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.

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.

Microglia are abundantly distributed throughout the central nervous system (CNS) to play critical roles in neural development and homeostasis, and act as immune sentinels to constantly monitor their surrounding neural environment. Given their high reactivity to brain insults, we hypothesised that the cerebral microenvironment altered by ischaemic stroke would significantly impact microglial morphology and function in a spatially dependent manner. To investigate this, we examined regional gene expression changes associated with microglial activation and neuroinflammation, microglial morphology using 3D image reconstruction and unbiased proteomics at 24 h after transient middle cerebral artery occlusion (tMCAO). We found the microenvironment within the ischaemic infarct core has a distinct proinflammatory profile versus that of the sham-operated controls. Moreover, stroke induces region-specific changes to microglia morphology with those closer to the infarct displaying a more ameboid shape and less complex dendritic processes. Additionally, we identified 108 differentially expressed proteins in microglia that were isolated from the ipsilateral ischaemic hemisphere compared to those isolated from the contralateral hemisphere. These differentially expressed proteins are predicted to influence signalling pathways that mediate TNFα superfamily cytokine production, chemokine activities and leukocyte chemotaxis and migration. These findings support microglia as critical regulators of the inflammatory signalling after stroke.