Diagnosis: Nanosensors in Diagnosis and Medical Monitoring
Harry F. Tibbals in Medical Nanotechnology and Nanomedicine, 2017
The emergence of proteomics comes from the growing base of DNA sequence information and new analysis technologies. The proteomics field has been fed by a range of new methods for determining protein localization, protein-protein interactions, posttranslational modifications, and the alteration of protein composition (e.g., differential expression) in tissues and body fluids. Protein analysis is used to characterize gene function, to understand functional relationships between protein molecules, and to provide insight into the mechanisms of complex biological process networks. High throughput techniques such as yeast two-hybrid analysis and affinity tag purification are used to build protein-protein interaction maps. Large-scale protein tagging with subcellular-specific localization provides information about protein function in the cell, and for intercell signaling. MS has emerged as a powerful tool for the analysis of protein complexes. Recent developments in protein microarray technology provide versatile tools for analysis of protein-protein, protein-nucleic acid, protein-lipid, enzyme-substrate, and protein-drug interactions [392-395].
Biochemical Markers in Ophthalmology
Ching-Yu Cheng, Tien Yin Wong in Ophthalmic Epidemiology, 2022
High-throughput methods include protein microarrays [145]. This process involves the application of small amounts of sample to a “chip” for analysis. Antibodies are subsequently fixated to the chip surface and used to capture target proteins in a complex model. This process is often referred to as analytical protein microarray [145]. Functional microarrays allow for the characterization of protein functions, including enzyme substrate turnover and protein–RNA interactions [146]. Reverse-phase protein microarray involves the process of using both healthy and diseased tissue bound to a chip, which is subsequently probed with antibodies against target proteins. MS-based proteomics is also a form of complex gel-free methods of separating proteins. This includes isotope-coded affinity tag, stable isotope labeling with amino acids in culture, and isobaric tags [147].
The Precision Medicine Approach in Oncology
David E. Thurston, Ilona Pysz in Chemistry and Pharmacology of Anticancer Drugs, 2021
More recently, protein microarray technology has been introduced to enhance throughput in proteomics. Originally based only on the immunoassay principal with antibodies attached to the surface of the array, the latest approaches employ a large range of capture and detection technologies, and are used for applications including protein expression profiling, molecular interaction mapping, biomarker and drug discovery, disease diagnosis and vaccine development (Figure 11.7). Summary of key protein microarray technologies and their applications in proteomics (Figure from Hongyan Sun, Grace Y.J. Chen, Shao Q. Yao (2013), “Recent Advances in Microarray Technologies for Proteomics”, Chemistry & Biology, 20, 5, pp685–699, (https://doi.org/10.1016/j.chembiol.2013.04.009). Copyright © 2013 Elsevier Ltd).
Advances in cell-free protein array methods
Published in Expert Review of Proteomics, 2018
Xiaobo Yu, Brianne Petritis, Hu Duan, Danke Xu, Joshua LaBaer
These landmark biomarkers were discovered in the 1970s and 1980s using traditional DNA sequencing, immunoprecipitation and cytogenetic techniques, respectively [7–9]. Like other discoveries at that time, they relied on testing ‘best guesses’ that arose from a reductionist approach to pathway discovery. Since then, biomedicine has recognized vast heterogeneity in disease and has embraced more complex systems, including the need to examine full genomes and proteomes. As part of this ‘omics’ revolution, a key tool, the protein microarray, was developed as a high throughput method to examine thousands of proteins simultaneously. First introduced in the late 1990s, it has been utilized increasingly to identify disease biomarkers and other biomedical discoveries [10–17]. See [18,19] for recent reviews of different protein microarray methods.
Recent insights into human bronchial proteomics – how are we progressing and what is next?
Published in Expert Review of Proteomics, 2018
Heng Wee Tan, Yan-Ming Xu, Dan-Dan Wu, Andy T. Y. Lau
In addition to MS-based technologies, microarray-based methods using antibodies are another compelling and rapidly advancing tools in proteomics [37,38]. High-throughput protein microarray, or the ‘western array’, can detect thousands of different targeted proteins in a single experiment. The commercially available HuProt™ Human Proteome Microarray is currently the world’s largest microarray platform as it contains >20,000 proteins and covers about 75% of the human proteome [39]. An ELISA-based array, the Extracellular Vesicle Array (EV Array), has been designed to detect LC-related exosomes using an antibody panel targeting the extracellular domain of selected membrane or membrane-associated proteins [40]. The EV array contains several exosome markers (e.g. CD9, CD63, CD81, and TSG101) and up to 24 cancer markers and have emerged as a promising screening tool for LC patients. Furthermore, high-throughput IHC and fluorescence in situ hybridization tests can be conveniently done using tissue microarrays (TMAs) and next-generation TMAs [41]. TMAs are capable of analyzing more than 1000 tissue samples in parallel and are particularly useful in analyzing tumor samples. These antibody-based proteomic approaches harbor an advantage over other proteomic methods by being able to sensitively and rapidly detect a large number of proteins simultaneously in a cost-effective manner.
Protein array-based companion diagnostics in precision medicine
Published in Expert Review of Molecular Diagnostics, 2020
Thomas B. G. Poulsen, Azra Karamehmedovic, Christopher Aboo, Malene Møller Jørgensen, Xiaobo Yu, Xiangdong Fang, Jonathan M. Blackburn, Claus H. Nielsen, Tue W. Kragstrup, Allan Stensballe
Multiple protein array technologies have been established based on the nature of active surface reactivity, chemistry, or protein complement [15]. Firstly, protein arrays that either utilize antibodies or antigens spotted on array surface enable relative quantitation of protein levels in biological samples (termed forward-phase protein arrays) and assessment of protein–protein interaction or antiprotein antibody levels [16,17]. In contrast, protein arrays can be constructed by immobilizing the whole repertoire of patient proteins that represent the transformed or dysregulated cell populations on the active surface (termed reverse-phase protein arrays (RPPA)) [18–20]. Each array format (forward-phase or reverse-phase protein arrays) has its own advantages and disadvantages, and their usefulness as CDx assay may vary, depending upon the specific clinical question. RPPA has been used both as a biomarker discovery platform but also as a tool for precision medicine in large clinical trial studies [21–23]. One study based on the I-SPY1 clinical trial was able to identify a subtype of patients with breast cancer with high levels of phosphorylated HER2 expression but no overexpression resulting in these patients being excluded from a potentially beneficial treatment effect from HER2 targeted therapy [23]. These trials and their results demonstrate the power of RPPA in biomarker research. However, this review will not focus on RPPA but on other widely used commercially available microarray platforms that we see suitable for CDx. Examples of such platforms include but are not limited to: Human Proteome Microarray (HuProt), ProtoArray, NAPPA arrays, Human Protein Fragment arrays, and Immunome arrays. These platforms allow the measurement of autoantibody reactions with thousands of unique human proteins simultaneously [24,25]. A quick summary of selected protein microarray platforms can be found in Table 1, while a more thorough description will follow below.
Related Knowledge Centers
- Antibody Microarray
- DNA Microarray
- Microarray
- Proteomics
- Messenger Rna
- High-Throughput Screening
- Microplate
- Hybridization Probe
- Laser Scanning
- Post-Translational Modification