Proteomics最新文献

The central dogma of molecular biology, traditionally focused on nucleic acids and proteins, has historically overlooked the crucial involvement of carbohydrates (sugars/glycans) in cellular processes. Carbohydrates combine with lipids, proteins, and RNA to form glycoconjugates-glycolipids, glycoproteins, and glycoRNAs-that mediate signaling, recognition, and dynamic cellular responses. A glycomics-centered perspective within the paracentral dogma extends the central dogma by incorporating additional biomacromolecular modifications, illustrating how glycans function as context-dependent molecular signals synthesized through non-template enzymatic processes that are partly genetically constrained yet structurally unpredictable. Recognized as the "third alphabet of life" after nucleic acids (the first) and amino acids (the second), the glycan encodes rich information that regulates cellular communication, immunity, and disease processes.Glycoconjugates with the recently discovered glycoRNAs demonstrate how glycan modifications integrate with nucleic acids, while O-GlcNAcylation in DNA synthesis and DNA damage response, exemplified by O-GlcNAc transferase and O-GlcNAcase, modulates genome stability and cellular homeostasis. Advances in glycomics, framed within the concept of paracentral dogma, provide deep insights into glycoconjugates and their sugar-encoded information, offering novel avenues for vaccination, targeted interventions and glycomedicine.

Prostate cancer (PCa) is a leading male malignancy worldwide, with metabolic reprogramming being a critical hallmark of its progression. Extracellular vesicles (EVs) derived from tissues directly reflect the tumor microenvironment, offering unique insights into cancer pathophysiology that are unattainable through cell line or biofluid-derived EVs. However, the functional roles of tissue-derived EVs in PCa metabolism remain poorly understood. Leveraging our expertise in murine PCa model establishment and EV isolation from prostate tissue, this study aimed to characterize functional differences between PCa and normal prostate tissue via proteomic analysis of tissue-derived sEVs. We orthotopically implanted luciferase-labeled PCa cells into nude mice to establish an in situ PCa model, confirmed tumor formation via in vivo imaging, and harvested tissues after 4 weeks. sEVs were isolated using ultracentrifugation combined with an iodixanol density cushion and characterized by transmission electron microscopy, nanoparticle tracking analysis, and protein marker profiling. Proteomic analysis identified 28 upregulated and 24 downregulated proteins in PCa-derived sEVs compared to normal controls. Subcellular localization revealed enrichment in the cytoplasm, while pathway analysis highlighted significant involvement in metabolic processes, particularly glycolysis, amino acid biogenesis, carbon metabolism, and pyruvate metabolism. Our study establishes a robust method for isolating prostate tissue sEVs and provides the first evidence that PCa tissue-derived sEVs exhibit profound metabolic pathway alterations. These findings enhance our understanding of PCa progression mechanisms and may facilitate the development of novel diagnostic biomarkers and therapeutic strategies targeting metabolic dysregulation in PCa. SUMMARY: In this study, we created a method to isolate prostate tissue small EVs, based on our knowledge of the murine prostate cancer model building. Our data suggested that prostate tissue small EVs proteins significantly changed in many metabolism pathways, such as Glycolysis, Biogenesis of amino acids, Carbon metabolism and Pyruvate metabolism. In this study, we are the first to report prostate tissue-derived EVs proteins enriched in alterations of cancer metabolism. These differential proteins in PCa tissue EVs reflect metabolic changes in PCa and may provide insights into the development of early diagnostic biomarkers or novel therapeutic strategies.

Myofiber regeneration and membrane repair play crucial roles in maintaining the continuous physiological functioning of the neuromuscular system. A swift and efficient repair mechanism enables the rapid restoration of sarcolemmal integrity following cellular impairment in damaged skeletal muscles. Members of the annexin family of proteins, which are characterized by the peripheral binding to acidic phospholipid membranes, are intrinsically involved in this myofiber repair process. The biochemical and proteomic profiling of dystrophinopathy, a severe and highly progressive neuromuscular disorder of early childhood, is outlined in this article with special focus on skeletal muscle-associated annexins and their role in membrane repair, myofiber regeneration and the cellular pathogenesis of Duchenne muscular dystrophy. Findings from comparative mass spectrometry-based surveys are described, and dystrophinopathy-related alterations in annexin expression patterns are discussed regarding the establishment of improved biomarker signatures of skeletal muscle wasting disorders. Mass spectrometry-based proteomic profiling is highly suitable for the systematic study of complex pathobiochemical alterations and inherent adaptations in dystrophinopathy. Disease-specific changes in annexins and related proteins of the membrane repair machinery can now be used to improve diagnosis, evaluation of disease severity, prognosis and therapeutic monitoring, and identify novel therapeutic targets to treat X-linked muscular dystrophy.

Proteomics has demonstrated that each protein consists of various proteoforms that provide an additional layer of biological data next to gene-, transcript-, or protein expression levels. As a result, proteome analyses are increasingly being complemented with proteoform maps. Identification and quantification of the type, site, and dynamics of a proteoform modification contribute to a better understanding of human biology. Testing the hypothesis that proteoform-resolved data can provide novel tools in precision medicine requires robust and high-throughput proteoform measurements. The prime candidate for this purpose is top-down proteomics (TDP), commonly performed with mass spectrometry. In this Special Issue: Top-Down Proteomics, Fornelli et al. report a comparative analysis of various SDS-removal methods that are needed for proteoform mapping in TDP experiments. Their work provides technical guidance on an important aspect of the TDP sample preparation process.

Extracellular vesicles (EVs) are heterogeneous lipid membrane-bound nanoparticles that carry diverse biomolecular cargos, including proteins, nucleic acids, lipids, and metabolites. Serving as fundamental mediators of intercellular communication in both physiological and pathological contexts, EVs have become a central focus in basic and translational research. Their participation in diverse biological processes-from immune regulation and tissue homeostasis to cancer progression and neurodegenerative diseases-highlights their dual functional roles. However, the intrinsic heterogeneity of EVs poses significant challenges for accurate characterization using conventional ensemble-averaging methods. Nano-flow cytometry (nFCM) represents a transformative technological advancement for single-particle EV analysis, offering high sensitivity, throughput, and multiparametric detection capabilities. This review first examines recent progress in nFCM instrumentation that improves sensitivity and resolution. We then summarize key applications of nFCM in uncovering previously inaccessible biophysical and biochemical characteristics of EVs at the single-particle level. Finally, we discuss current limitations hindering broader implementation and outline future directions to advance the field.