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Zhou L, Huang G, Wang S, Wu J, Lee WG, Chen Y, Xu F, Lu T. Advances in cell-based biosensors using three-dimensional cell-encapsulating hydrogels. Biotechnol J 2012; 6:1466-76. [PMID: 22162496 DOI: 10.1002/biot.201100098] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Cell-based biosensors (CBBs) have emerged as promising biotechnical tools whereby various cell types can be used as basic sensing units to detect external stimuli. Specifically, CBBs have been applied in environmental monitoring, drug screening, clinical diagnosis and biosecurity. For these applications, CBBs offer several advantages over conventional molecular-based biosensors or living animal-based approaches, such as the capability to better mimic physiological situations, to enhance detection specificity and sensitivity, and to detect unknown compounds and toxins. On the other hand, existing CBBs suffer from several limitations, such as weak cell-substrate attachment, two-dimensional (2D) cell microenvironment, and limited shelf life. An emerging method for scaffold-free three-dimensional (3D) cell culture uses hydrogels to encapsulate cells. Advances in novel biomaterials and nano/microscale technologies have enabled encapsulation of cells in hydrogels to fabricate 3D CBBs, which hold great potential for addressing the limitation in existing 2D CBBs. Here, we present an overview of the emerging hydrogel-based CBBs, their applications in pathogen/toxin detection, drug screening and screening of cell-biomaterials interaction, and the associated challenges and potential solutions.
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Affiliation(s)
- Lihong Zhou
- Biomedical Engineering and Biomechanics Center, Xi'an Jiaotong University, Xi'an, P R China
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52
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Hvastkovs EG, Schenkman JB, Rusling JF. Metabolic toxicity screening using electrochemiluminescence arrays coupled with enzyme-DNA biocolloid reactors and liquid chromatography-mass spectrometry. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2012; 5:79-105. [PMID: 22482786 PMCID: PMC3399491 DOI: 10.1146/annurev.anchem.111808.073659] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
New chemicals or drugs must be guaranteed safe before they can be marketed. Despite widespread use of bioassay panels for toxicity prediction, products that are toxic to a subset of the population often are not identified until clinical trials. This article reviews new array methodologies based on enzyme/DNA films that form and identify DNA-reactive metabolites that are indicators of potentially genotoxic species. This molecularly based methodology is designed in a rapid screening array that utilizes electrochemiluminescence (ECL) to detect metabolite-DNA reactions, as well as biocolloid reactors that provide the DNA adducts and metabolites for liquid chromatography-mass spectrometry (LC-MS) analysis. ECL arrays provide rapid toxicity screening, and the biocolloid reactor LC-MS approach provides a valuable follow-up on structure, identification, and formation rates of DNA adducts for toxicity hits from the ECL array screening. Specific examples using this strategy are discussed. Integration of high-throughput versions of these toxicity-screening methods with existing drug toxicity bioassays should allow for better human toxicity prediction as well as more informed decision making regarding new chemical and drug candidates.
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Affiliation(s)
- Eli G. Hvastkovs
- Department of Chemistry, East Carolina University, Greenville, North Carolina 27858;
| | - John B. Schenkman
- Department of Cell Biology, University of Connecticut Health Center, Farmington, Connecticut 06269;
| | - James F. Rusling
- Department of Cell Biology, University of Connecticut Health Center, Farmington, Connecticut 06269;
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269;
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53
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Miniaturized, microarray-based assays for chemical proteomic studies of protein function. Methods Mol Biol 2012; 800:133-62. [PMID: 21964787 DOI: 10.1007/978-1-61779-349-3_10] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Systematic analysis of protein and enzyme function typically requires scale-up of protein expression and purification prior to assay development; this can often be limiting. Miniaturization of assays provides an alternative approach, but simple, generic methods are in short supply. Here we show how custom microarrays can be adapted to this purpose. We discuss the different routes to array fabrication and describe in detail one facile approach in which the purification and immobilization procedures are combined into a single step, significantly simplifying the array fabrication process. We illustrate this approach by reference to the creation of arrays of human protein kinases and of human cytochrome P450s. We discuss methods for both ligand-binding and turnover-based assays, as well as data analysis on such arrays.
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Szymański P, Markowicz M, Mikiciuk-Olasik E. Adaptation of high-throughput screening in drug discovery-toxicological screening tests. Int J Mol Sci 2011; 13:427-52. [PMID: 22312262 PMCID: PMC3269696 DOI: 10.3390/ijms13010427] [Citation(s) in RCA: 179] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Revised: 12/11/2011] [Accepted: 12/19/2011] [Indexed: 11/23/2022] Open
Abstract
High-throughput screening (HTS) is one of the newest techniques used in drug design and may be applied in biological and chemical sciences. This method, due to utilization of robots, detectors and software that regulate the whole process, enables a series of analyses of chemical compounds to be conducted in a short time and the affinity of biological structures which is often related to toxicity to be defined. Since 2008 we have implemented the automation of this technique and as a consequence, the possibility to examine 100,000 compounds per day. The HTS method is more frequently utilized in conjunction with analytical techniques such as NMR or coupled methods e.g., LC-MS/MS. Series of studies enable the establishment of the rate of affinity for targets or the level of toxicity. Moreover, researches are conducted concerning conjugation of nanoparticles with drugs and the determination of the toxicity of such structures. For these purposes there are frequently used cell lines. Due to the miniaturization of all systems, it is possible to examine the compound's toxicity having only 1-3 mg of this compound. Determination of cytotoxicity in this way leads to a significant decrease in the expenditure and to a reduction in the length of the study.
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Affiliation(s)
- Paweł Szymański
- Department of Pharmaceutical Chemistry and Drug Analysis, Medical University of Lodz, Muszyńskiego 1, Lodz 90-151, Poland; E-Mails: (P.S.); (E.M.-O.)
| | - Magdalena Markowicz
- Department of Pharmaceutical Chemistry and Drug Analysis, Medical University of Lodz, Muszyńskiego 1, Lodz 90-151, Poland; E-Mails: (P.S.); (E.M.-O.)
| | - Elżbieta Mikiciuk-Olasik
- Department of Pharmaceutical Chemistry and Drug Analysis, Medical University of Lodz, Muszyńskiego 1, Lodz 90-151, Poland; E-Mails: (P.S.); (E.M.-O.)
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55
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LI HAIRUI, KOCHHAR JASPREETSINGH, PAN JING, CHAN SUIYUNG, KANG LIFENG. NANO/MICROSCALE TECHNOLOGIES FOR DRUG DELIVERY. J MECH MED BIOL 2011. [DOI: 10.1142/s021951941100406x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Nano- and microscale technologies have made a marked impact on the development of drug delivery systems. The loading efficiency and particle size of nano/micro particles can be better controlled with these new technologies than conventional methods. Moreover, drug delivery systems are moving from simple particles to smart particles and devices with programmable functions. These technologies are also contributing to in vitro and in vivo drug testing, which are important to evaluate drug delivery systems. For in vitro tests, lab-on-a-chip models are potentially useful as alternatives to animal models. For in vivo test, nano/micro-biosensors are developed for testing chemicals and biologics with high sensitivity and selectivity. Here, we review the recent development of nanoscale and microscale technologies in drug delivery including drug delivery systems, in vitro and in vivo tests.
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Affiliation(s)
- HAIRUI LI
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore 117543, Singapore
| | - JASPREET SINGH KOCHHAR
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore 117543, Singapore
| | - JING PAN
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore 117543, Singapore
| | - SUI YUNG CHAN
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore 117543, Singapore
| | - LIFENG KANG
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore 117543, Singapore
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56
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Lan SF, Starly B. Alginate based 3D hydrogels as an in vitro co-culture model platform for the toxicity screening of new chemical entities. Toxicol Appl Pharmacol 2011; 256:62-72. [DOI: 10.1016/j.taap.2011.07.013] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2011] [Revised: 07/18/2011] [Accepted: 07/21/2011] [Indexed: 12/16/2022]
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57
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Hsiung LC, Chiang CL, Wang CH, Huang YH, Kuo CT, Cheng JY, Lin CH, Wu V, Chou HY, Jong DS, Lee H, Wo AM. Dielectrophoresis-based cellular microarray chip for anticancer drug screening in perfusion microenvironments. LAB ON A CHIP 2011; 11:2333-42. [PMID: 21629948 DOI: 10.1039/c1lc20147f] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
We present a dielectrophoresis (DEP)-based cellular microarray chip for cell-based anticancer drug screening in perfusion microenvironments. Human breast cancer cells, MCF7, were seeded into the chip and patterned via DEP forces onto the planar interdigitated ring electrode (PIRE) arrays. Roughly, only one third of the cell amount was required for the chip compared to that for a 96-well plate control. Drug concentrations (cisplatin or docetaxel) were stably generated by functional integration of a concentration gradient generator (CGG) and an anti-crosstalk valve (ACV) to treat cells for 24 hours. Cell viability was quantified using a dual staining method. Results of cell patterning show substantial uniformity of patterned cells (92 ± 5 cells per PIRE). Furthermore, after 24 hour drug perfusion, no statistical significance in dose-responses between the chip and the 96-well plate controls was found. The IC(50) value from the chip also concurred with the values from the literature. Moreover, the perfusion culture exhibited reproducibility of drug responses of cells on different PIREs in the same chamber. The chip would enable applications where cells are of limited supply, and supplement microfluidic perfusion cultures for clinical practices.
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Affiliation(s)
- Lo-Chang Hsiung
- Institute of Applied Mechanics, National Taiwan University, Taipei, Taiwan
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58
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Xu F, Wu J, Wang S, Durmus NG, Gurkan UA, Demirci U. Microengineering methods for cell-based microarrays and high-throughput drug-screening applications. Biofabrication 2011; 3:034101. [PMID: 21725152 DOI: 10.1088/1758-5082/3/3/034101] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Screening for effective therapeutic agents from millions of drug candidates is costly, time consuming, and often faces concerns due to the extensive use of animals. To improve cost effectiveness, and to minimize animal testing in pharmaceutical research, in vitro monolayer cell microarrays with multiwell plate assays have been developed. Integration of cell microarrays with microfluidic systems has facilitated automated and controlled component loading, significantly reducing the consumption of the candidate compounds and the target cells. Even though these methods significantly increased the throughput compared to conventional in vitro testing systems and in vivo animal models, the cost associated with these platforms remains prohibitively high. Besides, there is a need for three-dimensional (3D) cell-based drug-screening models which can mimic the in vivo microenvironment and the functionality of the native tissues. Here, we present the state-of-the-art microengineering approaches that can be used to develop 3D cell-based drug-screening assays. We highlight the 3D in vitro cell culture systems with live cell-based arrays, microfluidic cell culture systems, and their application to high-throughput drug screening. We conclude that among the emerging microengineering approaches, bioprinting holds great potential to provide repeatable 3D cell-based constructs with high temporal, spatial control and versatility.
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Affiliation(s)
- Feng Xu
- Department of Medicine, Demirci Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Center for Biomedical Engineering, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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59
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Kwon CH, Wheeldon I, Kachouie NN, Lee SH, Bae H, Sant S, Fukuda J, Kang JW, Khademhosseini A. Drug-eluting microarrays for cell-based screening of chemical-induced apoptosis. Anal Chem 2011; 83:4118-25. [PMID: 21476591 PMCID: PMC3105158 DOI: 10.1021/ac200267t] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Traditional high-throughput screening (HTS) is carried out in centralized facilities that require extensive robotic liquid and plate handling equipment. This model of HTS is restrictive as such facilities are not accessible to many researchers. We have designed a simple microarray platform for cell-based screening that can be carried out at the benchtop. The device creates a microarray of 2100 individual cell-based assays in a standard microscope slide format. A microarray of chemical-laden hydrogels addresses a matching array of cell-laden microwells thus creating a microarray of sealed microscale cell cultures each with unique conditions. We demonstrate the utility of the device by screening the extent of apoptosis and necrosis in MCF-7 breast cancer cells in response to exposure to a small library of chemical compounds. From a set of screens we produced a rank order of chemicals that preferentially induce apoptosis over necrosis in MCF-7 cells. Treatment with doxorubicin induced high levels of apoptosis in comparison with staurosporine, ethanol, and hydrogen peroxide, whereas treatment with 100 μM ethanol induced minimal apoptosis with high levels of necrosis. We anticipate broad application of the device for various research and discovery applications as it is easy to use, scalable, and can be fabricated and operated with minimal peripheral equipment.
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Affiliation(s)
- Cheong Hoon Kwon
- Center for Biomedical Engineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Ian Wheeldon
- Center for Biomedical Engineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115
| | - Nezamoddin N. Kachouie
- Center for Biomedical Engineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Seung Hwan Lee
- Center for Biomedical Engineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Hojae Bae
- Center for Biomedical Engineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Shilpa Sant
- Center for Biomedical Engineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115
| | - Junji Fukuda
- Graduate School of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Japan 305-8573
| | - Jeong Won Kang
- Department of Chemical and Biological Engineering, Korea University, 5-Ga Anam-Dong, Sungbuk-Ku, Seoul, South Korea 136-701
| | - Ali Khademhosseini
- Center for Biomedical Engineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115
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Abstract
In the past decade, the tendency to move from a global, one-size-fits-all treatment philosophy to personalized medicine is based, in part, on the nuanced differences and sub-classifications of disease states. Our knowledge of these varied states stems from not only the ability to diagnose, classify, and perform experiments on cell populations as a whole, but also from new technologies that allow interrogation of cell populations at the individual cell level. Such departures from conventional thinking are driven by the recognition that clonal cell populations have numerous activities that manifest as significant levels of non-genetic heterogeneity. Clonal populations by definition originate from a single genetic origin so are regarded as having a high level of homogeneity as compared to genetically distinct cell populations. However, analysis at the single cell level has revealed a different phenomenon; cells and organisms require an inherent level of non-genetic heterogeneity to function properly, and in some cases, to survive. The growing understanding of this occurrence has lead to the development of methods to monitor, analyze, and better characterize the heterogeneity in cell populations. Following the trend of DNA- and protein microarrays, platforms capable of simultaneously monitoring each cell in a population have been developed. These cellular microarray platforms and other related formats allow for continuous monitoring of single live cells and simultaneously generate individual cell and average population data that are more descriptive and information-rich than traditional bulk methods. These technological advances have helped develop a better understanding of the intricacies associated with biological processes and afforded greater insight into complex biological systems. The associated instruments, techniques, and reagents now allow for highly multiplexed analyses, which enable multiple cellular activities, processes, or pathways to be monitored simultaneously. This critical review will discuss the paradigm shift associated with cellular heterogeneity, speak to the key developments that have lead to our better understanding of systems biology, and detail the future directions of the discipline (281 references).
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Affiliation(s)
- Maureen A Walling
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave., Albany, NY 12222, USA
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61
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Satterwhite JE, Pugh AM, Danell AS, Hvastkovs EG. Electrochemical detection of anti-benzo[a]pyrene diol epoxide DNA damage on TP53 codon 273 oligomers. Anal Chem 2011; 83:3327-35. [PMID: 21428456 DOI: 10.1021/ac103091v] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
DNA damage from (+/-)-anti-benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide (BPDE) at a hotspot TP53 gene sequence was electrochemically detected. BPDE was exposed to gold electrode immobilized double-stranded DNA oligomers followed by voltammetric measurements in the presence of redox-active C(12)H(25)V(2+)C(6)H(12)V(2+)C(12)H(25) (V(2+) = 4,4'-bipyridyl or viologen, C12-viologen). Square wave voltammograms from BPDE-exposed DNA-modified electrodes showed the emergence of a C12-viologen-DNA complex at -0.37 V versus Ag/AgCl. The peak current intensity of this redox wave was dependent on both BPDE concentration and exposure time. Controls with alternate xenobiotics and DNA sequences showed this redox wave to be primarily due to BPDE damage at the wild-type DNA sequence. The detection limit was determined to be approximately 170 nM BPDE. Mass spectrometry and UV thermal melting experiments provided insight into the BPDE reaction and mirrored the sensor results. This report demonstrates that an electrochemical hybridization sensor can be used to detect sequence-related xenobiotic DNA damage.
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Affiliation(s)
- Jennifer E Satterwhite
- Department of Chemistry, East Carolina University, Greenville, North Carolina 27858, United States
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62
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Chang G, Morigaki K, Tatsu Y, Hikawa T, Goto T, Imaishi H. Vertically Integrated Human P450 and Oxygen Sensing Film for the Assays of P450 Metabolic Activities. Anal Chem 2011; 83:2956-63. [DOI: 10.1021/ac103059k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gang Chang
- National Institute of Advanced Industrial, Science and Technology (AIST), Midorigaoka, Ikeda 563-8577, Japan
- Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, Faculty of Materials Sciences and Engineering, Hubei University, No. 11 Xueyuan Road, Wuchang, Wuhan 430062, China
| | - Kenichi Morigaki
- National Institute of Advanced Industrial, Science and Technology (AIST), Midorigaoka, Ikeda 563-8577, Japan
- Research Center for Environmental Genomics, Kobe University, Rokkodaicho 1-1, Nada, Kobe 657-8501 Japan
| | - Yoshiro Tatsu
- National Institute of Advanced Industrial, Science and Technology (AIST), Midorigaoka, Ikeda 563-8577, Japan
| | - Takashi Hikawa
- Research Center for Environmental Genomics, Kobe University, Rokkodaicho 1-1, Nada, Kobe 657-8501 Japan
| | - Tatsushi Goto
- Research Center for Environmental Genomics, Kobe University, Rokkodaicho 1-1, Nada, Kobe 657-8501 Japan
| | - Hiromasa Imaishi
- Research Center for Environmental Genomics, Kobe University, Rokkodaicho 1-1, Nada, Kobe 657-8501 Japan
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63
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Shumiantseva VV, Suprun EV, Bulko TV, Dobrynina OV, Archakov AI. [Sensor systems for medical application based on hemoproteins and nanocomposite materials]. BIOMEDITSINSKAIA KHIMIIA 2011; 56:55-71. [PMID: 21328911 DOI: 10.18097/pbmc20105601055] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Recent advances in nanotechnologies stimulate the development of sensor systems based on nanocomposite materials. This review discusses the prospects and challenges of sensors coupled with functionally important for medicine hemoproteins and nanoscale materials. Authors summarized their own experimental results and literature data on hemoprotein-based sensor systems. Mechanisms and the main function principles of electrochemical nanosensors are also discussed.
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64
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Tsagué Manfo FP, Chao WF, Moundipa PF, Pugeat M, Wang PS. Effects of maneb on testosterone release in male rats. Drug Chem Toxicol 2011; 34:120-8. [DOI: 10.3109/01480545.2010.482589] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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65
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Li H, Leulmi RF, Juncker D. Hydrogel droplet microarrays with trapped antibody-functionalized beads for multiplexed protein analysis. LAB ON A CHIP 2011; 11:528-34. [PMID: 21125085 DOI: 10.1039/c0lc00291g] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Antibody microarrays are a powerful tool for rapid, multiplexed profiling of proteins. 3D microarray substrates have been developed to improve binding capacity, assay sensitivity, and mass transport, however, they often rely on photopolymers which are difficult to manufacture and have a small pore size that limits mass transport and demands long incubation time. Here, we present a novel 3D antibody microarray format based on the entrapment of antibody-coated microbeads within alginate droplets that were spotted onto a glass slide using an inkjet. Owing to the low concentration of alginate used, the gels were highly porous to proteins, and together with the 3D architecture helped enhance mass transport during the assays. The spotting parameters were optimized for the attachment of the alginate to the substrate. Beads with 0.2 µm, 0.5 µm and 1 µm diameter were tested and 1 µm beads were selected based on their superior retention within the hydrogel. The beads were found to be distributed within the entire volume of the gel droplet using confocal microscopy. The assay time and the concentration of beads in the gels were investigated for maximal binding signal using one-step immunoassays. As a proof of concept, six proteins including cytokines (TNFα, IL-8 and MIP/CCL4), breast cancer biomarkers (CEA and HER2) and one cancer-related protein (ENG) were profiled in multiplex using sandwich assays down to pg mL(-1) concentrations with 1 h incubation without agitation in both buffer solutions and 10% serum. These results illustrate the potential of beads-in-gel microarrays for highly sensitive and multiplexed protein analysis.
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Affiliation(s)
- Huiyan Li
- Biomedical Engineering Department, McGill University, Montréal, QC H3A 1A4, Canada
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66
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Kool J, de Kloe G, Denker AD, van Altena K, Smoluch M, van Iperen D, Nahar TT, Limburg RJ, Niessen WMA, Lingeman H, Leurs R, de Esch IJP, Smit AB, Irth H. Nanofractionation Spotter Technology for Rapid Contactless and High-Resolution Deposition of LC Eluent for Further Off-Line Analysis. Anal Chem 2010; 83:125-32. [DOI: 10.1021/ac102001g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jeroen Kool
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
| | - Gerdien de Kloe
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
| | - Arnoud D. Denker
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
| | - Klaas van Altena
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
| | - Marek Smoluch
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
| | - Dick van Iperen
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
| | - Tariq T. Nahar
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
| | - Rob J. Limburg
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
| | - Wilfried M. A. Niessen
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
| | - Henk Lingeman
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
| | - Rob Leurs
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
| | - Iwan J. P. de Esch
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
| | - August B. Smit
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
| | - Hubertus Irth
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
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67
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Wu J, Wheeldon I, Guo Y, Lu T, Du Y, Wang B, He J, Hu Y, Khademhosseini A. A sandwiched microarray platform for benchtop cell-based high throughput screening. Biomaterials 2010; 32:841-8. [PMID: 20965560 DOI: 10.1016/j.biomaterials.2010.09.026] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Accepted: 09/14/2010] [Indexed: 01/24/2023]
Abstract
The emergence of combinatorial chemistries and the increased discovery of natural compounds have led to the production of expansive libraries of drug candidates and vast numbers of compounds with potentially interesting biological activities. Despite broad interest in high throughput screening (HTS) across varied fields of biological research, there has not been an increase in accessible HTS technologies. Here, we present a simple microarray sandwich system suitable for screening chemical libraries in cell-based assays at the benchtop. The microarray platform delivers chemical compounds to isolated cell cultures by 'sandwiching' chemical-laden arrayed posts with cell-seeded microwells. In this way, an array of sealed cell-based assays was generated without cross-contamination between neighbouring assays. After chemical exposure, cell viability was analyzed by fluorescence detection of cell viability assays on a per microwell basis using a standard microarray scanner. We demonstrate the efficacy of the system by generating four hits from toxicology screens towards MCF-7 human breast cancer cells. Three of the hits were identified in a combinatorial screen of a library of natural compounds in combination with verapamil, a P-glycoprotein inhibitor. A fourth hit, 9-methoxy-camptothecin, was identified by screening the natural compound library in the absence of verapamil. The method developed here miniaturizes existing HTS systems and enables the screening of a wide array of individual or combinatorial libraries in a reproducible and scalable manner. We anticipate broad application of such a system as it is amenable to combinatorial drug screening in a simple, robust and portable platform.
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Affiliation(s)
- Jinhui Wu
- Center for Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA 02139, USA
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68
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Monton MRN, Lebert JM, Little JRL, Nair JJ, McNulty J, Brennan JD. A Sol−Gel-Derived Acetylcholinesterase Microarray for Nanovolume Small-Molecule Screening. Anal Chem 2010; 82:9365-73. [PMID: 20949898 DOI: 10.1021/ac101949s] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maria Rowena N. Monton
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St. W, Hamilton, Ontario L8S 4M1, Canada
| | - Julie M. Lebert
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St. W, Hamilton, Ontario L8S 4M1, Canada
| | - Jessamyn R. L. Little
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St. W, Hamilton, Ontario L8S 4M1, Canada
| | - Jerald James Nair
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St. W, Hamilton, Ontario L8S 4M1, Canada
| | - James McNulty
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St. W, Hamilton, Ontario L8S 4M1, Canada
| | - John D. Brennan
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St. W, Hamilton, Ontario L8S 4M1, Canada
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69
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Microarray-based enzyme profiling: Recent advances and applications (Review). Biointerphases 2010; 5:FA24-31. [DOI: 10.1116/1.3462969] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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70
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Zhang H, Lee MY, Hogg MG, Dordick JS, Sharfstein ST. Gene delivery in three-dimensional cell cultures by superparamagnetic nanoparticles. ACS NANO 2010; 4:4733-4743. [PMID: 20731451 DOI: 10.1021/nn9018812] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Three-dimensional (3D) cellular assays closely mimic the in vivo milieu, providing a rapid, inexpensive system for screening drug candidates for toxicity or efficacy in the early stages of drug discovery. However, 3D culture systems may suffer from mass transfer limitations, particularly in delivery of large polypeptide or nucleic acid compounds. Nucleic acids (e.g., genes, silencing RNA) are of particular interest both as potential therapeutics and due to a desire to modulate the gene-expression patterns of cells exposed to small-molecule pharmacological agents. In the present study, polyethylenimine (PEI)-coated superparamagnetic nanoparticles (SPMNs) were designed to deliver interfering RNA and green fluorescent protein (GFP) plasmids through a collagen-gel matrix into 3D cell cultures driven by an external magnetic field. The highest transfection efficiency achieved was 64% for siRNA and 77% for GFP plasmids. Delivery of an shRNA plasmid against GFP by PEI-coated SPMNs silenced the GFP expression with 82% efficiency. We further demonstrated that this delivery approach could be used for screening interfering RNA constructs for therapeutic or toxic effects for cells grown in 3D cultures. Four known toxic shRNA plasmids were delivered by PEI-coated SPMNs into 3D cell cultures, and significant toxicities (41-51% cell death) were obtained.
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Affiliation(s)
- Haiyuan Zhang
- Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Science, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
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71
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Abstract
This article describes two kinds of "Cell Programmable Assay" (CPA) chips that utilize passive pumping for the culture and autonomous staining of cells to simply common protocols. One is a single timer channel CPA (sCPA) chip that has one timer channel and one main channel containing a cell culture chamber. The sCPA is used to culture and stain cells using Hoechst nuclear staining dye (a 2 step staining process). The other is a dual timer channel CPA (dCPA) chip that has two timer channels and one main channel with a chamber for cell culture. The dCPA is used here to culture, fix, permeablize, and stain cells using DAPI. The additional timer channel of the dCPA chip allows for automation of 3 steps. The CPA chips were successfully evaluated using HEK 293 cells. In addition, we provide a simplified equation for tuning or redesigning CPA chips to meet the needs of a variety of protocols that may require different timings. The equation is easy to use as it only depends upon the dimensions of microchannel and the volume of the reagent drops. The sCPA and dCPA chips can be readily modified to apply to a wide variety of common cell culture methods and procedures.
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Affiliation(s)
- Jongil Ju
- Department of Biomedical Engineering & Wisconsin Institutes for Medical Research, University of Wisconsin-Madison, Madison, WI 53705, USA
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72
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Fernandes TG, Kwon SJ, Bale SS, Lee MY, Diogo MM, Clark DS, Cabral JMS, Dordick JS. Three-dimensional cell culture microarray for high-throughput studies of stem cell fate. Biotechnol Bioeng 2010; 106:106-18. [PMID: 20069558 DOI: 10.1002/bit.22661] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We have developed a novel three-dimensional (3D) cellular microarray platform to enable the rapid and efficient tracking of stem cell fate and quantification of specific stem cell markers. This platform consists of a miniaturized 3D cell culture array on a functionalized glass slide for spatially addressable high-throughput screening. A microarray spotter was used to deposit cells onto a modified glass surface to yield an array consisting of cells encapsulated in alginate gel spots with volumes as low as 60 nL. A method based on an immunofluorescence technique scaled down to function on a cellular microarray was also used to quantify specific cell marker protein levels in situ. Our results revealed that this platform is suitable for studying the expansion of mouse embryonic stem (ES) cells as they retain their pluripotent and undifferentiated state. We also examined neural commitment of mouse ES cells on the microarray and observed the generation of neuroectodermal precursor cells characterized by expression of the neural marker Sox-1, whose levels were also measured in situ using a GFP reporter system. In addition, the high-throughput capacity of the platform was tested using a dual-slide system that allowed rapid screening of the effects of tretinoin and fibroblast growth factor-4 (FGF-4) on the pluripotency of mouse ES cells. This high-throughput platform is a powerful new tool for investigating cellular mechanisms involved in stem cell expansion and differentiation and provides the basis for rapid identification of signals and conditions that can be used to direct cellular responses.
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Affiliation(s)
- Tiago G Fernandes
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
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73
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Shumyantseva VV, Suprun EV, Bulko TV, Dobrynina OV, Archakov AI. Sensor systems for medical application based on hemoproteins and nanocomposite materials. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2010. [DOI: 10.1134/s199075081001004x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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74
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Metabolic enzyme microarray coupled with miniaturized cell-culture array technology for high-throughput toxicity screening. Methods Mol Biol 2010; 632:221-37. [PMID: 20217581 PMCID: PMC5293182 DOI: 10.1007/978-1-60761-663-4_14] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Due to poor drug candidate safety profiles that are often identified late in the drug development process, the clinical progression of new chemical entities to pharmaceuticals remains hindered, thus resulting in the high cost of drug discovery. To accelerate the identification of safer drug candidates and improve the clinical progression of drug candidates to pharmaceuticals, it is important to develop high-throughput tools that can provide early-stage predictive toxicology data. In particular, in vitro cell-based systems that can accurately mimic the human in vivo response and predict the impact of drug candidates on human toxicology are needed to accelerate the assessment of drug candidate toxicity and human metabolism earlier in the drug development process. The in vitro techniques that provide a high degree of human toxicity prediction will be perhaps more important in cosmetic and chemical industries in Europe, as animal toxicity testing is being phased out entirely in the immediate future.We have developed a metabolic enzyme microarray (the Metabolizing Enzyme Toxicology Assay Chip, or MetaChip) and a miniaturized three-dimensional (3D) cell-culture array (the Data Analysis Toxicology Assay Chip, or DataChip) for high-throughput toxicity screening of target compounds and their metabolic enzyme-generated products. The human or rat MetaChip contains an array of encapsulated metabolic enzymes that is designed to emulate the metabolic reactions in the human or rat liver. The human or rat DataChip contains an array of 3D human or rat cells encapsulated in alginate gels for cell-based toxicity screening. By combining the DataChip with the complementary MetaChip, in vitro toxicity results are obtained that correlate well with in vivo rat data.
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75
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Dash A, Inman W, Hoffmaster K, Sevidal S, Kelly J, Obach RS, Griffith LG, Tannenbaum SR. Liver tissue engineering in the evaluation of drug safety. Expert Opin Drug Metab Toxicol 2009; 5:1159-74. [PMID: 19637986 PMCID: PMC4110978 DOI: 10.1517/17425250903160664] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Assessment of drug-liver interactions is an integral part of predicting the safety profile of new drugs. Existing model systems range from in vitro cell culture models to FDA-mandated animal tests. Data from these models often fail, however, to predict human liver toxicity, resulting in costly failures of clinical trials. In vitro screens based on cultured hepatocytes are now commonly used in early stages of development, but many toxic responses in vivo seem to be mediated by a complex interplay among several different cell types. We discuss some of the evolving trends in liver cell culture systems applied to drug safety assessment and describe an experimental model that captures complex liver physiology through incorporation of heterotypic cell-cell interactions, 3D architecture and perfused flow. We demonstrate how heterotypic interactions in this system can be manipulated to recreate an inflammatory environment and apply the model to test compounds that potentially exhibit idiosyncratic drug toxicity. Finally, we provide a perspective on how the range of existing and emerging in vitro liver culture approaches, from simple to complex, might serve needs across the range of stages in drug discovery and development, including applications in molecular therapeutics.
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Affiliation(s)
- Ajit Dash
- Underwood-Prescott Professor of Toxicology and Chemistry, Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Office 56-731A, Cambridge, MA 02139, USA
| | - Walker Inman
- Underwood-Prescott Professor of Toxicology and Chemistry, Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Office 56-731A, Cambridge, MA 02139, USA
| | - Keith Hoffmaster
- Novartis Institute of Biomedical Research, 350 Massachusetts Avenue, Cambridge, Massachusetts, MA 02139, USA
| | - Samantha Sevidal
- Pfizer Research Technology Center, Cambridge, Massachusetts, MA 02139, USA
| | - Joan Kelly
- Pfizer Research Technology Center, Cambridge, Massachusetts, MA 02139, USA
| | - R Scott Obach
- Pfizer Research Technology Center, Cambridge, Massachusetts, MA 02139, USA
| | - Linda G Griffith
- Underwood-Prescott Professor of Toxicology and Chemistry, Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Office 56-731A, Cambridge, MA 02139, USA
| | - Steven R Tannenbaum
- Underwood-Prescott Professor of Toxicology and Chemistry, Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Office 56-731A, Cambridge, MA 02139, USA
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76
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Carnes EC, Harper JC, Ashley CE, Lopez DM, Brinker LM, Liu J, Singh S, Brozik SM, Brinker CJ. Cell-Directed Localization and Orientation of a Functional Foreign Transmembrane Protein within a Silica Nanostructure. J Am Chem Soc 2009; 131:14255-7. [DOI: 10.1021/ja906055m] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Eric C. Carnes
- Department of Chemical and Nuclear Engineering and Department of Molecular Genetics and Microbiology, University of New Mexico, Albuquerque, New Mexico 87131, and Sandia National Laboratories, Albuquerque, New Mexico 87106
| | - Jason C. Harper
- Department of Chemical and Nuclear Engineering and Department of Molecular Genetics and Microbiology, University of New Mexico, Albuquerque, New Mexico 87131, and Sandia National Laboratories, Albuquerque, New Mexico 87106
| | - Carlee E. Ashley
- Department of Chemical and Nuclear Engineering and Department of Molecular Genetics and Microbiology, University of New Mexico, Albuquerque, New Mexico 87131, and Sandia National Laboratories, Albuquerque, New Mexico 87106
| | - DeAnna M. Lopez
- Department of Chemical and Nuclear Engineering and Department of Molecular Genetics and Microbiology, University of New Mexico, Albuquerque, New Mexico 87131, and Sandia National Laboratories, Albuquerque, New Mexico 87106
| | - Lina M. Brinker
- Department of Chemical and Nuclear Engineering and Department of Molecular Genetics and Microbiology, University of New Mexico, Albuquerque, New Mexico 87131, and Sandia National Laboratories, Albuquerque, New Mexico 87106
| | - Juewen Liu
- Department of Chemical and Nuclear Engineering and Department of Molecular Genetics and Microbiology, University of New Mexico, Albuquerque, New Mexico 87131, and Sandia National Laboratories, Albuquerque, New Mexico 87106
| | - Seema Singh
- Department of Chemical and Nuclear Engineering and Department of Molecular Genetics and Microbiology, University of New Mexico, Albuquerque, New Mexico 87131, and Sandia National Laboratories, Albuquerque, New Mexico 87106
| | - Susan M. Brozik
- Department of Chemical and Nuclear Engineering and Department of Molecular Genetics and Microbiology, University of New Mexico, Albuquerque, New Mexico 87131, and Sandia National Laboratories, Albuquerque, New Mexico 87106
| | - C. Jeffrey Brinker
- Department of Chemical and Nuclear Engineering and Department of Molecular Genetics and Microbiology, University of New Mexico, Albuquerque, New Mexico 87131, and Sandia National Laboratories, Albuquerque, New Mexico 87106
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77
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Stoevesandt O, Taussig MJ, He M. Protein microarrays: high-throughput tools for proteomics. Expert Rev Proteomics 2009; 6:145-57. [PMID: 19385942 PMCID: PMC7105755 DOI: 10.1586/epr.09.2] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein microarrays are versatile tools for parallel, miniaturized screening of binding events involving large numbers of immobilized proteins in a time- and cost-effective manner. They are increasingly applied for high-throughput protein analyses in many research areas, such as protein interactions, expression profiling and target discovery. While conventionally made by the spotting of purified proteins, recent advances in technology have made it possible to produce protein microarrays through in situ cell-free synthesis directly from corresponding DNA arrays. This article reviews recent developments in the generation of protein microarrays and their applications in proteomics and diagnostics.
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Affiliation(s)
- Oda Stoevesandt
- Babraham Bioscience Technologies Ltd., Babraham Research Campus, Cambridge, CB22 3AT, UK.
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78
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Fernandes TG, Diogo MM, Clark DS, Dordick JS, Cabral JMS. High-throughput cellular microarray platforms: applications in drug discovery, toxicology and stem cell research. Trends Biotechnol 2009; 27:342-9. [PMID: 19398140 DOI: 10.1016/j.tibtech.2009.02.009] [Citation(s) in RCA: 177] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2009] [Revised: 02/13/2009] [Accepted: 02/18/2009] [Indexed: 02/08/2023]
Abstract
Cellular microarrays are powerful experimental tools for high-throughput screening of large numbers of test samples. Miniaturization increases assay throughput while reducing reagent consumption and the number of cells required, making these systems attractive for a wide range of assays in drug discovery, toxicology, stem cell research and potentially therapy. Here, we provide an overview of the emerging technologies that can be used to generate cellular microarrays, and we highlight recent significant advances in the field. This emerging and multidisciplinary approach offers new opportunities for the design and control of stem cells in tissue engineering and cellular therapies and promises to expedite drug discovery in the biotechnology and pharmaceutical industries.
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Affiliation(s)
- Tiago G Fernandes
- Institute for Biotechnology and Bioengineering (IBB), Centre for Biological and Chemical Engineering, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
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79
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Shumyantseva VV, Bulko TV, Kuznetsova GP, Samenkova NF, Archakov AI. Electrochemistry of cytochromes P450: Analysis of current-voltage characteristics of electrodes with immobilized cytochromes P450 for the screening of substrates and inhibitors. BIOCHEMISTRY (MOSCOW) 2009; 74:438-44. [DOI: 10.1134/s0006297909040129] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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80
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Hlavica P. Assembly of non-natural electron transfer conduits in the cytochrome P450 system: A critical assessment and update of artificial redox constructs amenable to exploitation in biotechnological areas. Biotechnol Adv 2009; 27:103-21. [DOI: 10.1016/j.biotechadv.2008.10.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2008] [Revised: 09/29/2008] [Accepted: 10/04/2008] [Indexed: 10/21/2022]
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81
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Ma B, Zhang G, Qin J, Lin B. Characterization of drug metabolites and cytotoxicity assay simultaneously using an integrated microfluidic device. LAB ON A CHIP 2009; 9:232-8. [PMID: 19107278 DOI: 10.1039/b809117j] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
An integrated microfluidic device was developed for the characterization of drug metabolites and a cytotoxicity assay simultaneously. The multi-layer device was composed of a quartz substrate with embedded separation microchannels and a perforated three-microwell array containing sol-gel bioreactors of human liver microsome (HLM), and two PDMS layers. By aligning the microwell array on the quartz substrate with cell culture chambers on the bottom PDMS layer, drug metabolism studies related to functional units, including metabolite generation, detection and incubation with cultured cells to assess metabolism induced cytotoxicity, were all integrated into the microfluidic device. To validate the feasibility of drug metabolism study on the microfluidic chip, UDP-glucuronosyltransferase (UGT) metabolism of acetaminophen (AP) and its effect on hepG2 cytotoxicity were studied first. Then metabolism based drug-drug interaction between AP and phenytoin (PH), which resulted in increased hepG2 cytotoxicity, was proved on this device. All this demonstrated that the developed microfluidic device could be a potential useful tool for drug metabolism and metabolism based drug-drug interaction research.
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Affiliation(s)
- Bo Ma
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
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82
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Kim KO, Lim SY, Hahn GH, Lee SH, Park CB, Kim DM. Cell-free synthesis of functional proteins using transcription/translation machinery entrapped in silica sol-gel matrix. Biotechnol Bioeng 2009; 102:303-7. [DOI: 10.1002/bit.22022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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83
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Sincic RS, Chang-Yen DA, Eddings M, Barrows LR, Gale BK. Parallel determination of phenotypic cytotoxicity with a micropattern of mutant cell lines. Biomed Microdevices 2008; 11:443-52. [PMID: 19067175 DOI: 10.1007/s10544-008-9250-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
This work presents a novel tool, the Continuous Flow Microspotter (CFM) and its use in patterning cellular microarrays of multiple cell types into the bottom of a tissue culture well. The CFM uses a system of isolated microfluidic channels to make an array of localized microspots of adhesion dependent cells in the bottom of a conventional tissue culture well. With this device we have created micropatterns of multiple cell lines in a single tissue culture well and used this system to conduct simultaneous cytotoxicity tests and recover dose survival curves in a parallel study. This mechanism of parallel testing allows the researcher to employ the use of positive and negative controls, as well as compare the chemical response of phenotypes in a tightly controlled microenvironment. For the experiments presented in this paper we have fabricated a CFM with a set of ten microchannels (five inlet channels and five outlet channels) to pattern a row of five microspots consisting of four cellular microspots and one empty spot for background measurements. Micropatterns containing a set of four different Chinese hamster ovarian cell (CHO) mutant phenotypes were deposited into the bottom of commercially available tissue culture wells then interrogated with mitomycin C, a chemotherapeutic agent. This study shows statistically significant (P < 0.05) hypersensitivity of the UV20 CHO mutant to a DNA interstrand cross-linking agent (mitomycin C). Because the CFM is also capable of depositing proteins and other biomolecules to the individual microspots of the array we foresee capabilities of the 48 microspot CFM to multiplex 48 cell types with 48 chemical reagents all within the confines of a 60 mm(2) area.
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Affiliation(s)
- Ryan S Sincic
- Department of Biomedical Engineering, University of Utah, 50 S. Central Campus Dr., Rm. 2480 MEB, Salt Lake City, UT 84112-9202, USA.
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84
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Combes R, Grindon C, Cronin MT, Roberts DW, Garrod JF. Integrated Decision-tree Testing Strategies for Acute Systemic Toxicity and Toxicokinetics with Respect to the Requirements of the EU REACH Legislation. Altern Lab Anim 2008; 36 Suppl 1:91-109. [DOI: 10.1177/026119290803601s08] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Liverpool John Moores University and FRAME conducted a joint research project, sponsored by Defra, on the status of alternatives to animal testing with regard to the European Union REACH (Registration, Evaluation and Authorisation of Chemicals) system for the safety testing and risk assessment of chemicals. The project covered all the main toxicity endpoints associated with REACH. This paper focuses on the use of alternative (non-animal) methods (both in vitro and in silico) for acute systemic toxicity and toxicokinetic testing. The paper reviews in vitro tests based on basal cytotoxicity and target organ toxicity, along with QSAR models and expert systems available for this endpoint. The use of PBPK modelling for the prediction of ADME properties is also discussed. These tests are then incorporated into a decision-tree style, integrated testing strategy, which also includes the use of refined in vivo acute toxicity tests, as a last resort. The implementation of the strategy is intended to minimise the use of animals in the testing of acute systemic toxicity and toxicokinetics, whilst satisfying the scientific and logistical demands of the EU REACH legislation.
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Affiliation(s)
| | | | - Mark T.D. Cronin
- School of Pharmacy and Chemistry, Liverpool John Moores University, Liverpool, UK
| | - David W. Roberts
- School of Pharmacy and Chemistry, Liverpool John Moores University, Liverpool, UK
| | - John F. Garrod
- Chemicals and Nanotechnologies Division, Defra, London, UK
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85
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Fernandes TG, Kwon SJ, Lee MY, Clark DS, Cabral JMS, Dordick JS. On-chip, cell-based microarray immunofluorescence assay for high-throughput analysis of target proteins. Anal Chem 2008; 80:6633-9. [PMID: 18656951 PMCID: PMC5292206 DOI: 10.1021/ac800848j] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have developed an immunofluorescence-based assay for high-throughput analysis of target proteins on a three-dimensional cellular microarray platform. This process integrates the use of three-dimensional cellular microarrays, which should better mimic the cellular microenvironment, with sensitive immunofluorescence detection and provides quantitative information on cell function. To demonstrate this assay platform, we examined the accumulation of the alpha subunit of the hypoxia-inducible factor (HIF-1alpha) after chemical stimulation of human pancreatic tumor cells encapsulated in 3D alginate spots in volumes as low as 60 nL. We also tested the effect of the known dysregulator of HIF-1alpha, 2-methoxyestradiol (2ME2), on the levels of HIF-1alpha using a dual microarray stamping technique. This chip-based in situ Western immunoassay protocol was able to provide quantitative information on cell function, namely, the cellular response to hypoxia mimicking conditions and the reduction of HIF-1alpha levels after cell treatment with 2ME2. This system is the first to enable high-content screening of cellular protein levels on a 3D human cell microarray platform.
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86
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Lebert JM, Forsberg EM, Brennan JD. Solid-phase assays for small molecule screening using sol-gel entrapped proteins. Biochem Cell Biol 2008; 86:100-10. [PMID: 18443623 DOI: 10.1139/o08-010] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
With compound libraries exceeding one million compounds, the ability to quickly and effectively screen these compounds against relevant pharmaceutical targets has become crucial. Solid-phase assays present several advantages over solution-based methods. For example, a higher degree of miniaturization can be achieved, functional- and affinity-based studies are possible, and a variety of detection methods can be used. Unfortunately, most protein immobilization methods are either too harsh or require recombinant proteins and thus are not amenable to delicate proteins such as kinases and membrane-bound receptors. Sol-gel encapsulation of proteins in an inorganic silica matrix has emerged as a novel solid-phase assay platform. In this minireview, we discuss the development of sol-gel derived protein microarrays and sol-gel based monolithic bioaffinity columns for the high-throughput screening of small molecule libraries and mixtures.
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Affiliation(s)
- Julie M Lebert
- Chemical Biology Program, Department of Chemistry, McMaster University, 1280 Main St. W, Hamilton, ON L8S4M1, Canada
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87
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Krishnan S, Hvastkovs EG, Bajrami B, Choudhary D, Schenkman JB, Rusling JF. Synergistic metabolic toxicity screening using microsome/DNA electrochemiluminescent arrays and nanoreactors. Anal Chem 2008; 80:5279-85. [PMID: 18563913 PMCID: PMC3483639 DOI: 10.1021/ac800763r] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Platforms based on thin enzyme/DNA films were used in two-tier screening of chemicals for reactive metabolites capable of producing toxicity. Microsomes were used for the first time as sources of cytochrome (cyt) P450 enzymes in these devices. Initial rapid screening involved electrochemiluminescent (ECL) arrays featuring spots containing ruthenium poly(vinylpyridine), DNA, and rat liver microsomes or bicistronically expressed human cyt P450 2E1 (h2E1). Cyt P450 enzymes were activated via the NADPH/reductase cycle. When bioactivation of substrates in the films gives reactive metabolites, they are trapped by covalent attachment to DNA bases. The rate of increase in ECL with enzyme reaction time reflects relative DNA damage rates. "Toxic hits" uncovered by the array were studied in structural detail by using enzyme/DNA films on silica nanospheres as "nanoreactors" to provide nucleobase adducts from reactive metabolites. The utility of this synergistic approach was demonstrated by estimating relative DNA damage rates of three mutagenic N-nitroso compounds and styrene. Relative enzyme turnover rates for these compounds using ECL arrays and LC-UV-MS correlated well with TD 50 values for liver tumor formation in rats. Combining ECL array and nanoreactor/LC-MS technologies has the potential for rapid, high-throughput, cost-effective screening for reactive metabolites and provides chemical structure information that is complementary to conventional toxicity bioassays.
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88
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Combes R, Grindon C, Cronin MTD, Roberts DW, Garrod JF. Integrated decision-tree testing strategies for acute systemic toxicity and toxicokinetics with respect to the requirements of the EU REACH legislation. Altern Lab Anim 2008; 36:45-63. [PMID: 18333714 DOI: 10.1177/026119290803600107] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Liverpool John Moores University and FRAME conducted a joint research project, sponsored by Defra, on the status of alternatives to animal testing with regard to the European Union REACH (Registration, Evaluation and Authorisation of Chemicals) system for the safety testing and risk assessment of chemicals. The project covered all the main toxicity endpoints associated with REACH. This paper focuses on the use of alternative (non-animal) methods (both in vitro and in silico) for acute systemic toxicity and toxicokinetic testing. The paper reviews in vitro tests based on basal cytotoxicity and target organ toxicity, along with QSAR models and expert systems available for this endpoint. The use of PBPK modelling for the prediction of ADME properties is also discussed. These tests are then incorporated into a decision-tree style, integrated testing strategy, which also includes the use of refined in vivo acute toxicity tests, as a last resort. The implementation of the strategy is intended to minimise the use of animals in the testing of acute systemic toxicity and toxicokinetics, whilst satisfying the scientific and logistical demands of the EU REACH legislation.
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89
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Lee MY, Kumar RA, Sukumaran SM, Hogg MG, Clark DS, Dordick JS. Three-dimensional cellular microarray for high-throughput toxicology assays. Proc Natl Acad Sci U S A 2008; 105:59-63. [PMID: 18160535 PMCID: PMC2224231 DOI: 10.1073/pnas.0708756105] [Citation(s) in RCA: 261] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2007] [Indexed: 01/21/2023] Open
Abstract
We have developed a miniaturized 3D cell-culture array (the Data Analysis Toxicology Assay Chip or DataChip) for high-throughput toxicity screening of drug candidates and their cytochrome P450-generated metabolites. The DataChip consists of human cells encapsulated in collagen or alginate gels (as small as 20 nl) arrayed on a functionalized glass slide for spatially addressable screening against multiple compounds. A single DataChip containing 1,080 individual cell cultures, used in conjunction with the complementary human P450-containing microarray (the Metabolizing Enzyme Toxicology Assay Chip or MetaChip), simultaneously provided IC(50) values for nine compounds and their metabolites from CYP1A2, CYP2D6, and CYP3A4 and a mixture of the three P450s designed to emulate the human liver. Similar responses were obtained with the DataChip and conventional 96-well plate assays, demonstrating that the near 2,000-fold miniaturization does not influence the cytotoxicity response. The DataChip may therefore enable toxicity analyses of drug candidates and their metabolites at throughputs compatible with the availability of compounds at early-stage drug discovery.
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Affiliation(s)
- Moo-Yeal Lee
- *Solidus Biosciences, Inc., Troy, NY 12180
- Departments of Chemical and Biological Engineering and
| | - R. Anand Kumar
- Department of Chemical Engineering, University of California, Berkeley, CA 94720
| | | | - Michael G. Hogg
- *Solidus Biosciences, Inc., Troy, NY 12180
- Departments of Chemical and Biological Engineering and
| | - Douglas S. Clark
- Department of Chemical Engineering, University of California, Berkeley, CA 94720
| | - Jonathan S. Dordick
- Departments of Chemical and Biological Engineering and
- Biology, Rensselaer Polytechnic Institute, Troy, NY 12180; and
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90
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Houck KA, Kavlock RJ. Understanding mechanisms of toxicity: insights from drug discovery research. Toxicol Appl Pharmacol 2007; 227:163-78. [PMID: 18063003 DOI: 10.1016/j.taap.2007.10.022] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2007] [Revised: 09/28/2007] [Accepted: 10/11/2007] [Indexed: 12/18/2022]
Abstract
Toxicology continues to rely heavily on use of animal testing for prediction of potential for toxicity in humans. Where mechanisms of toxicity have been elucidated, for example endocrine disruption by xenoestrogens binding to the estrogen receptor, in vitro assays have been developed as surrogate assays for toxicity prediction. This mechanistic information can be combined with other data such as exposure levels to inform a risk assessment for the chemical. However, there remains a paucity of such mechanistic assays due at least in part to lack of methods to determine specific mechanisms of toxicity for many toxicants. A means to address this deficiency lies in utilization of a vast repertoire of tools developed by the drug discovery industry for interrogating the bioactivity of chemicals. This review describes the application of high-throughput screening assays as experimental tools for profiling chemicals for potential for toxicity and understanding underlying mechanisms. The accessibility of broad panels of assays covering an array of protein families permits evaluation of chemicals for their ability to directly modulate many potential targets of toxicity. In addition, advances in cell-based screening have yielded tools capable of reporting the effects of chemicals on numerous critical cell signaling pathways and cell health parameters. Novel, more complex cellular systems are being used to model mammalian tissues and the consequences of compound treatment. Finally, high-throughput technology is being applied to model organism screens to understand mechanisms of toxicity. However, a number of formidable challenges to these methods remain to be overcome before they are widely applicable. Integration of successful approaches will contribute towards building a systems approach to toxicology that will provide mechanistic understanding of the effects of chemicals on biological systems and aid in rationale risk assessments.
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Affiliation(s)
- Keith A Houck
- National Center for Computational Toxicology, Office Research and Development, United Stated Environmental Protection Agency, Research Triangle Park, NC 27711, USA.
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91
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Brennan JD. Biofriendly sol-gel processing for the entrapment of soluble and membrane-bound proteins: toward novel solid-phase assays for high-throughput screening. Acc Chem Res 2007; 40:827-35. [PMID: 17458927 DOI: 10.1021/ar6000268] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The last decade has seen a revolution in the area of sol-gel-derived biomaterials since the demonstration that these materials can be used to encapsulate biological species such as enzymes, antibodies, and other proteins in a functional state. In particular, recent years have seen tremendous progress in the development of more "protein-friendly" sol-gel processing methods and their use for immobilization of delicate proteins, including key drug targets such as kinases and membrane-bound receptors. The latter example is particularly impressive, given the inherently low stability of membrane receptors and the need to stabilize an amphiphilic bilayer lipid membrane to maintain receptor function. In this Account, we provide an overview of the advances in biofriendly sol-gel processing methods developed in our research group and others and highlight recent accomplishments in the immobilization of both soluble and membrane-bound proteins, with particular emphasis on enzymes and membrane receptors that are drug targets. Emerging applications of sol-gel-entrapped proteins, focusing on the development platforms for high-throughput screening of small molecules, are also described.
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Affiliation(s)
- John D Brennan
- Department of Chemistry, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada.
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92
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Kwon SJ, Lee MY, Ku B, Sherman DH, Dordick JS. High-throughput, microarray-based synthesis of natural product analogues via in vitro metabolic pathway construction. ACS Chem Biol 2007; 2:419-25. [PMID: 17530734 DOI: 10.1021/cb700033s] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The generation of biological diversity by engineering the biosynthetic gene assembly of metabolic pathway enzymes has led to a wide range of "unnatural" variants of natural products. However, current biosynthetic techniques do not allow the rapid manipulation of pathway components and are often fundamentally limited by the compatibility of new pathways, their gene expression, and the resulting biosynthetic products and pathway intermediates with cell growth and function. To overcome these limitations, we have developed an entirely in vitro approach to synthesize analogues of natural products in high throughput. Using several type III polyketide synthases (PKS) together with oxidative post-PKS tailoring enzymes, we performed 192 individual and multienzymatic reactions on a single glass microarray. Subsequent array-based screening with a human tyrosine kinase led to the identification of three compounds that acted as modest inhibitors in the low-micromolar range. This approach, therefore, enables the rapid construction of analogues of natural products as potential pharmaceutical lead compounds.
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Affiliation(s)
- Seok Joon Kwon
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
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93
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Ueda Y, Morigaki K, Tatsu Y, Yumoto N, Imaishi H. Immobilization and activity assay of cytochrome P450 on patterned lipid membranes. Biochem Biophys Res Commun 2007; 355:926-31. [PMID: 17335776 DOI: 10.1016/j.bbrc.2007.02.058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2007] [Accepted: 02/12/2007] [Indexed: 10/23/2022]
Abstract
We report on a methodology for immobilizing cytochrome P450 on the surface of micropatterned lipid bilayer membranes and measuring the enzymatic activity. The patterned bilayer comprised a matrix of polymeric lipid bilayers and embedded fluid lipid bilayers. The polymeric lipid bilayer domains act as a barrier to confine fluid lipid bilayers in defined areas and as a framework to stabilize embedded membranes. The fluid bilayer domains, on the other hand, can contain lipid compositions that facilitate the fusion between lipid membranes, and are intended to be used as the binding agent of microsomes containing rat CYP1A1. By optimizing the membrane compositions of the fluid bilayers, we could selectively immobilize microsomal membranes on these domains. The enzymatic activity was significantly higher on lipid bilayer substrates compared with direct adsorption on glass. Furthermore, competitive assay experiment between two fluorogenic substrates demonstrated the feasibility of bioassays based on immobilized P450s.
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Affiliation(s)
- Yoshihiro Ueda
- Research Center for Environmental Genomics, Kobe University, Rokkodaicho 1-1, Nada, Kobe 657-8501, Japan
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94
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Lemaire F, Mandon CA, Reboud J, Papine A, Angulo J, Pointu H, Diaz-Latoud C, Lajaunie C, Chatelain F, Arrigo AP, Schaack B. Toxicity assays in nanodrops combining bioassay and morphometric endpoints. PLoS One 2007; 2:e163. [PMID: 17235363 PMCID: PMC1769465 DOI: 10.1371/journal.pone.0000163] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2006] [Accepted: 09/18/2006] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Improved chemical hazard management such as REACH policy objective as well as drug ADMETOX prediction, while limiting the extent of animal testing, requires the development of increasingly high throughput as well as highly pertinent in vitro toxicity assays. METHODOLOGY This report describes a new in vitro method for toxicity testing, combining cell-based assays in nanodrop Cell-on-Chip format with the use of a genetically engineered stress sensitive hepatic cell line. We tested the behavior of a stress inducible fluorescent HepG2 model in which Heat Shock Protein promoters controlled Enhanced-Green Fluorescent Protein expression upon exposure to Cadmium Chloride (CdCl2), Sodium Arsenate (NaAsO2) and Paraquat. In agreement with previous studies based on a micro-well format, we could observe a chemical-specific response, identified through differences in dynamics and amplitude. We especially determined IC50 values for CdCl2 and NaAsO2, in agreement with published data. Individual cell identification via image-based screening allowed us to perform multiparametric analyses. CONCLUSIONS Using pre/sub lethal cell stress instead of cell mortality, we highlighted the high significance and the superior sensitivity of both stress promoter activation reporting and cell morphology parameters in measuring the cell response to a toxicant. These results demonstrate the first generation of high-throughput and high-content assays, capable of assessing chemical hazards in vitro within the REACH policy framework.
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Affiliation(s)
- Frédéric Lemaire
- Commissariat à l'Energie Atomique, DSV, Cellular Responses and Dynamics Department, Laboratoire Biopuces, Commissariat à l'Energie Atomique Centre de Grenoble, Grenoble, France
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95
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Abstract
Drug metabolism information is a necessary component of drug discovery and development. The key issues in drug metabolism include identifying: the enzyme(s) involved, the site(s) of metabolism, the resulting metabolite(s), and the rate of metabolism. Methods for predicting human drug metabolism from in vitro and computational methodologies and determining relationships between the structure and metabolic activity of molecules are also critically important for understanding potential drug interactions and toxicity. There are numerous experimental and computational approaches that have been developed in order to predict human metabolism which have their own limitations. It is apparent that few of the computational tools for metabolism prediction alone provide the major integrated functions needed to assist in drug discovery. Similarly the different in vitro methods for human drug metabolism themselves have implicit limitations. The utilization of these methods for pharmaceutical and other applications as well as their integration is discussed as it is likely that hybrid methods will provide the most success.
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Affiliation(s)
- Larry J Jolivette
- Preclinical Drug Discovery, Cardiovascular and Urogenital Centre of Excellence in Drug Discovery, GlaxoSmithKline, King of Prussia, Pennsylvania, USA
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96
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Ptacek J, Snyder M. 14 Yeast Protein Microarrays. J Microbiol Methods 2007. [DOI: 10.1016/s0580-9517(06)36014-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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97
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Lewandowski AT, Yi H, Luo X, Payne GF, Ghodssi R, Rubloff GW, Bentley WE. Protein assembly onto patterned microfabricated devices through enzymatic activation of fusion pro-tag. Biotechnol Bioeng 2007; 99:499-507. [PMID: 17625789 DOI: 10.1002/bit.21580] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We report a versatile approach for covalent surface-assembly of proteins onto selected electrode patterns of pre-fabricated devices. Our approach is based on electro-assembly of the aminopolysaccharide chitosan scaffold as a stable thin film onto patterned conductive surfaces of the device, which is followed by covalent assembly of the target protein onto the scaffold surface upon enzymatic activation of the protein's "pro-tag." For our demonstration, the model target protein is green fluorescent protein (GFP) genetically fused with a pentatyrosine pro-tag at its C-terminus, which assembles onto both two-dimensional chips and within fully packaged microfluidic devices in situ and under flow. Our surface-assembly approach enables spatial selectivity and orientational control under mild experimental conditions. We believe that our integrated approach harnessing genetic manipulation, in situ enzymatic activation, and electro-assembly makes it advantageous for a wide variety of bioMEMS and biosensing applications that require facile "biofunctionalization" of microfabricated devices.
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Affiliation(s)
- Angela T Lewandowski
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland, USA
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98
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Lee MY, Dordick JS. High-throughput human metabolism and toxicity analysis. Curr Opin Biotechnol 2006; 17:619-27. [PMID: 17046235 DOI: 10.1016/j.copbio.2006.09.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2006] [Revised: 08/19/2006] [Accepted: 09/22/2006] [Indexed: 02/04/2023]
Abstract
Poor drug candidate safety profiles are often identified late in the drug development process, manifesting themselves in the preclinical and clinical phases and significantly contributing to the high cost and low yield of drug discovery. As a result, new tools are needed to accelerate the assessment of drug candidate toxicity and human metabolism earlier in the drug development process, from primary drug candidate screening to lead optimization. Although high-throughput screens exist for much of the discovery phase of drug development, translating such screening techniques into platforms that can accurately mimic the human in vivo response and predict the impact of drug candidates on human toxicology has proven difficult. Nevertheless, some success has been achieved in recent years, which may ultimately yield widespread acceptance in the pharmaceutical industry.
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Affiliation(s)
- Moo-Yeal Lee
- Solidus Biosciences, Inc., 1223 Peoples Avenue, Troy, New York 12180, USA.
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99
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Wang J, Uttamchandani M, Sun H, Yao S. Small Molecule Microarrays: Applications Using Specially Tagged Chemical Libraries. ACTA ACUST UNITED AC 2006. [DOI: 10.1002/qsar.200640083] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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100
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Chen Y, Monshouwer M, Fitch WL. Analytical Tools and Approaches for Metabolite Identification in Early Drug Discovery. Pharm Res 2006; 24:248-57. [PMID: 17048114 DOI: 10.1007/s11095-006-9162-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2006] [Accepted: 06/07/2006] [Indexed: 11/30/2022]
Abstract
Determination of the chemical structures of metabolites is a critical part of the early pharmaceutical discovery process. Understanding the structures of metabolites is useful both for optimizing the metabolic stability of a drug as well as rationalizing the drug safety profile. This review describes the current state of the art in this endeavor. The likely outcome of metabolism is first predicted by comparison to the literature. Then metabolites are synthesized in a variety of in vitro systems. The various approaches to LC/UV/MS are applied to learn information about these metabolites and structure hypotheses are made. Structures are confirmed by synthesis or NMR. The special topic of reactive metabolite structure determination is briefly addressed.
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Affiliation(s)
- Yuan Chen
- Drug Metabolism and Pharmacokinetics, Roche Palo Alto, 3431 Hillview Ave., Palo Alto, California 94304, USA
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