Superswelling Microneedle Arrays for Dermal Interstitial Fluid (Prote)Omics

The noninvasive sampling of dermal interstitial fluid (ISF) for the monitoring of clinical biomarkers is a greatly appealing area of research. The identification of molecular biomarkers in biological fluids has been accelerated with -omics analyses but remains limited in ISF because of its time-consuming and complex extraction process. Here, the generation of microneedle (MN) patches made of superabsorbent acrylate-based hydrogels for the rapid sampling of dermal ISF is described to explore its proteome. In depth, iterative optimization allows the identification of novel acrylate-based compositions with the required chemical, mechanical, and biocompatibility properties allowing proteomic analysis of the extracted ISF for the first time after sampling with swelling MNs. The generated MN arrays show no cytotoxic effect, successfully cross the stratum corneum, and can collect up to 6 µL of dermal ISF in 10 min in vivo. Proteomics lead to the detection of 176 clinically relevant biomarkers in the collected samples validating the use of ISF as a relevant bodily fluid for disease monitoring and diagnostic. Importantly, it is discovered that extraction fingerprint is strongly dependent on the MNs chemistry, and thus specific biomarkers could be selectively extracted by tuning the composition of the patch, making the system versatile and specific.     

α-Methylene-β-Lactone Scaffold for Developing Chemical Probes at the Two Ends of the Selectivity Spectrum

The utilities of an α-methylene-β-lactone (MeLac) moiety as a warhead composed of multiple electrophilic sites are reported. We demonstrate that a MeLac-alkyne not only reacts with diverse proteins as a broadly reactive measurement probe, but also recruits reduced endogenous glutathione (GSH) to assemble a selective chemical probe of GSH-β-lactone (GSH-Lac)-alkyne in live cells. Tandem mass spectrometry reveals that MeLac reacts with nucleophilic cysteine, serine, lysine, threonine, and tyrosine residues, through either Michael or acyl addition. A peptide-centric proteomics platform demonstrates that the proteomic selectivity profiles of orlistat and parthenolide, which have distinct reactivities, are measurable by MeLac-alkyne as a high-coverage probe. The GSH-Lac-alkyne selectively probes the glutathione S-transferase P responsible for multidrug resistance. The assembly of the GSH-Lac probe exemplifies a modular and scalable route to develop selective probes with different recognizing moieties.     

Gelatinised and hydrolysed corn starch is a cost-effective carbon source with higher production of L-lactic acid by Bacillus coagulans compared with glucose

L-lactic acid is an important organic acid widely used in pharmaceutical, food and textile industries. Bacillus coagulans BCS13002 can efficiently produce L-lactic acid with two kinds of carbon sources. BCS13002 produced L-lactic acid at a content of 10.23 ± 0.16 g/L and 11.67 ± 0.22 g/L, when glucose and gelatinised and hydrolysed corn starch （GHCS） were used, respectively. GHCS exhibits several advantages, including high yield of L-lactic acid and low cost. Proteomics analyses identified several key enzymes, which contributed to the higher production of L-lactic acid when GHCS was used as the carbon source. Those key enzymes were involved in the two-component system (SpoOF), pantothenate and CoA biosynthesis (pantothenate synthetase, 1.584-fold; dihydroxy-acid dehydratase, 1.517-fold), beta-alanine metabolism (1.605-fold) and valine, leucine and isoleucine biosynthesis (1.517-fold) pathways. This study provides a biological basis for using GHCS as a substitute of glucose in the production of L-lactic acid.     

Divide-and-Conquer Matrisome Protein (DC-MaP) Strategy: An MS-Friendly Approach to Proteomic Matrisome Characterization

Currently, the extracellular matrix (ECM) is considered a pivotal complex meshwork of macromolecules playing a plethora of biomolecular functions in health and disease beyond its commonly known mechanical role. Only by unraveling its composition can we leverage related tissue engineering and pharmacological efforts. Nevertheless, its unbiased proteomic identification still encounters some limitations mainly due to partial ECM enrichment by precipitation, sequential fractionation using unfriendly-mass spectrometry (MS) detergents, and resuspension with harsh reagents that need to be entirely removed prior to analysis. These methods can be technically challenging and labor-intensive, which affects the reproducibility of ECM identification and induces protein loss. Here, we present a simple new method applicable to tissue fragments of 10 mg and more. The technique has been validated on human ovarian tissue and involves a standardized procedure for sample processing with an MS-compatible detergent and combined centrifugation. This two-step protocol eliminates the need for laborious sample clarification and divides our samples into 2 fractions, soluble and insoluble, successively enriched with matrisome-associated (ECM-interacting) and core matrisome (structural ECM) proteins.     

Chemical Proteomics for Expanding the Druggability of Human Disease

Abstract . Over the past decade, chemical proteomics has emerged as a powerful technique to understand small molecule and protein function in the physiological system and plays a key role in unravelling the cellular targets of pharmacological modulators. Chemical proteomics that integrates activity-based protein profiling (ABPP) with mass spectrometry has been introduced to evaluate small-molecule and protein interaction and expand the druggable proteome. A much larger fraction of the human proteome can now be targeted by small molecules than estimated by past predictions of protein druggability.     

Mass spectrometry and the cellular surfaceome

The collection of exposed plasma membrane proteins, collectively termed the surfaceome, is involved in multiple vital cellular processes, such as the communication of cells with their surroundings and the regulation of transport across the lipid bilayer. The surfaceome also plays key roles in the immune system by recognizing and presenting antigens, with its possible malfunctioning linked to disease. Surface proteins have long been explored as potential cell markers, disease biomarkers, and therapeutic drug targets. Despite its importance, a detailed study of the surfaceome continues to pose major challenges for mass spectrometry-driven proteomics due to the inherent biophysical characteristics of surface proteins. Their inefficient extraction from hydrophobic membranes to an aqueous medium and their lower abundance compared to intracellular proteins hamper the analysis of surface proteins, which are therefore usually underrepresented in proteomic datasets. To tackle such problems, several innovative analytical methodologies have been developed. This review aims at providing an extensive overview of the different methods for surfaceome analysis, with respective considerations for downstream mass spectrometry-based proteomics.     

蛋白质组学技术在藻类研究中的应用现状与展望

藻类具有复杂多样的进化历史和生物学特征,不仅在生态系统中扮演着重要角色,而且具有许多独特的基因和生物过程。随着后基因时代的到来,组学技术受到各界学者的高度重视,近年来在藻类研究中也得到了应用。高通量技术在藻类研究领域中的应用,也大大促进了藻类蛋白质组学的发展。本文综述了蛋白质组学技术在藻类品质差异鉴定、养殖胁迫作用、生理机制方面的研究进展,并对其发展方向和应用前景进行了展望,为从事藻类组学的研究者提供参考。