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“Omics” Technologies in Vaccine Research
Published in Mesut Karahan, Synthetic Peptide Vaccine Models, 2021
A detailed picture of the protein-to-protein interactions related to the immune responses against infections, virulence of the pathogen, or host-pathogen interactions can be obtained via proteomics, and “interactome” of the cell is revealed. Proteins undergo modifications to gain their function or they are found in different locations of the cell. These certain groups of proteins can be isolated and identified using proteomics techniques. For instance, phosphorylated proteins playing roles in the signal transduction are identified via the phosphoproteomics technique, and the “kinome” of the cell is identified (Buonaguro and Pulendran 2011) or secreted proteins can be identified via “secretome” analysis (Bidmos et al. 2018).
Resistance Exercise Training and The Regulation of Muscle Protein Synthesis
Published in Peter M. Tiidus, Rebecca E. K. MacPherson, Paul J. LeBlanc, Andrea R. Josse, The Routledge Handbook on Biochemistry of Exercise, 2020
Nathan Hodson, Daniel R. Moore, Chris McGlory
In summary, resistance exercise represents a robust non-pharmacological means to enhance rates of MyoPS/MPS and skeletal muscle hypertrophy. Whilst the minutiae of resistance exercise prescription, such as the manipulation of repetition load and contraction mode, have received significant experimental attention, for the general population performing sufficient resistance exercise volume is often the primary barrier to maximizing gains in skeletal muscle mass with resistance exercise training (16, 75). However, it is known that there is large heterogeneity in the response of skeletal muscle size to resistance exercise training between individuals, even with high-volume resistance exercise training. In this regard, future work that aims to reveal the underlying mechanisms responsible for this “responder/non-responder” phenomenon would provide important information for the field. Although it is important to note that when examining a range of outcomes (i.e., changes in lean body mass, strength, and size), it is known that individuals will exhibit a positive adaptive response to resistance exercise training in at least one of these variables (16). Thus, from a public health standpoint, engagement in resistance exercise should be encouraged with the confidence that at the very least one aspect of musculoskeletal health will be improved (75). Additionally, recent evidence in rodents has challenged the long-established thesis that resistance exercise–induced gains in skeletal muscle mass are mTORC1-dependent. Future work using novel technologies such as phosphoproteomics and transcriptomics in humans will no doubt help elucidate novel molecular signals that regulate contraction-mediated up-regulation of translational control and rates of MPS (in all fractions of skeletal muscle) (113). Such information would not only assist with the design of post-exercise nutritional interventions aimed at maximizing muscle mass but also the development of targeted pharmacological interventions to combat musculoskeletal disease.
Oncoproteomic profiling of AML: moving beyond genomics
Published in Expert Review of Proteomics, 2022
Sunil K. Joshi, Cristina E. Tognon, Brian J. Druker, Karin D. Rodland
As demonstrated by Koschade et al., the combination of proteomics and phosphoproteomics led to the identification of the autophagy network – AKT/mTORC1/ULK1/ATG3 – as a primary node to FLT3 inhibitor resistance[12]. The authors employed a recently developed proteomics technology, termed translatome proteomics, which measures changes in the nascent cellular proteome and paired this approach with phosphoproteomics. The aggregate of proteomic analyses performed on cell lines, patient-derived xenografts, and primary AML cells ex vivo identified autophagy as a key pathway modulated upon FLT3 inhibition. Pharmacological or genetic inhibition of autophagy restored FLT3 inhibitor sensitivity and led to extended overall survival. It is important to note that the essential finding of autophagy hinges on the changes detected in the cellular proteome – changes that are unlikely to be detected with RNA-seq and which require the depth and quantitative characterization offered by translatome proteomics. This study lends additional support to the notion that transcriptomics is not a viable surrogate for investigating non-genetic mechanisms of resistance that manifest at the protein level.
Strategies for mass spectrometry-based phosphoproteomics using isobaric tagging
Published in Expert Review of Proteomics, 2021
Xinyue Liu, Rose Fields, Devin K. Schweppe, Joao A. Paulo
Sample multiplexing can offer several benefits for phosphoproteomics analysis. For instance, the sensitivity and dynamic range of phosphorylation profiling are limited by the general low abundance of phosphopeptides among all peptides, as well as the low stoichiometry of the phosphorylated peptide versus its unphosphorylated version. Sample multiplexing can essentially boost sensitivity as the intensities of chromatographic peaks, precursor ions, and fragment ions are increased due to the additive effects of a given peptide having identical mass and chromatographic properties across all isobaric tag-labeled samples. Moreover, missing values are reduced when samples are arranged in a single multiplexed experiment, eliminating the caveats of stochastic precursor sampling across multiple, individually analyzed samples. Overcoming the challenges of sensitivity and dynamic range is essential for acquiring comprehensive phosphoproteomics datasets and to extract biologically relevant findings therefrom. As such, progress in phosphopeptide enrichment methodologies, enhancements in instrumentation and data acquisition technologies, and further refinements in data analysis strategies will be key to improved tandem mass tag-centric phosphoproteomics studies.
Phosphoproteomics: a valuable tool for uncovering molecular signaling in cancer cells
Published in Expert Review of Proteomics, 2021
Jacqueline S. Gerritsen, Forest M. White
MS-based phosphoproteomics has made great strides over the past decade in terms of detection limits, speed, accuracy and resolution. Phosphoproteomics has emerged as a powerful tool for analysis of signaling networks in diseased tissues and model systems, both in vivo and in vitro. Nonetheless, one of the main challenges in MS-based phosphoproteomics is the application to limited sample amounts/low abundance model systems. Progress in this area has enabled successful phosphoproteomic analysis on extracellular vesicles secreted from cancer cells to identify potential biomarkers in glioblastoma-EGFRVIII variant [133]. Additionally, methods have emerged that address the challenge of limited starting material when working with patient tissue specimens [134], and phosphoproteomic analyses have now been successfully performed on FFPE tissue samples [26,135]. Simultaneously, given the value of patient samples and the importance of multi-omics analysis, methods are being developed that allow for simultaneous extraction of DNA, RNA and protein from samples [136].