Proteomics最新文献

Human males and females show differences in the incidence of neutrophil-associated diseases and differences in neutrophil responses such as a faster response to the chemorepellent Ser-Leu-Ile-Gly-Lys-Val-NH2 (SLIGKV) in males. Little is known about the basis of sex-based differences in human neutrophils. We used mass spectrometry to identify proteins and phosphoproteins in unstimulated human neutrophils and in neutrophils incubated with the SLIGKV, a protease-activated receptor 2 agonist. There were 132 proteins with higher levels in unstimulated male neutrophils; these proteins tended to be associated with RNA regulation, ribosome, and phosphoinositide signaling pathways, whereas 30 proteins with higher levels in unstimulated female neutrophils were associated with metabolic processes, proteasomes, and phosphatase regulatory proteins. Unstimulated male neutrophils had increased phosphorylation of 32 proteins compared to females. After exposure to SLIGKV, male neutrophils showed a faster response in terms of protein phosphorylation compared to female neutrophils. Male neutrophils have higher levels of proteins and higher phosphorylation of proteins associated with RNA processing and signaling pathways. Female neutrophils have higher levels of proteins associated with metabolism and proteolytic pathways. This suggests that male neutrophils might be more ready to adapt to a new environment, and female neutrophils might be more effective at responding to pathogens.

We aim to verify and validate low-abundant plasma proteins from severe COVID-19 cases and controls through a comparative analysis between Olink and Alamar performances. Eighty-three severe cases and 44 controls were measured for proteomics using three Olink panels and one Alamar panel, which share 94 targets. CV, pairwise correlation of intensity signals, and detectability range were compared across platforms. Statistical comparisons were performed using FDR-adjusted linear models with age as a covariate to construct differential protein abundance volcano plots between cases and controls per platform and heatmaps between our cohort and five public cohorts. Overall, pairwise comparisons (n = 94) showed strong correlations among cases (r = 0.82) and controls (r = 0.7). 60/94 proteins had mutual significance on both platforms; of which 54 showed concordant effect direction, and six showed opposite effect direction (IL-6R, IL-1R2, KITLG, TSLP, IL-17C, and IL-4R). Alamar verified 80 and 60 targets from cases and controls, respectively, along with 54 differential proteins from Olink. Compared to public cohorts measured by Olink, our Olink data showed consistent findings from 28 proteins, of which 27 were validated by Alamar.

CITE-Seq (Cellular Indexing of Transcriptomes and Epitopes by Sequencing) is an advanced single-cell sequencing method to profile both gene expression and protein abundance simultaneously in individual cells using single-cell mRNA sequencing techniques alongside antibody-derived tags (ADTs), for protein detection. The characterization of both the transcriptome and the proteome from the same cells provides a powerful and multiomic approach for understanding the mechanisms of complex biological processes. This review focuses on the workflow of CITE-Seq using a microwell-based single-cell analysis system as an example and provides key considerations for staining cells with ADTs. By highlighting critical information for CITE-Seq library preparation, sequencing, and data analysis, this review provides a practical guide with which to perform comprehensive CITE-Seq workflow.

The field of clinical proteomics has seen enormous growth in the past 20 years, with over 40,000 scientific manuscripts published to date. At the same time, actual clinical application of the reported findings is obviously scarce. In this viewpoint article, we discuss the key issues that may be responsible for this apparent lack of success. We conclude that success must not be assessed based on the number of publications, but via the impact on patient management and treatment. We proceed with specific suggestions for potential solutions, which include keeping a strict focus on potential patient benefit. We hope this article can help shape the field, so it can in fact deliver on its realistic promise to bring significant improvement in management and care to patients.

Fluctuating salinity is symptomatic of climate change challenging aquatic species. The melting of polar ice, rising sea levels, coastal surface and groundwater salinization, and increased evaporation in arid habitats alter salinity worldwide. Moreover, the frequency and intensity of extreme weather events such as rainstorms and floods increase, causing rapid shifts in brackish and coastal habitat salinity. Such salinity alterations disrupt homeostasis and ultimately diminish the fitness, of aquatic organisms by interfering with metabolism, reproduction, immunity, and other critical aspects of physiology. Proteins are central to these physiological mechanisms. They represent the molecular building blocks of phenotypes that govern organismal responses to environmental challenges. Environmental cues regulate proteins in a concerted fashion, necessitating holistic analyses of proteomes for comprehending salinity stress responses. Proteomics approaches reveal molecular causes of population declines and enable holistic bioindication geared toward timely interventions to prevent local extinctions. Proteomics analyses of salinity effects on aquatic organisms have been performed since the mid-1990s, propelled by the invention of two-dimensional protein gels, soft ionization techniques for mass spectrometry (MS), and nano-liquid chromatography in the 1970s and 1980s. This review summarizes the current knowledge on salinity regulation of proteomes from aquatic organisms, including key methodological advances over the past decades.