Microarray - 2007


Generally referring to an array of probes displayed on a matrix similar to a microscope slide which are used to analyzed complex mixtures for specific analytes. The sample is usually labeled with a signal such as a fluorescent dye. Both sample preparation and analysis are complex. See DNA microarray and protein microarray. See Schena, M., Heller, R.A., Theriault, T.P., et al,, Microarrays: biotechnology’s discovery platform for functional genomics, Trends Biotechnol. 16, 301-306, 1998; Gerhold, D., Rushmore, T., and Caskey, C.T., DNA chips: promising toys have become powerful tools, Trends Biochem Sci 24, 168-173, 1999; Ness, S.A., Basic microarray analysis: strategies for successful experiments, Methods Mol.Biol. 316, 13-33, 2006; Wang, S. and Cheng, Q., Microarray analysis in drug discovery and clinical applications, Methods Mol.Biol. 316, 49-65, 2006; Kozarova, A., Petrinac, S., Ali, A., and Hudson, J.W., Array of informatics: applications in modern research, J.Proteome Res. 5, 10551-1059, 2006; Sievertzon, M., Nilsson, P. and Lundeberg, J., Improving reliability and performance of DNA microarrays, Expert Rev.Mol.Diagn. 6, 481-492, 2006; Sobek, J., Bartscherer, K., Jacob, A., Hoheisel, J.D., and Angenendt, P., Microarray technology as a universal tool for high-throughput analysis of biological systems. Comb.Chem.High Throughput Screen. 9, 365-380, 2006; Pedroso, S. and Guillen, I.A., Microarray and nanotechnology applications of functional nanoparticles, Comb.Chem.High Througput Screen. 9, 389-397, 2006. Microarray analysis can also be applied to the study of multiple tissue specimens with tissue microarrays (Rimm, D.L., Camp, R.L, Charette, L.A., et al., Tissue microarray: a new technology for amplification of tissue resources, Cancer J. 7, 24-31, 2001; Bubendorf, L., Nocito, A., Moch, K., and Sauter, G., Tissue microarray (TMA) technology: Miniaturized pathology archives for high-throughput in situ studies, J.Pathol. 195, 72-79, 2001; Fedor, H.L. and De Marzo, A.M., Practical methods for tissue microarray construction, Methods Mol.Biol. 103, 89-101, 2005).

Microarray-2018


The term microarray refers to an analytical technology where probes of known composition are used to identify and quantify analytes (targets) in (usually) complex mixtures.  The probe is usually attached by either covalent or non-covalent binding to a matrix, frequently a modified glass slide, and a labeled sample applied to the sample; frequently a fluorescent label is used (1,2).  Use of PCR to amplify the signal increases sensitivity (3).  The data from DNA microarrays (and other probes such as proteins) can be expressed in the form of a heat map (4) to show increased or decreased gene expression (5).  There is considerable interest in the use of microarray technology to develop the lab-on-a-chip (6). There are systems where the target is placed on the microarray surface and analyzed with a labeled probe.  This approach has seen most use with proteins as an approach is referred to as reverse-phase protein microarray (7,8).  Microarray assays are based on high density of probes on a surface.  Microarrays may have 200 spots or elements/cm2 while a macroarray may have 20 spots or elements/cm2 (9).  I would note that the difference of the density of probes in microarray versus microarray is not generally accepted except that microarray spots are larger than microarray spots; macroarray density may be similar to that of conventional 96-well microplates which I estimate as 1-3 “spots” per cm2.  A macroarray spot contain 50-100 nmol compound while a microarray spot may contain 50-100 pmol compound (10).  Macroarrays have been used to establish conditions for reactions in microarrays (11).   As should be obvious from the above, the term microarray is used most often in DNA microarray.  The technology is based on the complementarity of DNA strands (molecular hybridization) as, for example, shown in the double helix (12,13).   DNA microarrays can process a very large number of samples so why the assay technology is relatively, although requiring robotics (14,15), the experimental design and data analysis is a continuing challenge (16-22).    Microarray technology has been useful in the analysis of proteins (23).   Antibody or antibody fragments have been used as probes for protein microarray analysis and purified proteins have been used to screen for antibodies as for example with hybridoma supernatant fractions (24).  Reverse Phase Protein Microarray (RPPM) is the term used to describe the use of proteins as probes for microarrays (25,26).   Aptamers have been used in the protein microarrays (27-28) developed with SELEX (Systematic Evaluation of ligands by exponential enrichment)(29) which is a form of combinatorial chemistry (30).  Peptide microarrays can be used for the assay/identification of proteolytic enzymes (31) and for the identification of epitopes (32).  Microarray analysis can also be applied to the study of multiple tissue specimens with tissue microarrays where small tissue samples (0.5 mm) can be placed on glass slide (33-36).  Carbohydrates can also serve as a probe for the analysis of complex mixtures (37).

References
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2.  Wagenknecht, H.A., Fluorescent DNA base modifications and substitutes: multiple fluorophore labeling and the DETEQ concept, Ann.N.Y.Acad.Sci. 1130, 122-130, 2008.
3.  Pierik, A.,Boamfa,M., van Zelst, M., et al., Real time quantitative amplification detection on a microarray: toward high multiplex quantitative PCR, Lab.Chip. 12, 1897-1902, 2012.
4.  Dresen, I.M., Hüsing, J., Kruse, E., Boes, T., and Jὅckel, K.H., Software packages for quantitative microarray-based gene expression analysis, Curr.Pharm.Biotechnol. 4, 417-437, 2003).
5.  Fridley, K.M., Nair, R., and McDevitt, T.C., Differential expression of extracellular matrix and growth factors by embryoid bodies in hydrodynamic and static cultures, Tissue Eng.Part C Methods 20, 931-940, 2014.
6.  Marzancola, M.G., Sedighi, A., and Li, P.C., DNA microarray-based diagnostics, Methods Mol.Biol. 1368, 161-178, 2016. 
7.  Tibes, R., Qiu, Y., Lu, Y., et al., Reverse-phase protein array: validation of a novel proteomic technology and utility for analysis of primary leukemia specimens and hematopoietic stem cells, Mol.Cacner  Ther. 5, 2512-2521, 2006.
8.  Masuda, M. and Yamada, T., Signaling pathway profiling by reverse-phase protein array for personalized cancer medicine, Biochim.Biophys.Acta 1854, 651-657, 2015. 
9.  Reimer, U., Reineke, U., and Schneiden-Mergener, J., Peptide arrays: from macro to micro, Curr.Opin.Biotechnol. 13, 315-329. 2002.
10. Blackwell, H.E., Hitting the SPOT: small-molecule macroarrays advance combinatorial synthesis, Curr.Opin.Chem.Biol. 10, 203-212, 2006.
11.  Stansfield, H.E., Kulczewski, B.P., Lyband, K.E., and Jamieson, E.R., Identifying protein interactions with metal-modified DNA using microarray technology, J.Biol.Inorg.Chem. 14, 193-199, 2009.
12.  12Southern, E.M., DNA microarrays History and Overview, in DNA Assays Methods and Protocols, ed. J.B. Rampal, Chapter 1, pps. 1-15, Humana Press, Totowa, New Jersey, USA, 2001.
13. Pirrung, M.C. and Southern, E.M., The genesis of microarrays, Biochem.Mol.Biol.Education 42, 106-113, 2014.
14. Auburn , R.P., Kreil, D.P., Meadows, L.A.,. et al., Robotic spotting of cDNA and oligonucleotide microarrays, Trends Biotechnol. 23, 374-279, 2005.
15. Ahmad, H., Sutherland, A., Shin, Y.S., et al., A robotics platform for automated batch fabrication of high density, microfluidics-based DNA microarrays, with applications to single cell, multiplex assays of secreted proteins, Rev.Sci.Instrum. 82(9):094301, 2011.
16.  Brazma, A., Hingamp, P., Quackenbush, J., et al., Minimum information about a microarray experiment (MIAME)-towards standards for microarray data, Nature Genetics 29, 365-371, 2001;.
17. Hackett, J.L. and Lesko, L.J., Microarray data – the US FDA, industry and academia, Nature 21, 742-743, 2003.
18.  Mehta, T., Tanik, M., and Allison, D.B., Towards some epistemological foundations of statistical methods for high-dimensional biology, Nature Genetics 36, 943-947, 2004.
19. Gorreta, F., Barzaghi, D., Van Meter, A.J., Chandhoke, V. and Del Diacco, L., Development of a new standard for microarray experiments, Biotechniques 36, 1002-1009, 2004.
20.  Knudsen, S., Guide to Analysis of DNA Microarray Data, Wiley-Liss,Hoboken, New Jersey, USA, 2004.
21.  Li, S. and Li, D., DNA Microarray Techology and Data Analysis in Cancer Research, World Scientific Publisher, Singapore, 2008.
22.  Amaratunga, D., Carbrera, J., and Shkedy,Z., Exploration and Analysis of DNA Microarray and Other High-Dimensional Data, 2nd edn.,Wiley, Hoboken, New Jersey, USA, 2014.
23.  Windren, C., Antibody-based proteomics, Adv.Exp.Med.Biol. 926, 163-179, 2016.
24.  Stoevesandt, O. and Taussig, M.J., Affinity proteomics: the role of specific binding reagents in human proteome analysis, Expert Rev.Proteomics 9, 401-414, 2012.
25.  25 Wulfkuhle, J.D., Aquino, J.A., Calvert, V.S., et al., Signal pathway profiling of ovarian cancer from human tissue specimens using revers-phase protein microarrays, Proteomics 3, 2085-2090, 2003.
26.  Pawlak, M. and Carragher, N.O.., Reverse phase protein arrays elucidate mechanisms-of-action and phenotypic response in 2D and 3D models, Drug Discov.Today.Technol; 23, 7-16, 2017.
27. Witt, M., Walter, J.G. and Stahl, F., Aptamer microarrays-Current status and future prospects, Microarrays (Basal) 4, 115-132, 2015.
28.  Albaba, D., Soomro, S., and Mohan, C., Aptamer-based screens of human body fluids for biomarkers, Microarrays (Basel) 4, 424-431, 2015.
29. Liu, X., Li, H., Jia, W., Chen, Z., and Xu, D., Selection of aptamers based on a protein microarray integrated with a microfluidic chip, Lab.Chip. 17, 178-185, 2016.
30. Lam, K.S. and Renil, M., From combinatorial chemistry to chemical microarray, Curr.Opin.Chem.Biol. 6, 353-358, 2002.
31.  Lei, Z., Chen, H., Zhang, H., et al., Evaluation of matrix metalloproteinase inhibition by peptide microarray-based fluorescence assay on polymer brush substrate and in vivo assessment, ACS Appld.Mater.Interfaces 9, 44241-44250, 2017.
32. Richer, J., Johnston, S.A., and Stafford, P., Epitope identification from fixed -complexity random-sequence peptide microarrays, Mol.Cell.Proeomics 14, 136-147, 2015.
33.  Rimm, D.L., Camp, R.L, Charette, L.A., et al., Tissue microarray: a new technology for amplification of tissue resources, Cancer J. 7, 24-31, 2001.
34.  Bubendorf, L., Nocito, A., Moch, K., and Sauter, G., Tissue microarray (TMA) technology: Miniaturized pathology archives for high-throughput in situ studies, J.Pathol. 195, 72-79, 2001.
35.  Fedor, H.L. and De Marzo, A.M., Practical methods for tissue microarray construction, Methods Mol.Biol. 103, 89-101, 2005.
36.   Dancau, A.-M., Simon, R., Mirlacher, M., and Sauter, G., Tissue microarrays, in Methods Mol.Biol. 1381(Cancer Gene Profiling. Methods and Protocols. ed.Grützmann and C.PIlarsky), Chapter 3, pps. 53-65, Springer Science-Business Media, New York, New York, USA, 2016.
37.  Zone, C., Venot, A., Li, X. et al., Heparan sulfate microarray reveals that heparan sulfate-protein binding exhibits different ligarnd requirements, J.Am.Chem.Soc. 139, 9534-9543, 2017.

© Roger L Lundblad August 4, 2018