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Gomes AR, Tavares-da-Silva EJ, Costa SC, Varela CL, Abrantes AM, Gonçalves AC, Alves R, Botelho MF, Roleira FMF, Pires AS. Steroidal epoxides as anticancer agents in lung, prostate and breast cancers: The case of 1,2-epoxysteroids. Biochem Pharmacol 2024; 225:116266. [PMID: 38710333 DOI: 10.1016/j.bcp.2024.116266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 05/08/2024]
Abstract
Cancer continues to be a serious threat to human health worldwide. Lung, prostate and triple-negative breast cancers are amongst the most incident and deadliest cancers. Steroidal compounds are one of the most diversified therapeutic classes of compounds and they were proven to be efficient against several types of cancer. The epoxide function has been frequently associated with anticancer activity, particularly the 1,2-epoxide function. For this reason, three 1,2-epoxysteroid derivatives previously synthesised (EP1, EP2 and EP3) and one synthesised for the first time (oxysteride) were evaluated against H1299 (lung), PC3 (prostate) and HCC1806 (triple-negative breast) cancer cell lines. A human non-tumour cell line, MRC-5 (normal lung cell line) was also used. EP2 was the most active compound in all cell lines with IC50 values of 2.50, 3.67 and 1.95 µM, followed by EP3 with IC50 values of 12.65, 15.10 and 14.16 µM in H1299, PC3 and HCC1806 cells, respectively. Additional studies demonstrated that EP2 and EP3 induced cell death by apoptosis at lower doses and apoptosis/necrosis at higher doses, proving that their effects were dose-dependent. Both compounds also exerted their cytotoxicity by ROS production and by inducing double-strand breaks. Furthermore, EP2 and EP3 proved to be much less toxic against a normal lung cell line, MRC5, indicating that both compounds might be selective, and they also demonstrated suitable in silico ADME and toxicity parameters. Finally, none of the compounds induced haemoglobin release. Altogether, these results point out the extreme relevance of both compounds, especially EP2, in the potential treatment of these types of cancer.
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Affiliation(s)
- Ana R Gomes
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) area of Environment Genetics and Oncobiology (CIMAGO), Biophysics Institute of Faculty of Medicine, Azinhaga de Santa Comba, Pólo III - Pólo das Ciências da Saúde, Coimbra, Portugal; Univ Coimbra, CERES, Faculty of Pharmacy, Laboratory of Pharmaceutical Chemistry, Azinhaga de Santa Comba, Pólo III - Pólo das Ciências da Saúde, Coimbra, Portugal; Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), Coimbra, Portugal
| | - Elisiário J Tavares-da-Silva
- Univ Coimbra, CERES, Faculty of Pharmacy, Laboratory of Pharmaceutical Chemistry, Azinhaga de Santa Comba, Pólo III - Pólo das Ciências da Saúde, Coimbra, Portugal.
| | - Saúl C Costa
- Univ Coimbra, Faculty of Pharmacy, Laboratory of Pharmaceutical Chemistry, Azinhaga de Santa Comba, Pólo III - Pólo das Ciências da Saúde, Coimbra, Portugal
| | - Carla L Varela
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), Coimbra, Portugal; Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), Azinhaga de Santa Comba, Pólo III - Pólo das Ciências da Saúde, Coimbra, Portugal; Univ Coimbra, CERES, Department of Chemical Engineering, 3030-790 Coimbra, Portugal
| | - Ana M Abrantes
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) area of Environment Genetics and Oncobiology (CIMAGO), Biophysics Institute of Faculty of Medicine, Azinhaga de Santa Comba, Pólo III - Pólo das Ciências da Saúde, Coimbra, Portugal; Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), Coimbra, Portugal; Clinical Academic Center of Coimbra (CACC), Praceta Professor Mota Pinto, Coimbra, Portugal
| | - Ana C Gonçalves
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), Coimbra, Portugal; Clinical Academic Center of Coimbra (CACC), Praceta Professor Mota Pinto, Coimbra, Portugal; Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) area of Environment Genetics and Oncobiology (CIMAGO), Laboratory of Oncobiology and Hematology and University Clinics of Hematology and Oncology, Faculty of Medicine, Portugal
| | - Raquel Alves
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), Coimbra, Portugal; Clinical Academic Center of Coimbra (CACC), Praceta Professor Mota Pinto, Coimbra, Portugal; Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) area of Environment Genetics and Oncobiology (CIMAGO), Laboratory of Oncobiology and Hematology and University Clinics of Hematology and Oncology, Faculty of Medicine, Portugal
| | - Maria F Botelho
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) area of Environment Genetics and Oncobiology (CIMAGO), Biophysics Institute of Faculty of Medicine, Azinhaga de Santa Comba, Pólo III - Pólo das Ciências da Saúde, Coimbra, Portugal; Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), Coimbra, Portugal; Clinical Academic Center of Coimbra (CACC), Praceta Professor Mota Pinto, Coimbra, Portugal
| | - Fernanda M F Roleira
- Univ Coimbra, CERES, Faculty of Pharmacy, Laboratory of Pharmaceutical Chemistry, Azinhaga de Santa Comba, Pólo III - Pólo das Ciências da Saúde, Coimbra, Portugal
| | - Ana S Pires
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) area of Environment Genetics and Oncobiology (CIMAGO), Biophysics Institute of Faculty of Medicine, Azinhaga de Santa Comba, Pólo III - Pólo das Ciências da Saúde, Coimbra, Portugal; Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), Coimbra, Portugal; Clinical Academic Center of Coimbra (CACC), Praceta Professor Mota Pinto, Coimbra, Portugal.
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Ashby G, Keng KE, Hayden CC, Stachowiak JC. A live cell imaging-based assay for tracking particle uptake by clathrin-mediated endocytosis. Methods Enzymol 2024; 700:413-454. [PMID: 38971609 DOI: 10.1016/bs.mie.2024.02.010] [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: 07/08/2024]
Abstract
A popular strategy for therapeutic delivery to cells and tissues is to encapsulate therapeutics inside particles that cells internalize via endocytosis. The efficacy of particle uptake by endocytosis is often studied in bulk using flow cytometry and Western blot analysis and confirmed using confocal microscopy. However, these techniques do not reveal the detailed dynamics of particle internalization and how the inherent heterogeneity of many types of particles may impact their endocytic uptake. Toward addressing these gaps, here we present a live-cell imaging-based method that utilizes total internal reflection fluorescence microscopy to track the uptake of a large ensemble of individual particles in parallel, as they interact with the cellular endocytic machinery. To analyze the resulting data, we employ an open-source tracking algorithm in combination with custom data filters. This analysis reveals the dynamic interactions between particles and endocytic structures, which determine the probability of particle uptake. In particular, our approach can be used to examine how variations in the physical properties of particles (size, targeting, rigidity), as well as heterogeneity within the particle population, impact endocytic uptake. These data impact the design of particles toward more selective and efficient delivery of therapeutics to cells.
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Affiliation(s)
- Grant Ashby
- Department of Biomedical Engineering, The University of Texas at Austin
| | - Kayla E Keng
- Department of Biomedical Engineering, The University of Texas at Austin
| | - Carl C Hayden
- Department of Biomedical Engineering, The University of Texas at Austin
| | - Jeanne C Stachowiak
- Department of Biomedical Engineering, The University of Texas at Austin; Department of Chemical Engineering, The University of Texas at Austin.
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3
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Lazarski CA, Hanley PJ. Review of flow cytometry as a tool for cell and gene therapy. Cytotherapy 2024; 26:103-112. [PMID: 37943204 PMCID: PMC10872958 DOI: 10.1016/j.jcyt.2023.10.005] [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: 08/16/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 11/10/2023]
Abstract
Quality control testing and analytics are critical for the development and manufacture of cell and gene therapies, and flow cytometry is a key quality control and analytical assay that is used extensively. However, the technical scope of characterization assays and safety assays must keep apace as the breadth of cell therapy products continues to expand beyond hematopoietic stem cell products into producing novel adoptive immune therapies and gene therapy products. Flow cytometry services are uniquely positioned to support the evolving needs of cell therapy facilities, as access to flow cytometers, new antibody clones and improved fluorochrome reagents becomes more egalitarian. This report will outline the features, logistics, limitations and the current state of flow cytometry within the context of cellular therapy.
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Affiliation(s)
- Christopher A Lazarski
- Program for Cell Enhancement and Technology for Immunotherapy, Center for Cancer and Immunology Research, Children's National Hospital, Washington, DC, USA; The George Washington University, Washington, DC, USA.
| | - Patrick J Hanley
- Program for Cell Enhancement and Technology for Immunotherapy, Center for Cancer and Immunology Research, Children's National Hospital, Washington, DC, USA; The George Washington University, Washington, DC, USA.
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4
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Ashby G, Keng KE, Hayden CC, Gollapudi S, Houser JR, Jamal S, Stachowiak JC. Selective Endocytic Uptake of Targeted Liposomes Occurs within a Narrow Range of Liposome Diameters. ACS APPLIED MATERIALS & INTERFACES 2023; 15:49988-50001. [PMID: 37862704 PMCID: PMC11165932 DOI: 10.1021/acsami.3c09399] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2023]
Abstract
Cell surface receptors facilitate signaling and nutrient uptake. These processes are dynamic, requiring receptors to be actively recycled by endocytosis. Due to their differential expression in disease states, receptors are often the target of drug-carrier particles, which are adorned with ligands that bind specifically to receptors. These targeted particles are taken into the cell by multiple routes of internalization, where the best-characterized pathway is clathrin-mediated endocytosis. Most studies of particle uptake have utilized bulk assays rather than observing individual endocytic events. As a result, the detailed mechanisms of particle uptake remain obscure. To address this gap, we employed a live-cell imaging approach to study the uptake of individual liposomes as they interact with clathrin-coated structures. By tracking individual internalization events, we find that the size of liposomes rather than the density of the ligands on their surfaces primarily determines their probability of uptake. Interestingly, targeting has the greatest impact on endocytosis of liposomes of intermediate diameters, with the smallest and largest liposomes being internalized or excluded, respectively, regardless of whether they are targeted. These findings, which highlight a previously unexplored limitation of targeted delivery, can be used to design more effective drug carriers.
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Affiliation(s)
- Grant Ashby
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas, 78712, United States of America
| | - Kayla E. Keng
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas, 78712, United States of America
| | - Carl C. Hayden
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas, 78712, United States of America
| | - Sadhana Gollapudi
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas, 78712, United States of America
| | - Justin R. Houser
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas, 78712, United States of America
| | - Sabah Jamal
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas, 78712, United States of America
| | - Jeanne C. Stachowiak
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas, 78712, United States of America
- Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas, 78712, United States of America
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Lourenço EMG, da Silva F, das Neves AR, Bonfá IS, Ferreira AMT, Menezes ACG, da Silva MEC, Dos Santos JT, Martines MAU, Perdomo RT, Toffoli-Kadri MC, G Barbosa E, Saba S, Beatriz A, Rafique J, de Arruda CCP, de Lima DP. Investigation of the Potential Targets behind the Promising and Highly Selective Antileishmanial Action of Synthetic Flavonoid Derivatives. ACS Infect Dis 2023; 9:2048-2061. [PMID: 37772925 DOI: 10.1021/acsinfecdis.3c00336] [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: 09/30/2023]
Abstract
Leishmaniases are among the neglected tropical diseases that still cause devastating health, social, and economic consequences to more than 350 million people worldwide. Despite efforts to combat these vector-borne diseases, their incidence does not decrease. Meanwhile, current antileishmanial drugs are old and highly toxic, and safer presentations are unaffordable to the most severely affected human populations. In a previous study by our research group, we synthesized 17 flavonoid derivatives that demonstrated impressive inhibition capacity against rCPB2.8, rCPB3, and rH84Y. These cysteine proteases are highly expressed in the amastigote stage, the target form of the parasite. However, although these compounds have been already described in the literature, until now, the amastigote effect of any of these molecules has not been proven. In this work, we aimed to deeply analyze the antileishmanial action of this set of synthetic flavonoid derivatives by correlating their ability to inhibit cysteine proteases with the action against the parasite. Among all the synthesized flavonoid derivatives, 11 of them showed high activity against amastigotes of Leishmania amazonensis, also providing safety to mammalian host cells. Furthermore, the high production of nitric oxide by infected cells treated with the most active cysteine protease B (CPB) inhibitors confirms a potential immunomodulatory response of macrophages. Besides, considering flavonoids as multitarget drugs, we also investigated other potential antileishmanial mechanisms. The most active compounds were selected to investigate another potential biological pathway behind their antileishmanial action using flow cytometry analysis. The results confirmed an oxidative stress after 48 h of treatment. These data represent an important step toward the validation of CPB as an antileishmanial target, as well as aiding in new drug discovery studies based on this protease.
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Affiliation(s)
- Estela M G Lourenço
- Laboratório de Síntese e Transformação de Moléculas Orgânicas -SINTMOL, Instituto de Química, Universidade Federal de Mato Grosso do Sul, Av. Senador Filinto Muller, Campo Grande, 79074-460 MS, Brazil
| | - Fernanda da Silva
- Laboratório de Parasitologia Humana, Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Campo Grande, 79070-900, MS, Brazil
| | - Amarith R das Neves
- Laboratório de Parasitologia Humana, Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Campo Grande, 79070-900, MS, Brazil
| | - Iluska S Bonfá
- Laboratório de Farmacologia e Inflamação, Faculdade de Ciências Farmacêuticas, Alimentos e Nutrição, Universidade Federal de Mato Grosso do Sul, Campo Grande, 79074-460 MS, Brazil
| | - Alda Maria T Ferreira
- Laboratório de Imunologia, Biologia Molecular e Bioensaios Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Campo Grande, 79070-900 MS, Brazil
| | - Adriana C G Menezes
- Biotério Central, Universidade Federal de Mato Grosso do Sul, Campo Grande, 79070-900 MS, Brazil
| | - Maria E C da Silva
- Laboratório de Síntese e Transformação de Moléculas Orgânicas -SINTMOL, Instituto de Química, Universidade Federal de Mato Grosso do Sul, Av. Senador Filinto Muller, Campo Grande, 79074-460 MS, Brazil
| | - Jéssica T Dos Santos
- Laboratório de Síntese e Transformação de Moléculas Orgânicas -SINTMOL, Instituto de Química, Universidade Federal de Mato Grosso do Sul, Av. Senador Filinto Muller, Campo Grande, 79074-460 MS, Brazil
| | - Marco A U Martines
- Instituto de Química, Universidade Federal de Mato Grosso do Sul, Av. Senador Filinto Muller, Campo Grande, 79074-460 MS, Brazil
| | - Renata T Perdomo
- Laboratório de Biologia Molecular e Cultura de Células, Faculdade de Ciências Farmacêuticas, Alimentos e Nutrição, Universidade Federal de Mato Grosso do Sul, Campo Grande, 79070-900 MS, Brazil
| | - Mônica C Toffoli-Kadri
- Laboratório de Farmacologia e Inflamação, Faculdade de Ciências Farmacêuticas, Alimentos e Nutrição, Universidade Federal de Mato Grosso do Sul, Campo Grande, 79074-460 MS, Brazil
| | - Euzébio G Barbosa
- Laboratório de Química Farmacêutica Computacional, Departamento de Farmácia, Universidade Federal do Rio Grande do Norte, Natal, 59012-570, RN, Brazil
| | - Sumbal Saba
- Laboratório de Síntese Sustentável e Organocalcogênio - LabSO, Instituto de Química, Universidade Federal de Goiás-UFG, Goiânia, 74690-900 GO, Brazil
| | - Adilson Beatriz
- Laboratório de Síntese e Transformação de Moléculas Orgânicas -SINTMOL, Instituto de Química, Universidade Federal de Mato Grosso do Sul, Av. Senador Filinto Muller, Campo Grande, 79074-460 MS, Brazil
| | - Jamal Rafique
- Laboratório de Síntese e Transformação de Moléculas Orgânicas -SINTMOL, Instituto de Química, Universidade Federal de Mato Grosso do Sul, Av. Senador Filinto Muller, Campo Grande, 79074-460 MS, Brazil
- Laboratório de Síntese Sustentável e Organocalcogênio - LabSO, Instituto de Química, Universidade Federal de Goiás-UFG, Goiânia, 74690-900 GO, Brazil
| | - Carla C P de Arruda
- Laboratório de Parasitologia Humana, Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Campo Grande, 79070-900, MS, Brazil
| | - Dênis P de Lima
- Laboratório de Síntese e Transformação de Moléculas Orgânicas -SINTMOL, Instituto de Química, Universidade Federal de Mato Grosso do Sul, Av. Senador Filinto Muller, Campo Grande, 79074-460 MS, Brazil
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6
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Ashby G, Keng KE, Hayden CC, Gollapudi S, Houser JR, Jamal S, Stachowiak JC. Selective endocytic uptake of targeted liposomes occurs within a narrow range of liposome diameter. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.06.548000. [PMID: 37461728 PMCID: PMC10350051 DOI: 10.1101/2023.07.06.548000] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/27/2023]
Abstract
Cell surface receptors facilitate signaling and nutrient uptake. These processes are dynamic, requiring receptors to be actively recycled by endocytosis. Due to their differential expression in disease states, receptors are often the target of drug-carrier particles, which are adorned with ligands that bind specifically to receptors. These targeted particles are taken into the cell by multiple routes of internalization, where the best-characterized pathway is clathrin-mediated endocytosis. Most studies of particle uptake have utilized bulk assays, rather than observing individual endocytic events. As a result, the detailed mechanisms of particle uptake remain obscure. To address this gap, we have employed a live-cell imaging approach to study the uptake of individual liposomes as they interact with clathrin-coated structures. By tracking individual internalization events, we find that the size of liposomes, rather than the density of the ligands on their surfaces, primarily determines their probability of uptake. Interestingly, targeting has the greatest impact on endocytosis of liposomes of intermediate diameters, with the smallest and largest liposomes being internalized or excluded, respectively, regardless of whether they are targeted. These findings, which highlight a previously unexplored limitation of targeted delivery, can be used to design more effective drug carriers.
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Affiliation(s)
- Grant Ashby
- Department of Biomedical Engineering, The University of Texas at Austin
| | - Kayla E Keng
- Department of Biomedical Engineering, The University of Texas at Austin
| | - Carl C Hayden
- Department of Biomedical Engineering, The University of Texas at Austin
| | - Sadhana Gollapudi
- Department of Biomedical Engineering, The University of Texas at Austin
| | - Justin R Houser
- Department of Biomedical Engineering, The University of Texas at Austin
| | - Sabah Jamal
- Department of Biomedical Engineering, The University of Texas at Austin
| | - Jeanne C Stachowiak
- Department of Biomedical Engineering, The University of Texas at Austin
- Department of Chemical Engineering, The University of Texas at Austin
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7
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Su Z, Brooks J, Pelker J, Andreyeva T, Sobon H, Gifford R, Powers M, Wang J, Dower C, Hegen M, Messing D, Sheehan AD, Brennan JJ. Studies with neutralizing antibodies suggest CXCL8-mediated neutrophil activation is independent of C-C motif chemokine receptor-like 2 (CCRL2) ligand binding function. PLoS One 2023; 18:e0280590. [PMID: 36662882 PMCID: PMC9858354 DOI: 10.1371/journal.pone.0280590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/03/2023] [Indexed: 01/22/2023] Open
Abstract
C-C motif chemokine receptor-like 2 (CCRL2) is a non-signaling 7 transmembrane receptor that binds chemotactic ligands to shape leukocyte recruitment to sites of inflammation. However, there is a lack of consensus on the ligands that directly bind CCRL2 or their functional impact. Studies with CCRL2 knockout mice have demonstrated that neutrophils have impaired degranulation and migration in response to CXCL8, where the underlying molecular mechanism is proposed to be due to the formation of CCRL2 heterodimers with the chemokine receptor CXCR2. Herein, we characterized the ligands that bind directly to CCRL2 and interrogated the impact of CCRL2 neutralization on CXCL8 signaling in neutrophils using pharmacological antibody tools. Using flow cytometry and Surface Plasmon Resonance microscopy (SPRm) cell binding experiments, we confirmed that chemerin, but not previously reported C-C chemokines, binds CCRL2. Furthermore, we identified human and mouse CCRL2 antibodies that neutralized chemerin binding to CCRL2. Unexpectedly, we found that neutralization of CCRL2 with these antibodies did not attenuate CXCL8-induced human neutrophil degranulation nor CXCL8-induced murine neutrophil recruitment to the peritoneum. Based on the observed differences in modulating CCRL2 function with neutralizing antibodies compared to the reported CCRL2 deficient murine models, we hypothesize that the ligand binding function of CCRL2 is dispensable for CXCL8 signaling in neutrophils. Finally, extensive profiling of CCRL2 expression on peripheral blood leukocytes revealed monocytes, dendritic cells (DC), and subpopulations of natural killer T (NKT) cells as additional targets, highlighting potential roles for CCRL2 in human cell types beyond neutrophils that warrants future investigation.
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Affiliation(s)
- Zhenwei Su
- BioMedicine Design, Pfizer, Cambridge, Massachusetts, United States of America
| | - Jonathan Brooks
- Inflammation and Immunology, Pfizer, Cambridge, Massachusetts, United States of America
| | - Jeffrey Pelker
- Inflammation and Immunology, Pfizer, Cambridge, Massachusetts, United States of America
| | - Tatyana Andreyeva
- Inflammation and Immunology, Pfizer, Cambridge, Massachusetts, United States of America
| | - Hanna Sobon
- Inflammation and Immunology, Pfizer, Cambridge, Massachusetts, United States of America
| | - Roger Gifford
- Inflammation and Immunology, Pfizer, Cambridge, Massachusetts, United States of America
| | - Matthew Powers
- Inflammation and Immunology, Pfizer, Cambridge, Massachusetts, United States of America
| | - Jing Wang
- BioMedicine Design, Pfizer, Cambridge, Massachusetts, United States of America
| | - Corey Dower
- BioMedicine Design, Pfizer, Cambridge, Massachusetts, United States of America
| | - Martin Hegen
- Inflammation and Immunology, Pfizer, Cambridge, Massachusetts, United States of America
| | - Dean Messing
- BioMedicine Design, Pfizer, Cambridge, Massachusetts, United States of America
| | | | - Joseph J. Brennan
- Inflammation and Immunology, Pfizer, Cambridge, Massachusetts, United States of America
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8
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Liu Y, Chen L, Yu J, Ye L, Hu H, Wang J, Wu B. Advances in Single-Cell Toxicogenomics in Environmental Toxicology. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:11132-11145. [PMID: 35881918 DOI: 10.1021/acs.est.2c01098] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The toxicity evaluation system of environmental pollutants has undergone numerous changes due to the application of new technologies. Single-cell toxicogenomics is rapidly changing our view on environmental toxicology by increasing the resolution of our analysis to the level of a single cell. Applications of this technology in environmental toxicology have begun to emerge and are rapidly expanding the portfolio of existing technologies and applications. Here, we first summarized different methods involved in single-cell isolation and amplification in single-cell sequencing process, compared the advantages and disadvantages of different methods, and analyzed their development trends. Then, we reviewed the main advances of single-cell toxicogenomics in environmental toxicology, emphatically analyzed the application prospects of this technology in identifying the target cells of pollutants in early embryos, clarifying the heterogeneous response of cell subtypes to pollutants, and finding pathogenic bacteria in unknown microbes, and highlighted the unique characteristics of this approach with high resolution, high throughput, and high specificity by examples. We also offered a prediction of the further application of this technology and the revolution it brings in environmental toxicology. Overall, these advances will provide practical solutions for controlling or mitigating exogenous toxicological effects that threaten human and ecosystem health, contribute to improving our understanding of the physiological processes affected by pollutants, and lead to the emergence of new methods of pollution control.
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Affiliation(s)
- Yuxuan Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
| | - Ling Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
| | - Jing Yu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
| | - Lin Ye
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
| | - Haidong Hu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
| | - Jinfeng Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
| | - Bing Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
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9
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Dragan P, Atzei A, Sanmukh SG, Latek D. Computational and experimental approaches to probe GPCR activation and signaling. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 193:1-36. [PMID: 36357073 DOI: 10.1016/bs.pmbts.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
G protein-coupled receptors (GPCRs) regulate different physiological functions, e.g., sensation, growth, digestion, reproductivity, nervous and immune systems response, and many others. In eukaryotes, they are also responsible for intercellular communication in response to pathogens. The major primary messengers binding to these cell-surface receptors constitute small-molecule or peptide hormones and neurotransmitters, nucleotides, lipids as well as small proteins. The simplicity of the way how GPCR signaling can be regulated by their endogenous agonists prompted the usage of GPCRs as major drug targets in modern pharmacology. Drugs targeting GPCRs inhibit pathological processes at the very beginning. This enables to significantly reduce the occurrence of morphological changes caused by diseases. Until recently, X-ray crystallography was the method of the first choice to obtain high-resolution structural information about GPCRs. Following X-ray crystallography, cryo-EM gained attention in GPCR studies as a quick and low-cost alternative. FRET microscopy is also widely used for GPCRs in the analysis of protein-protein interactions (PPIs) in intact cells as well as for screening purposes. Regarding computational methods, molecular dynamics (MD) for many years has proven its usefulness in studying the GPCR activation. MODELLER and Rosetta were widely used to generate preliminary homology models of GPCRs for MD simulation systems. Apart from the conventional all-atom approach with explicitly defined solvent, also other techniques have been applied to GPCRs, e.g., MARTINI or hybrid methods involving the coarse-grained representation, less demanding regarding computational resources, and thus offering much larger simulation timescales.
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Affiliation(s)
- Paulina Dragan
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | | | | | - Dorota Latek
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland.
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10
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de Rutte J, Dimatteo R, Zhu S, Archang MM, Di Carlo D. Sorting single-cell microcarriers using commercial flow cytometers. SLAS Technol 2022; 27:150-159. [PMID: 35058209 PMCID: PMC9018595 DOI: 10.1016/j.slast.2021.10.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The scale of biological discovery is driven by the vessels in which we can perform assays and analyze results, from multi-well plates to microfluidic compartments. We report on the compatibility of sub-nanoliter single-cell containers or "nanovials" with commercial fluorescence activated cell sorters (FACS). This recent lab on a particle approach utilizes 3D structured microparticles to isolate cells and perform single-cell assays at scale with existing lab equipment. Use of flow cytometry led to detection of fluorescently labeled protein with dynamic ranges spanning 2-3 log and detection limits down to ∼10,000 molecules per nanovial, which was the lowest amount tested. Detection limits were improved compared to fluorescence microscopy measurements using a 20X objective and a cooled CMOS camera. Nanovials with diameters between 35-85 µm could also be sorted with purity from 99-93% on different commercial instruments at throughputs up to 800 events/second. Cell-loaded nanovials were found to have unique forward and side (or back) scatter signatures that enabled gating of cell-containing nanovials using scatter metrics alone. The compatibility of nanovials with widely-available commercial FACS instruments promises to democratize single-cell assays used in discovery of antibodies and cell therapies, by enabling analysis of single cells based on secreted products and leveraging the unmatched analytical capabilities of flow cytometers to sort important clones.
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Affiliation(s)
- Joseph de Rutte
- Department of Bioengineering, University of California, Los Angeles, United States; Partillion Bioscience Corporation, Los Angeles, CA, United States.
| | - Robert Dimatteo
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, United States
| | - Sheldon Zhu
- Partillion Bioscience Corporation, Los Angeles, CA, United States
| | - Maani M Archang
- Department of Bioengineering, University of California, Los Angeles, United States
| | - Dino Di Carlo
- Department of Bioengineering, University of California, Los Angeles, United States; Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, United States; California NanoSystems Institute, University of California, Los Angeles, United States; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, United States
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11
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Avital-Shmilovici M, Liu X, Shaler T, Lowenthal A, Bourbon P, Snider J, Tambo-Ong A, Repellin C, Yniguez K, Sambucetti L, Madrid PB, Collins N. Mega-High-Throughput Screening Platform for the Discovery of Biologically Relevant Sequence-Defined Non-Natural Polymers. ACS CENTRAL SCIENCE 2022; 8:86-101. [PMID: 35106376 PMCID: PMC8796305 DOI: 10.1021/acscentsci.1c01041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Indexed: 06/14/2023]
Abstract
Combinatorial methods enable the synthesis of chemical libraries on scales of millions to billions of compounds, but the ability to efficiently screen and sequence such large libraries has remained a major bottleneck for molecular discovery. We developed a novel technology for screening and sequencing libraries of synthetic molecules of up to a billion compounds in size. This platform utilizes the fiber-optic array scanning technology (FAST) to screen bead-based libraries of synthetic compounds at a rate of 5 million compounds per minute (∼83 000 Hz). This ultra-high-throughput screening platform has been used to screen libraries of synthetic "self-readable" non-natural polymers that can be sequenced at the femtomole scale by chemical fragmentation and high-resolution mass spectrometry. The versatility and throughput of the platform were demonstrated by screening two libraries of non-natural polyamide polymers with sizes of 1.77M and 1B compounds against the protein targets K-Ras, asialoglycoprotein receptor 1 (ASGPR), IL-6, IL-6 receptor (IL-6R), and TNFα. Hits with low nanomolar binding affinities were found against all targets, including competitive inhibitors of K-Ras binding to Raf and functionally active uptake ligands for ASGPR facilitating intracellular delivery of a nonglycan ligand.
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12
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Continuous microfluidic 3D focusing enabling microflow cytometry for single-cell analysis. Talanta 2021; 221:121401. [DOI: 10.1016/j.talanta.2020.121401] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/04/2020] [Accepted: 07/08/2020] [Indexed: 02/06/2023]
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13
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Very rapid flow cytometric assessment of antimicrobial susceptibility during the apparent lag phase of microbial (re)growth. Microbiology (Reading) 2019; 165:439-454. [DOI: 10.1099/mic.0.000777] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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14
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Li L, Liao M, Chen Y, Shan B, Li M. Surface-enhanced Raman spectroscopy (SERS) nanoprobes for ratiometric detection of cancer cells. J Mater Chem B 2019; 7:815-822. [DOI: 10.1039/c8tb02828a] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A surface-enhanced Raman spectroscopic strategy is developed for ratiometric detection of cancer cells by quantifying the expression ratio of extracellular biomarkers.
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Affiliation(s)
- Linhu Li
- School of Materials Science and Engineering, State Key Laboratory for Power Metallurgy, Central South University
- Changsha
- China
| | - Mengling Liao
- School of Materials Science and Engineering, State Key Laboratory for Power Metallurgy, Central South University
- Changsha
- China
| | - Yingfan Chen
- School of Materials Science and Engineering, State Key Laboratory for Power Metallurgy, Central South University
- Changsha
- China
| | - Beibei Shan
- School of Materials Science and Engineering, State Key Laboratory for Power Metallurgy, Central South University
- Changsha
- China
| | - Ming Li
- School of Materials Science and Engineering, State Key Laboratory for Power Metallurgy, Central South University
- Changsha
- China
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15
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Joslin J, Gilligan J, Anderson P, Garcia C, Sharif O, Hampton J, Cohen S, King M, Zhou B, Jiang S, Trussell C, Dunn R, Fathman JW, Snead JL, Boitano AE, Nguyen T, Conner M, Cooke M, Harris J, Ainscow E, Zhou Y, Shaw C, Sipes D, Mainquist J, Lesley S. A Fully Automated High-Throughput Flow Cytometry Screening System Enabling Phenotypic Drug Discovery. SLAS DISCOVERY 2018; 23:697-707. [PMID: 29843542 PMCID: PMC6055113 DOI: 10.1177/2472555218773086] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The goal of high-throughput screening is to enable screening of compound libraries in an automated manner to identify quality starting points for optimization. This often involves screening a large diversity of compounds in an assay that preserves a connection to the disease pathology. Phenotypic screening is a powerful tool for drug identification, in that assays can be run without prior understanding of the target and with primary cells that closely mimic the therapeutic setting. Advanced automation and high-content imaging have enabled many complex assays, but these are still relatively slow and low throughput. To address this limitation, we have developed an automated workflow that is dedicated to processing complex phenotypic assays for flow cytometry. The system can achieve a throughput of 50,000 wells per day, resulting in a fully automated platform that enables robust phenotypic drug discovery. Over the past 5 years, this screening system has been used for a variety of drug discovery programs, across many disease areas, with many molecules advancing quickly into preclinical development and into the clinic. This report will highlight a diversity of approaches that automated flow cytometry has enabled for phenotypic drug discovery.
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Affiliation(s)
- John Joslin
- 1 Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - James Gilligan
- 1 Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Paul Anderson
- 1 Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Catherine Garcia
- 1 Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Orzala Sharif
- 1 Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Janice Hampton
- 1 Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Steven Cohen
- 1 Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Miranda King
- 1 Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Bin Zhou
- 1 Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Shumei Jiang
- 1 Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | | | - Robert Dunn
- 1 Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - John W Fathman
- 1 Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Jennifer L Snead
- 1 Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Anthony E Boitano
- 1 Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Tommy Nguyen
- 1 Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Michael Conner
- 1 Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Mike Cooke
- 1 Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Jennifer Harris
- 1 Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Ed Ainscow
- 1 Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Yingyao Zhou
- 1 Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Chris Shaw
- 1 Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Dan Sipes
- 1 Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - James Mainquist
- 1 Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Scott Lesley
- 1 Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
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16
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Bredemeyer AL, Edwards BS, Haynes MK, Morales AJ, Wang Y, Ursu O, Waller A, Sklar LA, Sleckman BP. High-Throughput Screening Approach for Identifying Compounds That Inhibit Nonhomologous End Joining. SLAS DISCOVERY 2017; 23:624-633. [PMID: 29232168 DOI: 10.1177/2472555217746324] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
DNA double-strand breaks (DSBs) are repaired primarily by homologous recombination (HR) or nonhomologous end joining (NHEJ). Compounds that modulate HR have shown promise as cancer therapeutics. The V(D)J recombination reaction, which assembles antigen receptor genes in lymphocytes, is initiated by the introduction of DNA DSBs at two recombining gene segments by the RAG endonuclease, followed by the NHEJ-mediated repair of these DSBs. Here, using HyperCyt automated flow cytometry, we develop a robust high-throughput screening (HTS) assay for NHEJ that utilizes engineered pre-B-cell lines where the V(D)J recombination reaction can be induced and monitored at a single-cell level. This approach, novel in processing four 384-well plates at a time in parallel, was used to screen the National Cancer Institute NeXT library to identify compounds that inhibit V(D)J recombination and NHEJ. Assessment of cell light scattering characteristics at the primary HTS stage (83,536 compounds) enabled elimination of 60% of apparent hits as false positives. Although all the active compounds that we identified had an inhibitory effect on RAG cleavage, we have established this as an approach that could identify compounds that inhibit RAG cleavage or NHEJ using new chemical libraries.
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Affiliation(s)
- Andrea L Bredemeyer
- 1 Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Bruce S Edwards
- 2 University of New Mexico Health Sciences Center and Cancer Research and Treatment Center, Department of Pathology, Cytometry, New Mexico Molecular Libraries Screening Center, Albuquerque, NM, USA
| | - Mark K Haynes
- 2 University of New Mexico Health Sciences Center and Cancer Research and Treatment Center, Department of Pathology, Cytometry, New Mexico Molecular Libraries Screening Center, Albuquerque, NM, USA
| | - Abigail J Morales
- 3 Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Yinan Wang
- 3 Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Oleg Ursu
- 2 University of New Mexico Health Sciences Center and Cancer Research and Treatment Center, Department of Pathology, Cytometry, New Mexico Molecular Libraries Screening Center, Albuquerque, NM, USA
| | - Anna Waller
- 2 University of New Mexico Health Sciences Center and Cancer Research and Treatment Center, Department of Pathology, Cytometry, New Mexico Molecular Libraries Screening Center, Albuquerque, NM, USA
| | - Larry A Sklar
- 2 University of New Mexico Health Sciences Center and Cancer Research and Treatment Center, Department of Pathology, Cytometry, New Mexico Molecular Libraries Screening Center, Albuquerque, NM, USA
| | - Barry P Sleckman
- 3 Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, USA
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17
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Precision toxicology based on single cell sequencing: an evolving trend in toxicological evaluations and mechanism exploration. Arch Toxicol 2017; 91:2539-2549. [DOI: 10.1007/s00204-017-1971-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 04/20/2017] [Indexed: 12/11/2022]
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18
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Luo Z, Samadzadeh KM, Nitin N. Rapid assessment of drug resistance of cancer cells to gefitinib and carboplatin using optical imaging. Anal Biochem 2016; 504:50-8. [DOI: 10.1016/j.ab.2016.03.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 03/14/2016] [Accepted: 03/28/2016] [Indexed: 12/19/2022]
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19
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Otvos RA, van Nierop P, Niessen WMA, Kini RM, Somsen GW, Smit AB, Kool J. Development of an Online Cell-Based Bioactivity Screening Method by Coupling Liquid Chromatography to Flow Cytometry with Parallel Mass Spectrometry. Anal Chem 2016; 88:4825-32. [DOI: 10.1021/acs.analchem.6b00455] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Reka A. Otvos
- Division
of BioAnalytical Chemistry, Vrije Universiteit Amsterdam, De Boelelaan
1083, 1081 HV Amsterdam, The Netherlands
- Department
of Molecular and Cellular Neurobiology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Pim van Nierop
- Department
of Molecular and Cellular Neurobiology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Wilfried M. A. Niessen
- Division
of BioAnalytical Chemistry, Vrije Universiteit Amsterdam, De Boelelaan
1083, 1081 HV Amsterdam, The Netherlands
- hyphen MassSpec, Herenweg 95, 2361
EK Warmond, The Netherlands
| | - R. Manjunatha Kini
- Department
of Biological Sciences, National University of Singapore, 14 Science
Drive 4, 117543, Singapore
| | - Govert W. Somsen
- Division
of BioAnalytical Chemistry, Vrije Universiteit Amsterdam, De Boelelaan
1083, 1081 HV Amsterdam, The Netherlands
| | - August B. Smit
- Department
of Molecular and Cellular Neurobiology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Jeroen Kool
- Division
of BioAnalytical Chemistry, Vrije Universiteit Amsterdam, De Boelelaan
1083, 1081 HV Amsterdam, The Netherlands
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20
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Gilchrist ML, Ahn K, Li YM. Imaging and Functional Analysis of γ-Secretase and Substrate in a Proteolipobead System with an Activity-Based Probe. Anal Chem 2016; 88:1303-11. [PMID: 26699370 PMCID: PMC4911041 DOI: 10.1021/acs.analchem.5b03762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Investigation of intramembranal protease catalysis demands the generation of intact biomembrane assemblies with structural integrity and lateral mobility. Here, we report the development of a microsphere supported-biomembrane platform enabling characterization of γ-secretase and substrate within proteolipobead assemblies via microscopy and flow cytometry. The active enzyme loading levels were tracked using an activity-based probe, with the biomembranes delineated by carbocyanine lipid reporters. Proteolipobeads formed from HeLa proteoliposomes gave rise to homogeneous distributions of active γ-secretase within supported biomembranes with native-like fluidity. The substrate loading into supported biomembranes was detergent-dependent, as evidenced by even colocalization of substrate and lipid tracers in confocal 3D imaging of individual proteolipobeads. Moreover, the loading level was tunable with bulk substrate concentration. γ-Secretase substrate cleavage and its inhibition within γ-secretase proteolipobeads were observed. This platform offers a means to visualize enzyme and substrate loading, activity, and inhibition in a controllable biomembrane microenvironment.
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Affiliation(s)
- M. Lane Gilchrist
- Department of Chemical Engineering and the Department of Biomedical Engineering, The City College of the City University of New York, 140th Street and Convent Avenue, New York, New York 10031, United States
| | - Kwangwook Ahn
- Chemistry Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, United States
| | - Yue-Ming Li
- Chemistry Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, United States
- Program of Pharmacology, Weill Graduate School of Medical Sciences of Cornell University, New York, New York 10021, United States
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21
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Haston KM, Finkbeiner S. Clinical Trials in a Dish: The Potential of Pluripotent Stem Cells to Develop Therapies for Neurodegenerative Diseases. Annu Rev Pharmacol Toxicol 2015; 56:489-510. [PMID: 26514199 PMCID: PMC4868344 DOI: 10.1146/annurev-pharmtox-010715-103548] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Neurodegenerative diseases are a leading cause of death. No disease-modifying therapies are available, and preclinical animal model data have routinely failed to translate into success for therapeutics. Induced pluripotent stem cell (iPSC) biology holds great promise for human in vitro disease modeling because these cells can give rise to any cell in the human brain and display phenotypes specific to neurodegenerative diseases previously identified in postmortem and clinical samples. Here, we explore the potential and caveats of iPSC technology as a platform for drug development and screening, and the future potential to use large cohorts of disease-bearing iPSCs to perform clinical trials in a dish.
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Affiliation(s)
- Kelly M Haston
- Gladstone Institute of Neurological Disease, San Francisco, California 94158;
| | - Steven Finkbeiner
- Gladstone Institute of Neurological Disease, San Francisco, California 94158;
- Taube/Koret Center for Neurodegenerative Disease and the Hellman Family Foundation Program in Alzheimer's Disease Research, San Francisco, California 94158
- Departments of Neurology and Physiology, University of California, San Francisco, California 94143
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22
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Robinson JP, Li N, Narayanan PK. High Throughput-Based Mitochondrial Function Assays by Multi-Parametric Flow Cytometry. ACTA ACUST UNITED AC 2015; 73:9.48.1-9.48.9. [PMID: 26132178 DOI: 10.1002/0471142956.cy0948s73] [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: 11/11/2022]
Abstract
Mitochondrial dysfunction has been increasingly implicated as an important mechanism for chemical-induced toxicity. In the present unit, we describe a multi-parametric flow cytometry assay to assess the effects of drug or chemical-induced mitochondrial dysfunction in cells. Cells are cultured in a glucose-supplemented medium and exposed to increasing concentrations of various chemicals. Several key mitochondrial/cellular parameters known to be directly impacted by mitochondrial dysfunction, such as mitochondrial membrane potential (MMP), mitochondrial reactive oxygen species (ROS) production, intracellular reduced glutathione (GSH) level, and cell viability, are simultaneously measured by flow cytometry.
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Affiliation(s)
- J Paul Robinson
- Purdue University Cytometry Laboratories, West Lafayette, Indiana
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23
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Janzen WP. Screening technologies for small molecule discovery: the state of the art. ACTA ACUST UNITED AC 2015; 21:1162-70. [PMID: 25237860 DOI: 10.1016/j.chembiol.2014.07.015] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 07/14/2014] [Accepted: 07/16/2014] [Indexed: 01/24/2023]
Abstract
Screening, high-throughput screening, and ultra-high-throughput screening are all really just points on a spectrum that represent differing applications of the same process: the creation of biologically relevant assays that are relevant, reproducible, reliable, and robust. Whether the discovery program is developing a pharmaceutical, an academic probe, cosmetics, pesticides, or a toxicity monitoring assay, the development of a screen focuses on generating a method that will reliably deliver reproducible results over a period of weeks, months, or years and that will generate consistent results for every test along the way. This review provides both historical perspective on how this unique scientific discipline evolved and commentary on the current state of the art technologies and techniques.
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Affiliation(s)
- William P Janzen
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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24
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Smurthwaite CA, Williams W, Fetsko A, Abbadessa D, Stolp ZD, Reed CW, Dharmawan A, Wolkowicz R. Genetic barcoding with fluorescent proteins for multiplexed applications. J Vis Exp 2015:52452. [PMID: 25938804 PMCID: PMC4541556 DOI: 10.3791/52452] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Fluorescent proteins, fluorescent dyes and fluorophores in general have revolutionized the field of molecular cell biology. In particular, the discovery of fluorescent proteins and their genes have enabled the engineering of protein fusions for localization, the analysis of transcriptional activation and translation of proteins of interest, or the general tracking of individual cells and cell populations. The use of fluorescent protein genes in combination with retroviral technology has further allowed the expression of these proteins in mammalian cells in a stable and reliable manner. Shown here is how one can utilize these genes to give cells within a population of cells their own biosignature. As the biosignature is achieved with retroviral technology, cells are barcoded 'indefinitely'. As such, they can be individually tracked within a mixture of barcoded cells and utilized in more complex biological applications. The tracking of distinct populations in a mixture of cells is ideal for multiplexed applications such as discovery of drugs against a multitude of targets or the activation profile of different promoters. The protocol describes how to elegantly develop and amplify barcoded mammalian cells with distinct genetic fluorescent markers, and how to use several markers at once or one marker at different intensities. Finally, the protocol describes how the cells can be further utilized in combination with cell-based assays to increase the power of analysis through multiplexing.
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25
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Flor A, Williams JH, Blaine KM, Duggan RC, Sperling AI, Schwartz DA, Kron SJ. DNA-directed assembly of antibody-fluorophore conjugates for quantitative multiparametric flow cytometry. Chembiochem 2014; 15:267-75. [PMID: 24375983 PMCID: PMC3925401 DOI: 10.1002/cbic.201300464] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Indexed: 02/07/2023]
Abstract
Multiparametric flow cytometry offers a powerful approach to single-cell analysis with broad applications in research and diagnostics. Despite advances in instrumentation, progress in methodology has lagged. Currently there is no simple and efficient method for antibody labeling or quantifying the number of antibodies bound per cell. Herein, we describe a DNA-directed assembly approach to fluorescent labeling that overcomes these barriers. Oligonucleotide-tagged antibodies and microparticles can be annealed to complementary oligonucleotides bearing fluorophores to create assay-specific labeling probes and controls, respectively. The ratio of the fluorescence intensity of labeled cells to the control particles allows direct conversion of qualitative data to quantitative units of antibody binding per cell. Importantly, a single antibody can be labeled with any fluorophore by using a simple mix-and-match labeling strategy. Thus, any antibody can provide a quantitative probe in any fluorescent channel, thus overcoming major barriers to the use of flow cytometry as a technique for systems biology and clinical diagnostics.
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Affiliation(s)
- Amy Flor
- University of Chicago, Chicago, Illinois 60637 (USA)
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26
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Xie J, Yea K, Zhang H, Moldt B, He L, Zhu J, Lerner RA. Prevention of cell death by antibodies selected from intracellular combinatorial libraries. ACTA ACUST UNITED AC 2014; 21:274-83. [PMID: 24440080 DOI: 10.1016/j.chembiol.2013.12.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 12/14/2013] [Accepted: 12/17/2013] [Indexed: 01/22/2023]
Abstract
One of the most important phenotypes in biology is cell death. One way to probe the mechanism(s) of cell death is to select molecules that prevent it and learn how this was accomplished. Here, intracellular combinatorial antibody libraries were used to select antibodies that protected cells from killing by rhinovirus infection. These rare antibodies functioned by inhibiting the virus-encoded protease that is necessary for viral maturation. Snapshots of the selection process after each round could be obtained by deep sequencing the ever-enriching populations. This detailed analysis of the enrichment process allowed an interesting look at a "test tube" selection process that pitted two replicating systems against each other. Thus, initially a minority of cells containing protective antibodies must compete against a majority of unprotected cells that continue to produce large amounts of virus.
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Affiliation(s)
- Jia Xie
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kyungmoo Yea
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 200031, China
| | - Hongkai Zhang
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Brian Moldt
- Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Linling He
- Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jiang Zhu
- Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Richard A Lerner
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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27
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Chandra H, Reddy PJ, Srivastava S. Protein microarrays and novel detection platforms. Expert Rev Proteomics 2014; 8:61-79. [DOI: 10.1586/epr.10.99] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Zhang B, Yang J, Zou Y, Gong M, Chen H, Hong G, Antaris AL, Li X, Liu CL, Chen C, Dai H. Plasmonic micro-beads for fluorescence enhanced, multiplexed protein detection with flow cytometry. Chem Sci 2014. [DOI: 10.1039/c4sc01206b] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The fluorescence enhancement of small molecule fluorophores was achieved on micro-beads through gold nano-island coating, enabling the detection of low-abundant protein biomarkers.
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Affiliation(s)
- Bo Zhang
- Department of Chemistry
- Stanford University
- Stanford, USA
| | - Jiang Yang
- Department of Chemistry
- Stanford University
- Stanford, USA
| | - Yingping Zou
- College of Chemistry and Chemical Engineering
- Central South University
- Changsha 410083, China
| | - Ming Gong
- Department of Chemistry
- Stanford University
- Stanford, USA
| | - Hui Chen
- Department of Chemistry
- Stanford University
- Stanford, USA
| | - Guosong Hong
- Department of Chemistry
- Stanford University
- Stanford, USA
| | | | - Xiaoyang Li
- Department of Chemistry
- Stanford University
- Stanford, USA
| | | | - Changxin Chen
- Department of Chemistry
- Stanford University
- Stanford, USA
| | - Hongjie Dai
- Department of Chemistry
- Stanford University
- Stanford, USA
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29
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Smurthwaite CA, Hilton BJ, O'Hanlon R, Stolp ZD, Hancock BM, Abbadessa D, Stotland A, Sklar LA, Wolkowicz R. Fluorescent genetic barcoding in mammalian cells for enhanced multiplexing capabilities in flow cytometry. Cytometry A 2013; 85:105-13. [DOI: 10.1002/cyto.a.22406] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 10/01/2013] [Accepted: 10/04/2013] [Indexed: 01/19/2023]
Affiliation(s)
| | - Brett J. Hilton
- Department of Biology; San Diego State University; San Diego California 92182
| | - Ryan O'Hanlon
- Department of Biology; San Diego State University; San Diego California 92182
| | - Zachary D. Stolp
- Department of Biology; San Diego State University; San Diego California 92182
| | - Bryan M. Hancock
- Department of Biology; San Diego State University; San Diego California 92182
| | - Darin Abbadessa
- Department of Biology; San Diego State University; San Diego California 92182
| | - Aleksandr Stotland
- Department of Biology; San Diego State University; San Diego California 92182
| | - Larry A. Sklar
- UNM Center for Molecular Discovery; University of New Mexico School of Medicine; Albuquerque New Mexico 87131
- Department of Pathology; University of New Mexico School of Medicine; Albuquerque New Mexico 87131
| | - Roland Wolkowicz
- Department of Biology; San Diego State University; San Diego California 92182
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30
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Alsaif M, Haenisch F, Guest PC, Rahmoune H, Bahn S. Challenges in drug target discovery in bipolar disorder. Expert Opin Ther Targets 2013; 17:565-77. [PMID: 23419165 DOI: 10.1517/14728222.2013.771169] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
INTRODUCTION Misdiagnosis and subsequent inappropriate treatment of patients with bipolar disorder (BD) can worsen their clinical condition and outcome. AREAS COVERED This review focuses on the therapeutic targets which have been implicated in BD, including the glycogen synthase kinase 3 (GSK-3) and phosphoinositide signaling pathways. In addition, evidence is presented for potential new molecular strategies which involve targeting neuropeptide-converting endopeptidases, glutamatergic excitotoxicity, insulin signaling and dysfunctions in mitochondrial metabolism. Current limitations in study design, molecular platforms, preclinical and cellular models in the context of BD drug target discovery, suggest that there are many areas for improvement. EXPERT OPINION For the future outlook, this review outlines the importance of developments such as the use of BD patient-derived cellular models for providing better understanding of the BD etiology and robust translational drug screening tools in combination with developments in the fields of bioinformatics and systems biology.
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Affiliation(s)
- Murtada Alsaif
- University of Cambridge, Institute of Biotechnology, Department of Chemical Engineering and Biotechnology , Tennis Court Road, Cambridge, CB2 1QT, Cambridgeshire, UK
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31
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Abstract
Since its birth in the late 1980s, the field of microfluidics has continued to mature, with a growing number of companies pursuing diagnostic applications. In 2009 the worldwide in vitro diagnostics market was estimated at >$40 billion USD, and microfluidic diagnostics are poised to reap a significant part of this market across a range of areas including laboratory diagnostics, point-of-care diagnostics, cancer diagnostics, and others. The potential economic advantages of microfluidics are numerous and compelling: lower reagent and/or sample volumes, lower equipment costs, improved portability, increased automation, and increased measurement speed. All of these factors may help put more information in the hands of doctors and patients sooner, enabling earlier disease detection and more tailored, effective treatments. This chapter reviews the microfluidic diagnostics commercial landscape and discusses potential commercialization challenges and opportunities.
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Affiliation(s)
- Lily Kim
- Wyss Institute of Biologically Inspired Engineering at Harvard University, Brookline, MA, USA,
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32
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Robinson JP, Patsekin V, Holdman C, Ragheb K, Sturgis J, Fatig R, Avramova LV, Rajwa B, Davisson VJ, Lewis N, Narayanan P, Li N, Qualls CW. High-throughput secondary screening at the single-cell level. ACTA ACUST UNITED AC 2012; 18:85-98. [PMID: 22968419 DOI: 10.1177/2211068212456978] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We have developed an automated system for drug screening using a single-cell-multiple functional response technology. The approach uses a semiautomated preparatory system, high-speed sample collection, and a unique analytical tool that provides instantaneous results for compound dilutions using 384-well plates. The combination of automation and rapid robotic sampling increases quality control and robustness. High-speed flow cytometry is used to collect single-cell results together with a newly defined analytical tool for extraction of IC(50) curves for multiple assays per cell. The principal advantage is the extreme speed of sample collection, with results from a 384-well plate being completed for both collection and data processing in less than 10 min. Using this approach, it is possible to extract detailed drug response information in a highly controlled fashion. The data are based on single-cell results, not populations. With simultaneous assays for different functions, it is possible to gain a more detailed understanding of each drug/compound interaction. Combined with integrated advanced data processing directly from raw data files, the process from sampling to analytical results is highly intuitive. Direct PubMed links allow review of drug structure and comparisons with similar compounds.
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Affiliation(s)
- J Paul Robinson
- Purdue University Cytometry Laboratories, Department of Basic Medical Sciences, Purdue University, West Lafayette, IN 47907, USA.
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33
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Chen J, Young SM, Allen C, Seeber A, Péli-Gulli MP, Panchaud N, Waller A, Ursu O, Yao T, Golden JE, Strouse JJ, Carter MB, Kang H, Bologa CG, Foutz TD, Edwards BS, Peterson BR, Aubé J, Werner-Washburne M, Loewith RJ, De Virgilio C, Sklar LA. Identification of a small molecule yeast TORC1 inhibitor with a multiplex screen based on flow cytometry. ACS Chem Biol 2012; 7:715-22. [PMID: 22260433 DOI: 10.1021/cb200452r] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
TOR (target of rapamycin) is a serine/threonine kinase, evolutionarily conserved from yeast to human, which functions as a fundamental controller of cell growth. The moderate clinical benefit of rapamycin in mTOR-based therapy of many cancers favors the development of new TOR inhibitors. Here we report a high-throughput flow cytometry multiplexed screen using five GFP-tagged yeast clones that represent the readouts of four branches of the TORC1 signaling pathway in budding yeast. Each GFP-tagged clone was differentially color-coded, and the GFP signal of each clone was measured simultaneously by flow cytometry, which allows rapid prioritization of compounds that likely act through direct modulation of TORC1 or proximal signaling components. A total of 255 compounds were confirmed in dose-response analysis to alter GFP expression in one or more clones. To validate the concept of the high-throughput screen, we have characterized CID 3528206, a small molecule most likely to act on TORC1 as it alters GFP expression in all five GFP clones in a manner analogous to that of rapamycin. We have shown that CID 3528206 inhibited yeast cell growth and that CID 3528206 inhibited TORC1 activity both in vitro and in vivo with EC(50)'s of 150 nM and 3.9 μM, respectively. The results of microarray analysis and yeast GFP collection screen further support the notion that CID 3528206 and rapamycin modulate similar cellular pathways. Together, these results indicate that the HTS has identified a potentially useful small molecule for further development of TOR inhibitors.
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Affiliation(s)
| | | | | | | | - Marie-Pierre Péli-Gulli
- Department of Biology, Division
of Biochemistry, University of Fribourg, CH-1700 Fribourg, Switzerland
| | - Nicolas Panchaud
- Department of Biology, Division
of Biochemistry, University of Fribourg, CH-1700 Fribourg, Switzerland
| | | | | | - Tuanli Yao
- University of Kansas Specialized
Chemistry Center, University of Kansas,
Lawrence, Kansas 66047, United States
| | - Jennifer E. Golden
- University of Kansas Specialized
Chemistry Center, University of Kansas,
Lawrence, Kansas 66047, United States
| | | | | | | | | | | | | | - Blake R. Peterson
- University of Kansas Specialized
Chemistry Center, University of Kansas,
Lawrence, Kansas 66047, United States
- Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas 66045, United
States
| | - Jeffrey Aubé
- University of Kansas Specialized
Chemistry Center, University of Kansas,
Lawrence, Kansas 66047, United States
- Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas 66045, United
States
| | | | | | - Claudio De Virgilio
- Department of Biology, Division
of Biochemistry, University of Fribourg, CH-1700 Fribourg, Switzerland
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34
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Abstract
High-throughput screening (HTS) is a key process used in drug discovery to identify hits from compound libraries that may become leads for medicinal chemistry optimization. This updated overview discusses the utilization of compound libraries, compounds derived from combinatorial and parallel synthesis campaigns and natural product sources; creation of mother and daughter plates; and compound storage, handling, and bar coding in HTS. The unit also presents an overview of established and emerging assay technologies (i.e., time-resolved fluorescence, fluorescence polarization, fluorescence-correlation spectroscopy, functional whole cell assays, and high-content assays) and their integration in automation hardware and IT systems. This revised unit provides updated descriptions of state-of-the-art instrumentation and technologies in this rapidly changing environment. The section on assay methodologies now also covers enzyme complementation assays and methods for high-throughput screening of ion channel activities. Finally, a section on criteria for assay robustness is included discussing the Z'-factor, which is now a widely accepted criterion for evaluation and validation of high throughput screening assays.
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Affiliation(s)
- Michael Entzeroth
- Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), Singapore
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35
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Cornelissen F, Cik M, Gustin E. Phaedra, a Protocol-Driven System for Analysis and Validation of High-Content Imaging and Flow Cytometry. ACTA ACUST UNITED AC 2012; 17:496-506. [DOI: 10.1177/1087057111432885] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
High-content screening has brought new dimensions to cellular assays by generating rich data sets that characterize cell populations in great detail and detect subtle phenotypes. To derive relevant, reliable conclusions from these complex data, it is crucial to have informatics tools supporting quality control, data reduction, and data mining. These tools must reconcile the complexity of advanced analysis methods with the user-friendliness demanded by the user community. After review of existing applications, we realized the possibility of adding innovative new analysis options. Phaedra was developed to support workflows for drug screening and target discovery, interact with several laboratory information management systems, and process data generated by a range of techniques including high-content imaging, multicolor flow cytometry, and traditional high-throughput screening assays. The application is modular and flexible, with an interface that can be tuned to specific user roles. It offers user-friendly data visualization and reduction tools for HCS but also integrates Matlab for custom image analysis and the Konstanz Information Miner (KNIME) framework for data mining. Phaedra features efficient JPEG2000 compression and full drill-down functionality from dose-response curves down to individual cells, with exclusion and annotation options, cell classification, statistical quality controls, and reporting.
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Affiliation(s)
- Frans Cornelissen
- Janssen Research & Development, a Division of Janssen Pharmaceutica NV, Beerse, Belgium
| | - Miroslav Cik
- Janssen Research & Development, a Division of Janssen Pharmaceutica NV, Beerse, Belgium
| | - Emmanuel Gustin
- Janssen Research & Development, a Division of Janssen Pharmaceutica NV, Beerse, Belgium
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36
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Mao H, Graziano J, Smider VV. Arrayed protein library technology for therapeutic biologic discovery. Biotechnol Genet Eng Rev 2012; 28:131-45. [DOI: 10.5661/bger-28-131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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37
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Abstract
The uptake of nanoparticles by cells is an important factor to assess nanotoxicity. In general, the nanoparticles taken up by the cells have been identified by transmission electron microscope, inductively coupled plasma mass spectrometry, etc.; however, the methods required an immense amount of time and effort. Flow cytometry (FCM) has been used and developed in the fields of biochemistry and clinical hematology, and has advantages to analyze thousands of cells in seconds. We recently clarified that the side-scatter(ed) light of FCM could be used as a guide to measure uptake potential of nanoparticles. Here, we describe the protocol for screening of the uptake potential of nanoparticles using FCM.
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Affiliation(s)
- Yuko Ibuki
- Institute for Environmental Sciences, University of Shizuoka, Shizuoka-shi, Japan.
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38
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Roy A, McDonald PR, Sittampalam S, Chaguturu R. Open access high throughput drug discovery in the public domain: a Mount Everest in the making. Curr Pharm Biotechnol 2011; 11:764-78. [PMID: 20809896 DOI: 10.2174/138920110792927757] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Accepted: 03/15/2010] [Indexed: 01/24/2023]
Abstract
High throughput screening (HTS) facilitates screening large numbers of compounds against a biochemical target of interest using validated biological or biophysical assays. In recent years, a significant number of drugs in clinical trails originated from HTS campaigns, validating HTS as a bona fide mechanism for hit finding. In the current drug discovery landscape, the pharmaceutical industry is embracing open innovation strategies with academia to maximize their research capabilities and to feed their drug discovery pipeline. The goals of academic research have therefore expanded from target identification and validation to probe discovery, chemical genomics, and compound library screening. This trend is reflected in the emergence of HTS centers in the public domain over the past decade, ranging in size from modestly equipped academic screening centers to well endowed Molecular Libraries Probe Centers Network (MLPCN) centers funded by the NIH Roadmap initiative. These centers facilitate a comprehensive approach to probe discovery in academia and utilize both classical and cutting-edge assay technologies for executing primary and secondary screening campaigns. The various facets of academic HTS centers as well as their implications on technology transfer and drug discovery are discussed, and a roadmap for successful drug discovery in the public domain is presented. New lead discovery against therapeutic targets, especially those involving the rare and neglected diseases, is indeed a Mount Everestonian size task, and requires diligent implementation of pharmaceutical industry's best practices for a successful outcome.
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Affiliation(s)
- Anuradha Roy
- High Throughput Screening Laboratory, Institute for Advancing Medical Innovations, University of Kansas, Lawrence, KS 66047, USA
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39
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Chen J, Carter MB, Edwards BS, Cai H, Sklar LA. High throughput flow cytometry based yeast two-hybrid array approach for large-scale analysis of protein-protein interactions. Cytometry A 2011; 81:90-8. [PMID: 21954189 DOI: 10.1002/cyto.a.21144] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 07/25/2011] [Accepted: 08/27/2011] [Indexed: 02/03/2023]
Abstract
The analysis of protein-protein interactions is a key focus of proteomics efforts. The yeast two-hybrid system (Y2H) has been the most commonly used method in genome-wide searches for protein interaction partners. However, the throughput of the current yeast two-hybrid array approach is hampered by the involvement of the time-consuming LacZ assay and/or the incompatibility of liquid handling automation due to the requirement for selection of colonies/diploids on agar plates. To facilitate large-scale Y2H assays, we report a novel array approach by coupling a GFP reporter based Y2H system with high throughput flow cytometry that enables the processing of a 96-well plate in as little as 3 min. In this approach, the yEGFP reporter has been established in both AH109 (MATa) and Y187 (MATα) reporter cells. It not only allows the generation of two copies of GFP reporter genes in diploid cells, but also allows the convenient determination of self-activators generated from both bait and prey constructs by flow cytometry. We demonstrate a Y2H array assay procedure that is carried out completely in liquid media in 96-well plates by mating bait and prey cells in liquid YPD media, selecting the diploids containing positive interaction pairs in selective media and analyzing the GFP reporter directly by flow cytometry. We have evaluated this flow cytometry based array procedure by showing that the interaction of the positive control pair P53/T is able to be reproducibly detected at 72 hr postmating compared with the negative control pairs. We conclude that our flow cytometry based yeast two-hybrid approach is robust, convenient, quantitative, and is amenable to large-scale analysis using liquid-handling automation.
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Affiliation(s)
- Jun Chen
- University of New Mexico Center for Molecular Discovery, Albuquerque, New Mexico 87131, USA.
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40
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Werner M, Merenda F, Piguet J, Salathé RP, Vogel H. Microfluidic array cytometer based on refractive optical tweezers for parallel trapping, imaging and sorting of individual cells. LAB ON A CHIP 2011; 11:2432-9. [PMID: 21655617 DOI: 10.1039/c1lc20181f] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Analysis of genetic and functional variability in populations of living cells requires experimental techniques capable of monitoring cellular processes such as cell signaling of many single cells in parallel while offering the possibility to sort interesting cell phenotypes for further investigations. Although flow cytometry is able to sequentially probe and sort thousands of cells per second, dynamic processes cannot be experimentally accessed on single cells due to the sub-second sampling time. Cellular dynamics can be measured by image cytometry of surface-immobilized cells, however, cell sorting is complicated under these conditions due to cell attachment. We here developed a cytometric tool based on refractive multiple optical tweezers combined with microfluidics and optical microscopy. We demonstrate contact-free immobilization of more than 200 yeast cells into a high-density array of optical traps in a microfluidic chip. The cell array could be moved to specific locations of the chip enabling us to expose in a controlled manner the cells to reagents and to analyze the responses of individual cells in a highly parallel format using fluorescence microscopy. We further established a method to sort single cells within the microfluidic device using an additional steerable optical trap. Ratiometric fluorescence imaging of intracellular pH of trapped yeast cells allowed us on the one hand to measure the effect of the trapping laser on the cells' viability and on the other hand to probe the dynamic response of the cells upon glucose sensing.
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Affiliation(s)
- Michael Werner
- Laboratory of Physical Chemistry of Polymers and Membranes, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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41
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Green CL, Brown L, Stewart JJ, Xu Y, Litwin V, Mc Closkey TW. Recommendations for the validation of flow cytometric testing during drug development: I instrumentation. J Immunol Methods 2011; 363:104-19. [DOI: 10.1016/j.jim.2010.07.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Revised: 07/12/2010] [Accepted: 07/12/2010] [Indexed: 10/25/2022]
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42
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Covey TM, Putta S, Cesano A. Single cell network profiling (SCNP): mapping drug and target interactions. Assay Drug Dev Technol 2010; 8:321-43. [PMID: 20158439 DOI: 10.1089/adt.2009.0251] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Measuring target coverage of small molecule inhibitors is paramount-first, for selection of molecules to progress through the drug development process and second, once a candidate drug moves to clinical testing, for guiding dose/schedule selection. Single cell network profiling (SCNP) using multiparameter flow cytometry can measure compound effects on multiple signaling cascades in a cell-type-specific manner. We applied SCNP to a panel of compounds with reported inhibitory effects on Jak/Stat signaling using a novel system where modulation of multiple signaling cascades are simultaneously measured in discrete cell subsets in whole (ie, unfractionated) blood. Jak2 vs. Jak3 selectivity as well as "off-target" effects on other cell signaling pathways were measured using a combination of cytokines that target different white blood cell subsets, namely GM-CSF (monocytes/granulocytes), IL-2 (T cells), and CD40L (B cells). The compounds were then rank-ordered by potency and selectivity against the different pathways tested. Notably, SCNP performed in whole unfractionated blood compared to fractionated peripheral blood mononuclear cells (PBMC) from the same donors revealed potency loss for all compounds, with one exception. These studies show that SCNP can be used to efficiently measure a drug candidate's potency and selectivity in a physiologically relevant environment (eg, whole blood) and that robust IC(50) are attainable from rare subpopulations (<100 cells). The ability to generate in vitro IC(50) measurements in whole blood can be used not only for the preclinical selection of lead molecules, but also to determine the target plasma concentration for clinical studies and to measure target coverage after drug administration in early phase clinical trials. Knowledge of the compound plasma concentration necessary to achieve biochemical coverage permits rational design of clinical trials based on biologically active dose vs. the traditional maximum tolerated dose (MTD) design, which is better suited for cytotoxic, nontargeted drugs.
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Affiliation(s)
- Todd M Covey
- Nodality Inc., South San Francisco, California, USA
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43
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Cheung KC, Di Berardino M, Schade-Kampmann G, Hebeisen M, Pierzchalski A, Bocsi J, Mittag A, Tárnok A. Microfluidic impedance-based flow cytometry. Cytometry A 2010; 77:648-66. [PMID: 20583276 DOI: 10.1002/cyto.a.20910] [Citation(s) in RCA: 164] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Microfabricated flow cytometers can detect, count, and analyze cells or particles using microfluidics and electronics to give impedance-based characterization. Such systems are being developed to provide simple, low-cost, label-free, and portable solutions for cell analysis. Recent work using microfabricated systems has demonstrated the capability to analyze micro-organisms, erythrocytes, leukocytes, and animal and human cell lines. Multifrequency impedance measurements can give multiparametric, high-content data that can be used to distinguish cell types. New combinations of microfluidic sample handling design and microscale flow phenomena have been used to focus and position cells within the channel for improved sensitivity. Robust designs will enable focusing at high flowrates while reducing requirements for control over multiple sample and sheath flows. Although microfluidic impedance-based flow cytometers have not yet or may never reach the extremely high throughput of conventional flow cytometers, the advantages of portability, simplicity, and ability to analyze single cells in small populations are, nevertheless, where chip-based cytometry can make a large impact.
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Affiliation(s)
- Karen C Cheung
- Department of Electrical and Computer Engineering, University of British Columbia, Vancouver, Canada.
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44
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Arterburn JB, Oprea TI, Prossnitz ER, Edwards BS, Sklar LA. Discovery of selective probes and antagonists for G-protein-coupled receptors FPR/FPRL1 and GPR30. Curr Top Med Chem 2010; 9:1227-36. [PMID: 19807662 DOI: 10.2174/156802609789753608] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Accepted: 07/29/2009] [Indexed: 01/04/2023]
Abstract
Recent technological advances in flow cytometry provide a versatile platform for high throughput screening of compound libraries coupled with high-content biological testing and drug discovery. The G protein-coupled receptors (GPCRs) constitute the largest class of signaling molecules in the human genome with frequent roles in disease pathogenesis, yet many examples of orphan receptors with unknown ligands remain. The complex biology and potential for drug discovery within this class provide strong incentives for chemical biology approaches seeking to develop small molecule probes to facilitate elucidation of mechanistic pathways and enable specific manipulation of the activity of individual receptors. We have initiated small molecule probe development projects targeting two distinct families of GPCRs: the formylpeptide receptors (FPR/FPRL1) and G protein-coupled estrogen receptor (GPR30). In each case the assay for compound screening involved the development of an appropriate small molecule fluorescent probe, and the flow cytometry platform provided inherently biological rich assays that enhanced the process of identification and optimization of novel antagonists. The contributions of cheminformatics analysis tools, virtual screening, and synthetic chemistry in synergy with the biomolecular screening program have yielded valuable new chemical probes with high binding affinity, selectivity for the targeted receptor, and potent antagonist activity. This review describes the discovery of novel small molecule antagonists of FPR and FPRL1, and GPR30, and the associated characterization process involving secondary assays, cell based and in vivo studies to define the selectivity and activity of the resulting chemical probes.
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Affiliation(s)
- Jeffrey B Arterburn
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM 88003, USA.
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45
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Früh V, IJzerman AP, Siegal G. How to catch a membrane protein in action: a review of functional membrane protein immobilization strategies and their applications. Chem Rev 2010; 111:640-56. [PMID: 20831158 DOI: 10.1021/cr900088s] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Virginie Früh
- Division of Medicinal Chemistry, Leiden Amsterdam Center for Drug Research, Leiden University, The Netherlands
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46
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Abstract
IMPORTANCE OF THE FIELD Flow cytometry is considered today as a mature technology. Recently, it has become an accurate tool for screening applications. Yet, not many studies have been published emphasizing flow cytometry as a tool of choice for drug screening except multiplex bead assay. AREAS COVERED IN THIS REVIEW Scanning the literature for technology breakouts in screening by flow is not an easy task. When a private industry has an accurate and fast screening technology on hands, why should they make public a tool precious for their screening applications? On the European academic side, there are regrettably few grants to help develop and publish screening methodologies. So, a less scientific way to find out is a close market survey seeking new instruments and associated kits or new methods. From here, can one expect flow cytometry to be a tool with new potential for drug discovery? WHAT THE READER WILL GAIN As the machines are getting simpler to use, a need for plug-and-analyze software has emerged. New analysis tools remain an important step as they will permit to analyze and compare several parameters in a multi-well format simultaneously and this for several cell types for cytomics: a multiparametric, dynamic approach to cell research as cytomics has a practical role to play in drug discovery within the immediate limitations of cell-based analyses. TAKE HOME MESSAGE Developing new software with multi-well comparison capabilities and most importantly real-time interaction on cytograms can easily circumvent the lack of fluorescent channels on small bench top machines.
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Affiliation(s)
- Jean Peluso
- Laboratoire d'Innovation Thérapeutique, Faculté de Pharmacie, Université de Strasbourg, UMR CNRS 7200, 74, Route du Rhin, B.P. 24, 67401 Illkirch, Cedex, France +33 3 68 85 42 71 ; +33 3 68 85 43 10 ;
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47
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Abstract
Cell-based assays represent approximately half of all high-throughput screens currently performed. Here, we review in brief the history and status of high-throughput screening (HTS), and summarize some of the challenges and benefits associated with the use of cell-based assays in HTS. Approaches for successful experimental design and execution of cell-based screens are introduced, including strategies for assay development, implementation of primary and secondary screens, and target identification. In doing so, we hope to provide a comprehensive review of the cell-based HTS process and an introduction to the methodologies and techniques used.
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Affiliation(s)
- W Frank An
- Chemical Biology Platform, The Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA.
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An Interview with Larry Sklar, Ph.D., ,and Bruce Edwards, Ph.D. . Assay Drug Dev Technol 2010; 8:397-407. [DOI: 10.1089/adt.2010.0804.pr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Randlev B, Huang LC, Watatsu M, Marcus M, Lin A, Shih SJ. Validation of a quantitative flow cytometer assay for monitoring HER-2/neu expression level in cell-based cancer immunotherapy products. Biologicals 2010; 38:249-59. [PMID: 20080049 DOI: 10.1016/j.biologicals.2009.12.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2009] [Revised: 10/08/2009] [Accepted: 12/02/2009] [Indexed: 11/26/2022] Open
Abstract
GVAX immunotherapy for prostate cancer is comprised of two genetically modified prostate cancer cell lines, CG1940 and CG8711, engineered to secrete granulocyte macrophage-colony-stimulating factor. As part of the matrix of potency assays, CG1940 and CG8711 are tested for the expression level of cell surface HER-2/neu using a quantitative flow cytometer assay. This assay reports the antibody binding capacity value of the cells as a measure of HER-2/neu expression using cells immediately after thawing from cryogenic storage. With optimized cell handling and staining procedure and appropriate system suitability controls, the assay was validated as a quantitative assay. The validation results showed that assay accuracy, specificity, precision, linearity, and range were suitable for the intended use of ensuring lot-to-lot consistency of HER-2/neu expression. Assay robustness was demonstrated using design of experiments that evaluated critical assay parameters. Finally, the assay was successfully transferred to a current good manufacturing practice Quality Control laboratory in a separate facility. Since the overall precision of this assay is better than that of ELISA methods and it can be performed with ease and high throughput, quantitative flow cytometer-based assays may be an appropriate immunological assay platform for Quality Control laboratories for characterization and release of cell-based therapies.
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Affiliation(s)
- Britta Randlev
- Assay Development, Cell Genesys, Inc., 500 Forbes Boulevard, South San Francisco, CA 94404, USA
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Prowse ABJ, Wilson J, Osborne GW, Gray PP, Wolvetang EJ. Multiplexed staining of live human embryonic stem cells for flow cytometric analysis of pluripotency markers. Stem Cells Dev 2009; 18:1135-40. [PMID: 19397457 DOI: 10.1089/scd.2009.0080] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Use of flow cytometry to detect pluripotency markers on or in human embryonic stem cells (hESCs) is a powerful analytical tool. However, current staining methodologies for high-content analysis of large numbers of samples utilize large quantities of primary and secondary antibodies, are time consuming, and may suffer from sample-to-sample variability. To circumvent these issues, we have developed a reproducible, quick, and cost-effective method of staining 12 populations of hESCs grown under different conditions by labeling each with a unique optical signature (UOS). The UOS for each population is achieved by combining different combinations and concentrations of 3 esterase activated, live cell, fluorescent indicators. The individually stained populations are then combined and an aliquot of the hESC samples stained for pluripotency or other markers of interest in the far-red region of the spectrum. Based on the unique fluorescent intensity and emission wavelengths of each population, the characteristics of each population are decoded in software after flow cytometric analysis. We have validated both our staining procedure and decoding methods by mixing populations of differentiated and undifferentiated hESCs and successfully quantifying differences in the pluripotency markers SSEA-4, Tra-1-60, GCTM2, and CD9 between the 12 different populations. Our multiplexing approach allows for the addition of internal controls and reduces sample-to-sample variation, while offering a significant reduction in time and reagent consumption. We anticipate that this method will be of great benefit to laboratories conducting high-content flow cytometric analysis of hESCs.
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Affiliation(s)
- Andrew B J Prowse
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
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