Protein array
Developments and Applications of Functional Protein MicroarraysFunctional protein microarray is a crucial tool in the study of proteins in native, unbiased, and high-throughput manner. There is a wide variety of applications, including the study of proteome-wide molecular interactions, analysis of post-translational modifications, identification of novel drug targets, and examination of pathogen-host interactions. Functional protein microarray is also useful in profiling antibody specificity, as well as in the discovery of novel biomarkers, especially for autoimmune diseases, infectious diseases, and cancers. Recently, the virion display method has been applied to produce functional GPCR array for various research and pharmaceutical applications.
Integration of IgA and IgG Autoantigens Improves Performance of Biomarker Panels for Early Diagnosis of Lung CancerLung cancer (LC) remains the leading cause of mortality from malignant tumors worldwide. To identify biomarkers for early detection of LC, we employed the HuProt array platform and ELISA tests to identify and validate for IgA-bound autoantigens, which were then combined with the previously validated IgG autoantigens for the identification and validation of integrated IgA/IgG biomarker panels. We discovered and validated an integrated biomarker panel, with the best performance of 73.5% sensitivity at 85% specificity for early LC diagnosis.
TCPA v3.0: An Integrative Platform to Explore the Pan-Cancer Analysis of Functional Proteomic DataReverse-phase protein arrays represent a powerful functional proteomics approach. Using this platform, we have characterized ∼8,000 patient samples of 32 cancer types through The Cancer Genome Atlas and built a widely used, open-access bioinformatic resource, The Cancer Proteome Atlas (TCPA). Here we have developed a new module called “TCGA Pan-Cancer Analysis,” which provides comprehensive protein-centric, pan-cancer analyses in rich context of TCGA data. This upgraded TCPA (v3.0) provides a more valuable tool for studying functional proteomics and making translational impacts.
Proteome-wide Tyrosine Phosphorylation Analysis Reveals Dysregulated Signaling Pathways in Ovarian TumorsA systematic, multiplexed approach interrogating enzyme-substrate relationships in context of PTMs is fundamental in understanding the dynamics of these pathways in disease processes. Multiplexed PTM reactions on HuProt arrays were developed and applied to 102 TCGA ovarian tumor samples. Data integration and networks analysis led to the prediction that 19 tyrosine kinases were elevated and potentially responsible for the dysregulated pTyr signaling pathways in ovarian tumors. Elevated kinase activities of PTK2 and PTK2B were confirmed in several ovarian cancer cell lines.
Deciphering Protein Glycosylation by Computational Integration of On-chip Profiling, Glycan-array Data, and Mass SpectrometryA new method is presented to decipher information about the isomeric variants of the glycans attached to purified proteins. The method takes advantage of the specificities of glycosidases and lectins, combined with computational integration of the data with information from glycan arrays and mass spectrometry. The application to microspots of proteins makes it compatible with analyzing low-abundance proteins, providing the potential for studying proteins derived from clinical specimens.