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Advances in Experimental Medicine and... 2016Antibody-based proteomic approaches play an important role in high-throughput, multiplexed protein expression profiling in health and disease. These antibody-based... (Review)
Review
Antibody-based proteomic approaches play an important role in high-throughput, multiplexed protein expression profiling in health and disease. These antibody-based technologies will provide (miniaturized) set-ups capable of the simultaneously profiling of numerous proteins in a specific, sensitive, and rapid manner, targeting high- as well as low-abundant proteins, even in crude proteomes such as serum. The generated protein expression patterns, or proteomic snapshots, can then be transformed into proteomic maps, or detailed molecular fingerprints, revealing the composition of the target (sample) proteome at a molecular level. By using bioinformatics, candidate biomarker signatures can be deciphered and evaluated for clinical applicability. The approaches will provide unique opportunities for e.g. disease diagnostics, biomarker discovery, patient stratification, predicting disease recurrence, and evidence-based therapy selection. In this review, we describe the current status of the antibody-based proteomic approaches, focusing on antibody arrays. Furthermore, the current benefits and limitations of the approaches, as well as a set of selected key applications outlining the applicative potential will be discussed.
Topics: Antibodies; Autoimmune Diseases; Gene Expression; Gene Expression Profiling; Humans; Hypersensitivity; Immunohistochemistry; Neoplasms; Protein Array Analysis; Proteome; Proteomics; Sensitivity and Specificity
PubMed: 27686812
DOI: 10.1007/978-3-319-42316-6_11 -
Current Protein & Peptide Science 2021Modern protein science is broadening horizons by moving toward the systemic description of proteins in their natural habitats. This implies a transition from a classical... (Review)
Review
Modern protein science is broadening horizons by moving toward the systemic description of proteins in their natural habitats. This implies a transition from a classical reductionist approach associated with consideration of the unique structure and specific biological activity of an individual protein in a purified form to studying entire proteomes and their functions. This minireview provides a brief description of structural, functional, and expression proteomics, the dark proteome (or unfoldome), and some of the tools utilized in the analyses of proteomes.
Topics: Humans; Proteome; Proteomics
PubMed: 34382522
DOI: 10.2174/1389203722666210812120751 -
Scientific Reports Aug 2020Cancer cells release small extracellular vesicles, exosomes, that have been shown to contribute to various aspects of cancer development and progression. Differential...
Cancer cells release small extracellular vesicles, exosomes, that have been shown to contribute to various aspects of cancer development and progression. Differential analysis of exosomal proteomes from cancerous and non-tumorigenic breast cell lines can provide valuable information related to breast cancer progression and metastasis. Moreover, such a comparison can be explored to find potentially new protein biomarkers for early disease detection. In this study, exosomal proteomes of MDA-MB-231, a metastatic breast cancer cell line, and MCF-10A, a non-cancerous epithelial breast cell line, were identified by nano-liquid chromatography coupled to tandem mass spectrometry. We also tested three exosomes isolation methods (ExoQuick, Ultracentrifugation (UC), and Ultrafiltration-Ultracentrifugation) and detergents (n-dodecyl β-D-maltoside, Triton X-100, and Digitonin) for solubilization of exosomal proteins and enhanced detection by mass spectrometry. A total of 1,107 exosomal proteins were identified in both cell lines, 726 of which were unique to the MDA-MB-231 breast cancer cell line. Among them, 87 proteins were predicted to be relevant to breast cancer and 16 proteins to cancer metastasis. Three exosomal membrane/surface proteins, glucose transporter 1 (GLUT-1), glypican 1 (GPC-1), and disintegrin and metalloproteinase domain-containing protein 10 (ADAM10), were identified as potential breast cancer biomarkers and validated with Western blotting and high-resolution flow cytometry. We demonstrated that exosomes are a rich source of breast cancer-related proteins and surface biomarkers that may be used for disease diagnosis and prognosis.
Topics: Biomarkers, Tumor; Breast Neoplasms; Exosomes; Female; Humans; Mass Spectrometry; Proteome; Proteomics; Tumor Cells, Cultured; Ultracentrifugation
PubMed: 32782317
DOI: 10.1038/s41598-020-70393-4 -
Expert Review of Proteomics 2023Alzheimer's disease (AD) is a neurodegenerative disorder characterized by progressive cognitive decline, memory loss, and changes in behavior. Accumulating evidence... (Review)
Review
INTRODUCTION
Alzheimer's disease (AD) is a neurodegenerative disorder characterized by progressive cognitive decline, memory loss, and changes in behavior. Accumulating evidence indicates that dysfunction of glial cells, including astrocytes, microglia, and oligodendrocytes, may contribute to the development and progression of AD. Large-scale analysis of glial proteins sheds light on their roles in cellular processes and diseases. In AD, glial proteomics has been utilized to understand glia-based pathophysiology and identify potential biomarkers and therapeutic targets.
AREA COVERED
In this review, we provide an updated overview of proteomic analysis of glia in the context of AD. Additionally, we discuss current challenges in the field, involving glial complexity and heterogeneity, and describe some cutting-edge proteomic technologies to address them.
EXPERT OPINION
Unbiased comprehensive analysis of glial proteomes aids our understanding of the molecular and cellular mechanisms of AD pathogenesis. These investigations highlight the crucial role of glial cells and provide novel insights into the mechanisms of AD pathology. A deeper understanding of the AD-related glial proteome could offer a repertoire of potential biomarkers and therapeutics. Further technical advancement of glial proteomics will enable us to identify proteins within individual cells and specific cell types, thus significantly enhancing our comprehension of AD pathogenesis.
Topics: Humans; Alzheimer Disease; Proteome; Proteomics; Neuroglia; Biomarkers
PubMed: 37724426
DOI: 10.1080/14789450.2023.2260955 -
Methods in Molecular Biology (Clifton,... 2022Plasma and serum are rich sources of proteins that are commonly used for clinical proteome profiling and biomarkers discovery. However, high-throughput plasma proteome...
Plasma and serum are rich sources of proteins that are commonly used for clinical proteome profiling and biomarkers discovery. However, high-throughput plasma proteome profiling and quantitative analysis using mass spectrometry are challenging because of the large dynamic range of protein abundance and complexity. To overcome these challenges, we developed a convenient high-throughput workflow of depleted plasma using the 4D-Proteomics feature of the Bruker timsTOF Pro mass spectrometer with data-dependent (PASEF) and data-independent acquisition (diaPASEF) method that can potentially be used in a clinical proteome profiling and biomarker discoveries. This workflow is robust, optimal for high throughput, high proteome depth, and is reproducible. In our sample preparation steps, we used immuno-depletion steps to remove high-abundance plasma proteins, and without any further cleanup steps, we can use depleted plasma samples directly for enzymatic digestion. Immuno-depletion steps and 4D-Proteomics features of timsTOF Pro increase the plasma proteome depth, and accuracy with the identification of >800 protein groups.
Topics: Biomarkers; Blood Proteins; Plasma; Proteome; Proteomics
PubMed: 36127608
DOI: 10.1007/978-1-0716-2565-1_36 -
Advances in Experimental Medicine and... 2021Autophagy is an evolutionarily conserved intracellular degradation process. Autophagy is closely involved in human health and diseases. In recent years, mass...
Autophagy is an evolutionarily conserved intracellular degradation process. Autophagy is closely involved in human health and diseases. In recent years, mass spectrometry-based proteomic methods have become important and powerful tools for autophagy studies. These types of techniques have been especially helpful to reveal the range of degradation substrates of autophagy through large-scale, unbiased analysis of cellular proteomes. At present, a variety of mass spectrometry-based proteomics methods have been successfully applied to autophagy research.
Topics: Autophagy; Humans; Mass Spectrometry; Proteome; Proteomics
PubMed: 34260034
DOI: 10.1007/978-981-16-2830-6_17 -
Journal of Proteomics Jul 2014Human individuals differ from one another in almost all of their genes due to single nucleotide polymorphisms (SNPs). When the maternal and the paternal genomes become... (Review)
Review
Human individuals differ from one another in almost all of their genes due to single nucleotide polymorphisms (SNPs). When the maternal and the paternal genomes become combined in a F1 individual, the two alleles of each gene represent arbitrary combinations. In consequence, individuals show high variability in protein expression. Furthermore, within a proteome, the proteins form networks of protein-protein interactions. These networks differ between individuals in robustness against genetic or/and environmental perturbation due to polymorphisms, which differ in type and composition between individuals, and modify the arrangement of proteins in the proteomic network. As a general conclusion, the robustness of a human individual against diseases may depend on the structure and expression of the protein-protein interaction network that varies in its functional efficiency between individuals due to "network-polymorphisms". This article is part of a Special Issue entitled: 20years of Proteomics in memory of Viatliano Pallini. Guest Editors: Luca Bini, Juan J. Calvete, Natacha Turck, Denis Hochstrasser and Jean-Charles Sanchez.
Topics: Anniversaries and Special Events; Female; Gene-Environment Interaction; History, 20th Century; History, 21st Century; Humans; Male; Polymorphism, Single Nucleotide; Precision Medicine; Proteome; Proteomics
PubMed: 24732725
DOI: 10.1016/j.jprot.2014.04.003 -
Biochimica Et Biophysica Acta Aug 2016Although major advances have been made during the past 20 years in our understanding of the genetic and genomic consequences of polyploidy, our knowledge of polyploidy... (Review)
Review
Although major advances have been made during the past 20 years in our understanding of the genetic and genomic consequences of polyploidy, our knowledge of polyploidy and the proteome is in its infancy. One of our goals is to stimulate additional study, particularly broad-scale proteomic analyses of polyploids and their progenitors. Although it may be too early to generalize regarding the extent to which transcriptomic data are predictive of the proteome of polyploids, it is clear that the proteome does not always reflect the transcriptome. Despite limited data, important observations on the proteomes of polyploids are emerging. In some cases, proteomic profiles show qualitatively and/or quantitatively non-additive patterns, and proteomic novelty has been observed. Allopolyploids generally combine the parental contributions, but there is evidence of parental dominance of one contributing genome in some allopolyploids. Autopolyploids are typically qualitatively identical to but quantitatively different from their parents. There is also evidence of parental legacy at the proteomic level. Proteomes clearly provide insights into the consequences of genomic merger and doubling beyond what is obtained from genomic and/or transcriptomic data. Translating proteomic changes in polyploids to differences in morphology and physiology remains the holy grail of polyploidy--this daunting task of linking genotype to proteome to phenotype should emerge as a focus of polyploidy research in the next decade. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.
Topics: Gene Expression Profiling; Plant Proteins; Plants; Polyploidy; Proteome; Proteomics
PubMed: 26993527
DOI: 10.1016/j.bbapap.2016.03.010 -
Biochimica Et Biophysica Acta. Proteins... Nov 2020Saliva is identified as functional equivalent to serum, reflecting the physiological state of the body, as well as hormonal, emotional, nutritional and metabolic... (Review)
Review
Saliva is identified as functional equivalent to serum, reflecting the physiological state of the body, as well as hormonal, emotional, nutritional and metabolic alterations. The application of mass spectrometry based approaches has allowed a thorough characterization of the saliva proteome and led to the discovery of putative biomarkers. Several salivary biomarkers have been recently explored as potentially useful screening tools in patients diagnosed with metabolic disorders. In this review, we provide an overview of saliva proteomics studies, with a focus on diabetes, and we explore the evidence for the utility of well identified markers for the diagnosis and monitoring of the disease. Emerging approaches in salivary diagnostics that may significantly advance the field of diabetes research are also highlighted.
Topics: Biomarkers; Diabetes Mellitus; Humans; Proteome; Proteomics; Saliva
PubMed: 32663525
DOI: 10.1016/j.bbapap.2020.140494 -
Expert Review of Proteomics 2022Schistosomes are long-lived blood dwelling helminth parasites using intricate mechanisms to invade, mature, and reproduce inside their vertebrate hosts, whilst...
INTRODUCTION
Schistosomes are long-lived blood dwelling helminth parasites using intricate mechanisms to invade, mature, and reproduce inside their vertebrate hosts, whilst simultaneously deploying immune evasion strategies. Their multi-tissue organization and solid body plan presents particular problems for the definition of sub-proteomes.
AREAS COVERED
Here, we focus on the two host-parasite interfaces of the adult worm accessible to the immune system, namely the tegument and the alimentary tract, but also on the secretions of the infective cercaria, the migrating schistosomulum and the mature egg. In parallel, we introduce the concepts of "leakyome' and 'disintegrome' to emphasize the importance of interpreting data in the context of schistosome biology so that misleading conclusions about the distinct proteome compositions are avoided. Lastly, we highlight the possible clinical implications of the reviewed proteomic findings for pathogenesis, vaccine design and diagnostics.
EXPERT OPINION
Proteomics has provided considerable insights into the biology of schistosomes, most importantly for rational selection of novel vaccine candidates that might confer protective immunity, but also into the pathogenesis of schistosomiasis. However, given the increasing sensitivity of mass spectrometric instrumentation, we stress the need for care in data interpretation since schistosomes do not deviate from the fundamental rules of eukaryotic cell biology.
Topics: Animals; Proteomics; Helminth Proteins; Schistosoma; Schistosomiasis; Vaccines; Proteome
PubMed: 36331139
DOI: 10.1080/14789450.2022.2142565