Post-Translational Modification Profiling--a High-Content Assay for Identifying Protein Modifications in Mammalian Cellular Systems

Phage Immunoprecipitation Sequencing (PhIP-Seq) for Analyzing Antibody Epitope Repertoires Against Food Antigens

While thousands of food and environmental allergens have been reported, conventional methods for allergy testing typically rely on measuring immunoglobulin E (IgE) binding against panels of dozens to hundreds of antigens. Beyond IgE, also the specificity of other Ig (sub-)classes such as IgG4, has gained interest because of a potential protective role toward allergy.Phage immunoprecipitation sequencing (PhIP-Seq) allows to study hundreds of thousands of rationally selected peptide antigens and to resolve binding specificities of different Ig classes. This technology combines synthetic DNA libraries encoding antigens, with the display on the surface of T7 bacteriophages and next-generation sequencing (NGS) for quantitative readouts. Thereby binding of entire Ig repertoires can be measured to detect the exact epitopes of food allergens and to study potential cross-reactivity.In this chapter, we provide a summary of both the key experimental steps and various strategies for analyzing PhIP-Seq datasets, as well as comparing the advantages and disadvantages of this methodology for measuring antibody responses against food antigens.

Protein microarray applications: Autoantibody detection and posttranslational modification

The discovery of DNA microarrays was a major milestone in genomics; however, it could not adequately predict the structure or dynamics of underlying protein entities, which are the ultimate effector molecules in a cell. Protein microarrays allow simultaneous study of thousands of proteins/peptides, and various advancements in array technologies have made this platform suitable for several diagnostic and functional studies. Antibody arrays enable researchers to quantify the abundance of target proteins in biological fluids and assess PTMs by using the antibodies. Protein microarrays have been used to assess protein-protein interactions, protein-ligand interactions, and autoantibody profiling in various disease conditions. Here, we summarize different microarray platforms with focus on its biological and clinical applications in autoantibody profiling and PTM studies. We also enumerate the potential of tissue microarrays to validate findings from protein arrays as well as other approaches, highlighting their significance in proteomics.

Post-translational modification profiling - A novel tool for mapping the protein modification landscape in cancer

The ubiquitin system plays an important role in essentially every cellular process, regulating numerous pathways ranging from development, transcription, DNA damage response, cell cycle, and signal transduction. Its best studied role involves removal of faulty proteins or those that are not necessary anymore. Aberrations in the ubiquitin system have been implicated in various pathologies including cancer, where specific mutations in E3 ligases such as Mdm2, pVHL, and BRCA1 have been linked to disease progression, prognosis, and resistance to drugs. Yet, there are hundreds of E3 ligases in the human genome and our knowledge of their target proteins and their dynamic regulation in the cellular environment is largely limited. In addition, fundamental questions related to recognition and specificity in ubiquitin conjugation remain unanswered. It is thus of major importance to characterize the ubiquitin landscape under various cellular conditions, and study how the regulatory network is altered in health and disease. To do so, analytical tools that allow identification of ubiquitin substrates, the conjugation and removal of ubiquitin, and the nature of specific ubiquitin linkages that are formed are needed. In this mini-review, we discuss common proteomic methodologies applied to studying the ubiquitome, and specifically focus on our recently developed post-translational modification (PTM) profiling approach. PTM profiling is a functional assay, amenable to biochemical manipulation, which allows the detection of protein modifications in a high-throughput manner. We discuss in detail the advantages and limitations of this system, focusing primarily on examples for analyzing the ubiquitin system in cancer. Uncovering the intricate signaling dynamics governed by and regulating ubiquitin modifications should clearly evolve into a new paradigm in understanding the molecular basis of malignant transformation and the development of novel therapeutic modalities.