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Expert Review of Proteomics Apr 2020Cellular senescence is a rapidly growing field with potential relevance for the treatment of multiple human diseases. In the last decade, cellular senescence and the... (Review)
Review
INTRODUCTION
Cellular senescence is a rapidly growing field with potential relevance for the treatment of multiple human diseases. In the last decade, cellular senescence and the senescence-associated secretory phenotype (SASP) have emerged as central drivers of aging and many chronic diseases, including cancer, neurodegeneration, heart disease and osteoarthritis. Major efforts are underway to develop drugs that selectively eliminate senescent cells (senolytics) or alter the SASP (senomorphics) to treat age-related diseases in humans. The translation of senescence-targeting therapies into humans is still in early stages. Nonetheless, it is clear that proteomic approaches will facilitate the discovery of important SASP proteins, development of senescence- and SASP-derived biomarkers, and identification of therapeutic targets for senolytic and senomorphic drugs.
AREAS COVERED
We review recent proteomic studies of cellular senescence and their translational relevance and, particularly, characterization of the secretory phenotype and preclinical development of biomarkers (from 2008-2020, PubMed). We focus on emerging areas, such as the heterogeneity of senescent cells and the SASP, extracellular vesicles released by senescent cells, and validating biomarkers of aging in vivo.
EXPERT OPINION
Proteomic and multi-omic approaches will be important for the development of senescence-based biomarkers to facilitate and monitor future therapeutic interventions that target senescent cells.
Topics: Animals; Cellular Senescence; Exosomes; Humans; Phenotype; Proteome; Proteomics
PubMed: 32425074
DOI: 10.1080/14789450.2020.1766976 -
The Journal of Physiology Feb 2005Proteomics, the study of the proteome (the collection of all the proteins expressed from the genome in all isoforms, polymorphisms and post-translational modifications),... (Review)
Review
Proteomics, the study of the proteome (the collection of all the proteins expressed from the genome in all isoforms, polymorphisms and post-translational modifications), is a rapidly developing field in which there are numerous new and often expensive technologies, making it imperative to use the most appropriate technology for the biological system and hypothesis being addressed. This review provides some guidelines on approaching a broad-based proteomics project, including strategies on refining hypotheses, choosing models and proteomic approaches with an emphasis on aspects of sample complexity (including abundance and protein characteristics), and separation technologies and their respective strengths and weaknesses. Finally, issues related to quantification, mass spectrometry and informatics strategies are discussed. The goal of this review is therefore twofold: the first section provides a brief outline of proteomic technologies, specifically with respect to their applications to broad-based proteomic approaches, and the second part provides more details about the application of these technologies in typical scenarios dealing with physiological and pathological processes. Proteomics at its best is the integration of carefully planned research and complementary techniques with the advantages of powerful discovery technologies that has the potential to make substantial contributions to the understanding of disease and disease processes.
Topics: Animals; Chromatography; Computer Simulation; Electrophoresis; Gene Expression Profiling; Humans; Mass Spectrometry; Models, Biological; Protein Array Analysis; Proteome; Proteomics; Research Design
PubMed: 15611015
DOI: 10.1113/jphysiol.2004.080341 -
BMC Bioinformatics Mar 2017High-accuracy mass spectrometry enables near comprehensive quantification of the components of the cellular proteomes, increasingly including their chemically modified...
BACKGROUND
High-accuracy mass spectrometry enables near comprehensive quantification of the components of the cellular proteomes, increasingly including their chemically modified variants. Likewise, large-scale libraries of quantified synthetic peptides are becoming available, enabling absolute quantification of chemically modified proteoforms, and therefore systems-level analyses of changes of their absolute abundance and stoichiometry. Existing computational methods provide advanced tools for mass spectral analysis and statistical inference, but lack integrated functions for quantitative analysis of post-translationally modified proteins and their modification stoichiometry.
RESULTS
Here, we develop ProteoModlR, a program for quantitative analysis of abundance and stoichiometry of post-translational chemical modifications across temporal and steady-state biological states. While ProteoModlR is intended for the analysis of experiments using isotopically labeled reference peptides for absolute quantitation, it also supports the analysis of labeled and label-free data, acquired in both data-dependent and data-independent modes for relative quantitation. Moreover, ProteoModlR enables functional analysis of sparsely sampled quantitative mass spectrometry experiments by inferring the missing values from the available measurements, without imputation. The implemented architecture includes parsing and normalization functions to control for common sources of technical variation. Finally, ProteoModlR's modular design and interchangeable format are optimally suited for integration with existing computational proteomics tools, thereby facilitating comprehensive quantitative analysis of cellular signaling.
CONCLUSIONS
ProteoModlR and its documentation are available for download at http://github.com/kentsisresearchgroup/ProteoModlR as a stand-alone R package.
Topics: Evaluation Studies as Topic; Isotope Labeling; Mass Spectrometry; Peptides; Protein Processing, Post-Translational; Proteome; Proteomics; Software
PubMed: 28259147
DOI: 10.1186/s12859-017-1563-6 -
Expert Review of Proteomics Feb 2015Effective traumatic brain injury (TBI) therapeutics remains stubbornly elusive. Efforts in the field have been challenged by the heterogeneity of clinical TBI, with... (Review)
Review
Effective traumatic brain injury (TBI) therapeutics remains stubbornly elusive. Efforts in the field have been challenged by the heterogeneity of clinical TBI, with greater complexity among underlying molecular phenotypes than initially conceived. Future research must confront the multitude of factors comprising this heterogeneity, representing a big data challenge befitting the coming informatics age. Proteomics is poised to serve a central role in prescriptive therapeutic development because it offers an efficient endpoint within which to assess post-TBI biochemistry. We examine rationale for multifactor TBI proteomic studies and the particular importance of temporal profiling in defining biochemical sequences and guiding therapeutic development. Finally, we offer perspective on repurposing biofluid proteomics to develop theragnostic assays with which to prescribe, monitor and assess pharmaceutics for improved translation and outcome for patients with TBI.
Topics: Animals; Biomarkers; Brain Injuries; Drug Discovery; Humans; Neuroprotective Agents; Proteome; Proteomics
PubMed: 25603864
DOI: 10.1586/14789450.2015.1000869 -
Free Radical Research 2015Lipid peroxidation is responsible for the generation of chemically reactive, diffusible lipid-derived electrophiles (LDEs) that covalently modify cellular protein... (Review)
Review
Lipid peroxidation is responsible for the generation of chemically reactive, diffusible lipid-derived electrophiles (LDEs) that covalently modify cellular protein targets. These protein modifications modulate protein activity and macromolecular interactions and induce adaptive and toxic cell signaling. Protein modifications induced by LDEs can be identified and quantified by affinity enrichment and liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based techniques. Tagged LDE analog probes with different electrophilic groups can be covalently captured by click chemistry for LC-MS/MS analyses, thereby enabling in-depth studies of proteome damage at the protein and peptide sequence levels. Conversely, click-reactive, thiol-directed probes can be used to evaluate thiol damage caused by LDE by difference. These analytical approaches permit systematic study of the dynamics of protein damage caused by LDE and mechanisms by which oxidative stress contribute to toxicity and diseases.
Topics: Chromatography, Liquid; Humans; Lipid Peroxidation; Protein Processing, Post-Translational; Proteome; Proteomics; Tandem Mass Spectrometry
PubMed: 25819163
DOI: 10.3109/10715762.2015.1019348 -
Quantitative proteomic strategies to study reproduction in farm animals: Female reproductive fluids.Journal of Proteomics Aug 2020Reproductive fluids from the female reproductive tract are gaining attention for their potential to support and optimize reproductive processes, including gamete... (Review)
Review
Reproductive fluids from the female reproductive tract are gaining attention for their potential to support and optimize reproductive processes, including gamete maturation and embryo culture in vitro. Quantitative proteomics is a powerful way to decipher the proteome of reproductive tract fluids and to identify biologically relevant proteins. The present review describes proteomic strategies for analysing female reproductive fluid proteins. In addition, it considers the strategies for the preparation of oviductal, uterine and follicular fluid samples. Finally, it highlights the main results of quantitative proteomic studies, providing insights into the biological processes related to reproductive biology in farm animals. SIGNIFICANCE: Assisted reproductive technologies (ARTs) have become vitally important for farm animal breeding and much effort is going into the optimization and refinement of the techniques. There are also attempts to imitate physiological conditions by adding reproductive fluids or individual fluid proteins to improve in vitro procedures. A detailed knowledge of the reproductive fluid proteomes is indispensable. The present review summarizes the most widely used quantitative proteomic approaches for the analysis of fluids from the female reproductive tract and highlights the potential of quantitative proteomics to delineate reproductive processes and identify candidate proteins for ARTs in farm animals.
Topics: Animals; Farms; Female; Humans; Oviducts; Proteome; Proteomics; Reproduction
PubMed: 32593762
DOI: 10.1016/j.jprot.2020.103884 -
Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue... Nov 2003Proteomics has its origins in two-dimensional gel electrophoresis (2-DE), a technique developed more than twenty years ago. 2-DE has a high-resolution capacity, and was... (Review)
Review
Proteomics has its origins in two-dimensional gel electrophoresis (2-DE), a technique developed more than twenty years ago. 2-DE has a high-resolution capacity, and was initially used primarily for separating and characterizing proteins in complex mixtures. 2-DE remains an important tool for protein identification, but is now normally coupled with mass spectrometry (MS), a technique which has advanced considerably in recent years. The recent completion of human genome project has produced a large DNA database which can be utilized through bioinformatics, and the next challenge for scientists is to uncover the entire proteome of a particular organism. The integration of genomic and proteomic data will help to elucidate the functions of proteins in the pathogenesis of diseases and the ageing process, and could lead to the discovery of novel drug target proteins and biomarkers of diseases. This review describes recent advances in proteomic technology and discusses the potential applications of proteomics in biomedical research.
Topics: Biomedical Research; Electrophoresis, Gel, Two-Dimensional; Humans; Protein Array Analysis; Proteome; Proteomics
PubMed: 14614532
DOI: No ID Found -
Molecular & Cellular Proteomics : MCP Jan 2016Bottom-up proteomics relies on the use of proteases and is the method of choice for identifying thousands of protein groups in complex samples. Top-down proteomics has...
Bottom-up proteomics relies on the use of proteases and is the method of choice for identifying thousands of protein groups in complex samples. Top-down proteomics has been shown to be robust for direct analysis of small proteins and offers a solution to the "peptide-to-protein" inference problem inherent with bottom-up approaches. Here, we describe the first large-scale integration of genomic, bottom-up and top-down proteomic data for the comparative analysis of patient-derived mouse xenograft models of basal and luminal B human breast cancer, WHIM2 and WHIM16, respectively. Using these well-characterized xenograft models established by the National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium, we compared and contrasted the performance of bottom-up and top-down proteomics to detect cancer-specific aberrations at the peptide and proteoform levels and to measure differential expression of proteins and proteoforms. Bottom-up proteomic analysis of the tumor xenografts detected almost 10 times as many coding nucleotide polymorphisms and peptides resulting from novel splice junctions than top-down. For proteins in the range of 0-30 kDa, where quantitation was performed using both approaches, bottom-up proteomics quantified 3,519 protein groups from 49,185 peptides, while top-down proteomics quantified 982 proteoforms mapping to 358 proteins. Examples of both concordant and discordant quantitation were found in a ∼60:40 ratio, providing a unique opportunity for top-down to fill in missing information. The two techniques showed complementary performance, with bottom-up yielding eight times more identifications of 0-30 kDa proteins in xenograft proteomes, but failing to detect differences in certain posttranslational modifications (PTMs), such as phosphorylation pattern changes of alpha-endosulfine. This work illustrates the potency of a combined bottom-up and top-down proteomics approach to deepen our knowledge of cancer biology, especially when genomic data are available.
Topics: Animals; Breast Neoplasms; Chromatography, High Pressure Liquid; Female; Genotype; Heterografts; Humans; Mice; Molecular Weight; Peptides; Polymorphism, Single Nucleotide; Proteome; Proteomics; Tandem Mass Spectrometry; Transplantation, Heterologous
PubMed: 26503891
DOI: 10.1074/mcp.M114.047480 -
Biochimica Et Biophysica Acta.... Jan 2022Though proteases were long regarded as nonspecific degradative enzymes, over time, it was recognized that they also hydrolyze peptide bonds very specifically with a... (Review)
Review
Though proteases were long regarded as nonspecific degradative enzymes, over time, it was recognized that they also hydrolyze peptide bonds very specifically with a limited substrate pool. This irreversible posttranslational modification modulates the fate and activity of many proteins, making proteolytic processing a master switch in the regulation of e.g., the immune system, apoptosis and cancer progression. N- and C-terminomics, the identification of protein termini, has become indispensable in elucidating protease substrates and therefore protease function. Further, terminomics has the potential to identify yet unknown proteoforms, e.g. formed by alternative splicing or the recently discovered alternative ORFs. Different strategies and workflows have been developed that achieve higher sensitivity, a greater depth of coverage or higher throughput. In this review, we summarize recent developments in both N- and C-terminomics and include the potential of top-down proteomics which inherently delivers information on both ends of analytes in a single analysis.
Topics: Animals; Humans; Proteolysis; Proteome; Proteomics; RNA Splicing
PubMed: 34626679
DOI: 10.1016/j.bbamcr.2021.119137 -
Proteomics Jan 2016Capillary zone electrophoresis (CZE) is emerging as a useful tool in proteomic analysis. Interest arises from dramatic improvements in performance that result from... (Review)
Review
Capillary zone electrophoresis (CZE) is emerging as a useful tool in proteomic analysis. Interest arises from dramatic improvements in performance that result from improvements in the background electrolyte used for the separation, the incorporation of advanced sample injection methods, the development of robust and sensitive electrospray interfaces, and the coupling with Orbitrap mass spectrometers with high resolution and sensitivity. The combination of these technologies produces performance that is rapidly approaching the performance of UPLC-based methods for microgram samples and exceeds the performance of UPLC-based methods for mid- to low nanogram samples. These systems now produce over 10 000 peptide IDs in a single 100-min analysis of the HeLa proteome.
Topics: Electrophoresis, Capillary; Humans; Proteome; Proteomics; Quality Improvement; Spectrometry, Mass, Electrospray Ionization
PubMed: 26508368
DOI: 10.1002/pmic.201500339