
| | - Marko Pregel
- 1 Rare Disease Research, Pfizer Inc., Cambridge, MA, USA
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Carmi I, De Battista M, Maddalena L, Carroll EC, Kienzler MA, Berlin S. Holographic two-photon activation for synthetic optogenetics. Nat Protoc 2019; 14:864-900. [PMID: 30804570 DOI: 10.1038/s41596-018-0118-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 12/17/2018] [Indexed: 12/25/2022]
Abstract
Optogenetic tools provide users the ability to photocontrol the activity of cells. Commonly, activation is achieved by expression of proteins from photosynthetic organisms, for example, microbial opsins (e.g., ChR2). Alternatively, a sister approach, synthetic optogenetics, enables photocontrol over proteins of mammalian origin by use of photoswitches, visible light (typically), and genetic modification. Thus, synthetic optogenetics facilitates interrogation of native neuronal signaling mechanisms. However, the poor tissue penetration of visible wavelengths impedes the use of the technique in tissue, as two-photon excitation (2PE) is typically required to access the near-infrared window. Here, we describe an alternative technique that uses 2PE-compatible photoswitches (section 1) for photoactivation of genetically modified glutamate receptors (section 2). Furthermore, for fast, multi-region photoactivation, we describe the use of 2P-digital holography (2P-DH) (section 3). We detail how to combine 2P-DH and synthetic optogenetics with electrophysiology, or with red fluorescence Ca2+ recordings, for all-optical neural interrogation. The time required to complete the methods, aside from obtaining the necessary reagents and illumination equipment, is ~3 weeks.
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Affiliation(s)
- Ido Carmi
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Marco De Battista
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Laura Maddalena
- Department of Imaging Physics, Delft University of Technology, Delft, the Netherlands
| | - Elizabeth C Carroll
- Department of Imaging Physics, Delft University of Technology, Delft, the Netherlands
| | | | - Shai Berlin
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel.
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