Systematic Evaluation of Affinity Enrichment Methods for O-GlcNAc Proteomics.

O-Linked ß-N-acetylglucosamine (O-GlcNAc) modification (i.e., O-GlcNAcylation) on proteins plays critical roles in the regulation of diverse biological processes. However, protein O-GlcNAcylation analysis, especially at a large scale, has been a challenge. So far, a number of enrichment materials and methods have been developed for site-specific O-GlcNAc proteomics in different biological settings. Despite the presence of multiple methods, their performance for the O-GlcNAc proteomics is largely unclear. In this work, by using the lysates of PANC-1 cells (a pancreatic cancer cell line), we provided a head-to-head comparison of three affinity enrichment methods and materials (i.e., antibody, lectin AANL6, and an OGA mutant) for site-specific O-GlcNAc proteomics. The enriched peptides were analyzed by HCD product-dependent EThcD (i.e., HCD-pd-EThcD) mass spectrometry. The resulting data files were processed by three different data analysis packages (i.e., Sequest HT, Byonic, and FragPipe). Our data suggest that each method captures a subpopulation of the O-GlcNAc proteins. Besides the enrichment methods, we also observe complementarity between the different data analysis tools. Thus, combining different approaches holds promise for enhanced coverage of O-GlcNAc proteomics.

Exploring the causal association between epigenetic clocks and menopause age: insights from a bidirectional Mendelian randomization study.

Background: Evidence suggests a connection between DNA methylation (DNAm) aging and reproductive aging. However, the causal relationship between DNAm and age at menopause remains uncertain. Methods: Employing established DNAm epigenetic clocks, such as DNAm Hannum age acceleration (Hannum), Intrinsic epigenetic age acceleration (IEAA), DNAm-estimated granulocyte proportions (Gran), DNAm GrimAge acceleration (GrimAgeAccel), DNAm PhenoAge acceleration (PhenoAgeAccel), and DNAm-estimated plasminogen activator inhibitor-1 levels (DNAmPAIadjAge), a bidirectional Mendelian randomization (MR) study was carried out to explore the potential causality between DNAm and menopausal age. The primary analytical method used was the inverse variance weighted (IVW) estimation model, supplemented by various other estimation techniques. Results: DNAm aging acceleration or deceleration, as indicated by Hannum, IEAA, Gran, GrimAgeAccel, PhenoAgeAccel, and DNAmPAIadjAge, did not exhibit a statistically significant causal effect on menopausal age according to forward MR analysis. However, there was a suggestive positive causal association between age at menopause and Gran (Beta = 0.0010; 95% confidence interval (CI): 0.0004, 0.0020) in reverse MR analysis. Conclusion: The observed increase in granulocyte DNAm levels in relation to menopausal age could potentially serve as a valuable indicator for evaluating the physiological status at the onset of menopause.

O-GlcNAc informatics: advances and trends.

As a post-translational modification, protein glycosylation is critical in health and disease. O-Linked ß-N-acetylglucosamine (O-GlcNAc) modification (O-GlcNAcylation), as an intracellular monosaccharide modification on proteins, was discovered 40 years ago. Thanks to technological advances, the physiological and pathological significance of O-GlcNAcylation has been gradually revealed and widely appreciated, especially in recent years. O-GlcNAc informatics has been quickly evolving. Clearly, O-GlcNAc informatics tools have not only facilitated O-GlcNAc functional studies, but also provided us a unique perspective on protein O-GlcNAcylation. In this article, we review O-GlcNAc-focused software tools and servers that have been developed for O-GlcNAc research over the past four decades. Specifically, we will (1) survey bioinformatics tools that have facilitated O-GlcNAc proteomics data analysis, (2) introduce databases/servers for O-GlcNAc proteins/sites that have been experimentally identified by individual research labs, (3) describe software tools that have been developed to predict O-GlcNAc sites, and (4) introduce platforms cataloging proteins that interact with the O-GlcNAc cycling enzymes (i.e., O-GlcNAc transferase and O-GlcNAcase). We hope these resources will provide useful information to both experienced researchers and new incomers to the O-GlcNAc field. We anticipate that this review provides a framework to stimulate the future development of more sophisticated informatic tools for O-GlcNAc research.

Translationally controlled tumor protein interacts with TaCIPK23 to positively regulate wheat resistance to Puccinia triticina.

Hypersensitive response-programmed cell death (HR-PCD) regulated by Ca2+ signal is considered the major regulator of resistance against Puccinia triticina (Pt.) infection in wheat. In this study, the bread wheat variety Thatcher and its near-isogenic line with the leaf rust resistance locus Lr26 were infected with the Pt. race 260 to obtain the compatible and incompatible combinations, respectively. The expression of translationally controlled tumor protein (TaTCTP) was upregulated upon infection with Pt., through a Ca2+-dependent mechanism in the incompatible combination. The knockdown of TaTCTP markedly increased the area of dying cell and the number of Pt. haustorial mother cells (HMCs) at the infection sites, whereas plants overexpressing the gene exhibited enhanced resistance. The interaction between TaTCTP and calcineurin B-like protein-interacting protein kinase 23 (TaCIPK23) was also investigated, and the interaction was found occurred in the endoplasmic reticulum. TaCIPK23 phosphorylated TaTCTP in vitro. The expression of a phospho-mimic TaTCTP mutant in Nicotiana benthamiana promoted HR-like cell death. Silencing TaCIPK23 or TaCIPK23/TaTCTP co-silencing resulted in the same results as silencing TaTCTP. This suggested that TaTCTP is a novel phosphorylation target of TaCIPK23, and both participate in the resistance of wheat to Pt. in the same pathway.

TaCAMTA4 negatively regulates H2O2-dependent wheat leaf rust resistance by activating catalase 1 expression.

Leaf rust, caused by Puccinia triticina Erikss. (Pt), is a serious disease threatening wheat (Triticum aestivum L.) production worldwide. Hydrogen peroxide (H2O2) triggered by Pt infection in resistant wheat cultivars cause oxidative damage directly to biomolecules or is activated by calcium signaling and mediates the hypersensitive response. Calmodulin-binding transcriptional activator 4 (TaCAMTA4) has been reported to negatively regulate wheat resistance to Pt. In this study, we found that TaCAMTA4 was induced by Pt race 165 in its compatible host harboring the Pt resistant locus Lr26, TcLr26, and silencing of TaCAMTA4 increased local H2O2 accumulation and Pt resistance. Subcellular localization and autoactivation tests revealed that TaCAMTA4 is a nucleus-localized transcriptional activator. Furthermore, four DNA motifs recognized by TaCAMTA4 were identified by transcription factor-centered Y1H. Through analyzing the transcriptome database, four gene clusters were identified, each containing a different DNA motif on each promoter. Among them, the expression of catalase 1 (TaCAT1) with motif-1 was highly induced in the compatible interaction and was decreased when TaCAMTA4 was silenced. The results of EMSA, ChIP-qPCR, and RT-qPCR further showed that TaCAMTA4 directly bound motif-1 in the TaCAT1 promoter. Furthermore, silencing of TaCAT1 resulted in enhanced resistance to Pt and increased local H2O2 accumulation in wheat, which is consistent with that of TaCAMTA4. Since CAMTAs are Ca2+ sensors and catalases catalyze the decomposition of H2O2, we hypothesize that Ca2+ regulates the plant immune networks that are controlled by H2O2 and implicate a potential mechanism for Pt to suppress resistance by inducing the expression of the TaCAMTA4-TaCAT1 module, which consequently enhances H2O2 scavenging and attenuates H2O2-dependent resistance.

Longitudinal analysis of the lung proteome reveals persistent repair months after mild to moderate COVID-19.

In order to assess homeostatic mechanisms in the lung after COVID-19, changes in the protein signature of bronchoalveolar lavage from 45 patients with mild to moderate disease at three phases (acute, recovery, and convalescent) are evaluated over a year. During the acute phase, inflamed and uninflamed phenotypes are characterized by the expression of tissue repair and host defense response molecules. With recovery, inflammatory and fibrogenic mediators decline and clinical symptoms abate. However, at 9 months, quantified radiographic abnormalities resolve in the majority of patients, and yet compared to healthy persons, all showed ongoing activation of cellular repair processes and depression of the renin-kallikrein-kinin, coagulation, and complement systems. This dissociation of prolonged reparative processes from symptom and radiographic resolution suggests that occult ongoing disruption of the lung proteome is underrecognized and may be relevant to recovery from other serious viral pneumonias.

Advances in analysis of atmospheric ultrafine particles and application in air quality, climate, and health research.

There is growing interest in the contribution of ultrafine particles to air quality, climate, and human health. Ultrafine particles are of central significance for the influence of radiative forcing of climate change by involving in the formation of clouds and precipitation. Moreover, exposure to ultrafine particles can enhance the disease burden. The determination of those effects of ultrafine particles strongly depends on their chemical composition and physicochemical properties. This review focuses on the advanced techniques for the characterization of chemical composition and physicochemical properties of ultrafine particles in the past five years. The current analytical methodologies are broadly classified into electron and X-ray microscopy, optical spectroscopy and microscopy, electrical mobility, and mass spectrometry, and then described and discussed its operation principle, advantages, and limitations. Besides measurements, application of the state-of-the-art techniques is briefly reviewed to help us to promote a better understanding of atmospheric ultrafine particles relevant to air quality, climate, and health.

Integrating HexNAcQuest with Glycoproteomics Data Analysis Software to Distinguish HexNAc Isomers on Peptides.

Recently, HexNAcQuest was developed to help distinguish peptides modified by HexNAc isomers, more specifically O-linked ß-N-acetylglucosamine (O-GlcNAc) and O-linked α-N-acetylgalactosamine (O-GalNAc, Tn antigen). To facilitate its usage (particularly for datasets from glycoproteomics studies), herein we present a detailed protocol. It describes example cases and procedures for which users might need to use HexNAcQuest to distinguish these two modifications.

A novel halloysite nanotubes-based hybrid monolith for in-tube solid-phase microextraction of polar cationic pesticides.

The accurate determination of polar cationic pesticides in food poses a challenge due to their high polarity and trace levels in complex matrices. This study hypothesized that the use of halloysite nanotubes (HNTs) can significantly enhance the extraction efficiency and sensitivity of these analytes because of their rich hydroxyl groups and cation exchange sites. Therefore, we chemically incorporated HNTs with organic polymer monoliths for in-tube solid-phase microextraction (SPME). This novel hybrid monolith extended service life, improved adsorption capacity, and exhibited excellent extraction performance for polar cationic pesticides. Based on these advancements, a robust and sensitive in-tube SPME-HILIC-MS/MS method was constructed to determine trace levels of polar cationic pesticides in complex food matrices. The method achieved limits of detection of 1.9, 2.1, and 0.1 µg/kg for maleic hydrazide, amitrole, and cyromazine, respectively. The spiked recoveries in five food samples ranged from 80.2 to 100.8%, with relative standard deviations below 10.7%.

Liberated bioactive bound phenolics during in vitro gastrointestinal digestion and colonic fermentation boost the prebiotic effects of triticale insoluble dietary fiber.

Phenolics in bound form extensively exist in cereal dietary fiber, especially insoluble fiber, while their release profile in gastrointestinal tract and contribution to the potential positive effects of dietary fiber in modulating gut microbiota still needs to be disclosed. In this work, the composition of bound phenolics (BPs) in triticale insoluble dietary fiber (TIDF) was studied, and in vitro gastrointestinal digestion as well as colonic fermentation were performed to investigate BPs liberation and their role in regulating intestinal flora of TIDF. It turned out that most BPs were unaccessible in digestion but partly released continuously during fermentation. 16 s rRNA sequencing demonstrated that TIDF possessed prebiotic effects by promoting anti-inflammatory while inhibiting proinflammatory bacteria alongside boosting SCFAs production and antioxidative BPs contributed a lot to these effects. Results indicated that TIDF held capabilities to regulate intestinal flora and BPs were important functional components to the health benefits of cereal dietary fiber.

In-Depth Endogenous Phosphopeptidomics of Serum with Zirconium(IV)-Grafted Mesoporous Silica Enrichment.

Detection of endogenous peptides, especially those with modifications (such as phosphorylation) in biofluids, can serve as an indicator of intracellular pathophysiology. Although great progress has been made in phosphoproteomics in recent years, endogenous phosphopeptidomics has largely lagged behind. One main hurdle in endogenous phosphopeptidomics analysis is the coexistence of proteins and highly abundant nonmodified peptides in complex matrices. In this study, we developed an approach using zirconium(IV)-grafted mesoporous beads to enrich phosphopeptides, followed by analysis with a high resolution nanoRPLC-MS/MS system. The bifunctional material was first tested with digests of standard phosphoproteins and HeLa cell lysates, with excellent enrichment performance achieved. Given the size exclusion nature, the beads were directly applied for endogenous phosphopeptidomic analysis of serum samples from pancreatic ductal adenocarcinoma (PDAC) patients and controls. In total, 329 endogenous phosphopeptides (containing 113 high confidence sites) were identified across samples, by far the largest endogenous phosphopeptide data set cataloged to date. In addition, the method was readily applied for phosphoproteomics of the same set of samples, with 172 phosphopeptides identified and significant changes in dozens of phosphopeptides observed. Given the simplicity and robustness of the proposed method, we envision that it can be readily used for comprehensive phosphorylation studies of serum and other biofluid samples.

Halloysite nanotubes-based hybrid silica monolithic spin tip for hydrophilic solid-phase extraction of sulbactam, cefoperazone, and cefuroxime in whole blood.

In this study, we proposed a novel method utilizing polyethyleneimine (PEI)-modified halloysite nanotubes (HNTs)-based hybrid silica monolithic spin tip to analyze hydrophilic ß-lactam antibiotics and ß-lactamases inhibitors in whole blood samples for the first time. HNTs were incorporated directly into the hybrid silica monolith via a sol-gel method, which improved the hydrophilicity of the matrix. The as-prepared monolith was further modified with PEI by glutaraldehyde coupling reaction. It was found that the PEI-modified HNTs-based hybrid silica monolith enabled a large adsorption capacity of cefoperazone at 35.7 mg g-1. The monolithic spin tip-based purification method greatly reduced the matrix effect of whole blood samples and had a detection limit as low as 0.1 - 0.2 ng mL-1. In addition, the spiked recoveries of sulbactam, cefuroxime, and cefoperazone in blank whole blood were in the range of 89.3-105.4 % for intra-day and 90.6-103.5 % for inter-day, with low relative standard deviations of 1.3-7.2 % and 4.9-10.5 %, respectively. This study introduces a new strategy for preparing nanoparticles incorporated in a hybrid silica monolith with a high adsorption capacity. Moreover, it offers a valuable tool to monitor sulbactam, cefoperazone, and cefuroxime in whole blood from pregnant women with the final aim of guiding their administration.

Secondary organic aerosols from oxidation of 1-methylnaphthalene: Yield, composition, and volatility.

Alkyl-PAHs (APAHs) have been identified worldwide, which could rapidly react with chlorine and OH radicals in the atmosphere. In this study, a comprehensive investigation is conducted for SOA generated by a representative alkyl-naphthalene (1-methyl naphthalene, 1-MN) initiated by Cl, including yield, chemical composition, and volatility of SOA. To better understand 1-MN atmospheric oxidation, reaction mechanisms of 1MN with Cl atoms and OH radicals are proposed and compared under different nitrogen oxides (NOx) conditions. The SOA yields are comparable for Cl-initiated and OH-initiated reactions under high NOx conditions but increased in Cl-initiated reactions under low NOx conditions. The compounds with ten carbons are more abundant in Cl-initiated SOA, while compounds with nine carbons have higher intensity, suggesting that Cl caused ring-retained and alkyl-lost products and OH produces ring-broken and alkyl-retained compounds. The volatility of SOA is remarkably low, and SOA formed from Cl oxidation is slightly higher than that from OH oxidation. These results reveal that 1MN-derived SOA with OH and Cl radicals would have different physical-chemical properties and may play an important role in air quality and health effects.

O-GlcNAcPRED-DL: Prediction of Protein O-GlcNAcylation Sites Based on an Ensemble Model of Deep Learning.

O-linked ß-N-acetylglucosamine (O-GlcNAc) is a post-translational modification (i.e., O-GlcNAcylation) on serine/threonine residues of proteins, regulating a plethora of physiological and pathological events. As a dynamic process, O-GlcNAc functions in a site-specific manner. However, the experimental identification of the O-GlcNAc sites remains challenging in many scenarios. Herein, by leveraging the recent progress in cataloguing experimentally identified O-GlcNAc sites and advanced deep learning approaches, we establish an ensemble model, O-GlcNAcPRED-DL, a deep learning-based tool, for the prediction of O-GlcNAc sites. In brief, to make a benchmark O-GlcNAc data set, we extracted the information on O-GlcNAc from the recently constructed database O-GlcNAcAtlas, which contains thousands of experimentally identified and curated O-GlcNAc sites on proteins from multiple species. To overcome the imbalance between positive and negative data sets, we selected five groups of negative data sets in humans and mice to construct an ensemble predictor based on connection of a convolutional neural network and bidirectional long short-term memory. By taking into account three types of sequence information, we constructed four network frameworks, with the systematically optimized parameters used for the models. The thorough comparison analysis on two independent data sets of humans and mice and six independent data sets from other species demonstrated remarkably increased sensitivity and accuracy of the O-GlcNAcPRED-DL models, outperforming other existing tools. Moreover, a user-friendly Web server for O-GlcNAcPRED-DL has been constructed, which is freely available at http://oglcnac.org/pred_dl.

Resistance to abemaciclib is associated with increased metastatic potential and lysosomal protein deregulation in breast cancer cells.

Cyclin dependent kinase 4 and 6 inhibitors such as abemaciclib are routinely used to treat metastatic estrogen receptor positive (ER+) breast cancer. However, adaptive mechanisms inhibit their effectiveness and allow for disease progression. Using ER+ breast cancer cell models, we show that acquired resistance to abemaciclib is accompanied by increase in metastatic potential. Mass spectrometry-based proteomics from abemaciclib sensitive and resistant cells showed that lysosomal proteins including CTSD (cathepsin D), cathepsin A and CD68 were significantly increased in resistant cells. Combination of abemaciclib and a lysosomal destabilizer, such as hydroxychloroquine (HCQ) or bafilomycin A1, resensitized resistant cells to abemaciclib. Also, combination of abemaciclib and HCQ decreased migration and invasive potential and increased lysosomal membrane permeability in resistant cells. Prosurvival B cell lymphoma 2 (BCL2) protein levels were elevated in resistant cells, and a triple treatment with abemaciclib, HCQ, and BCL2 inhibitor, venetoclax, significantly inhibited cell growth compared to treatment with abemaciclib and HCQ. Furthermore, resistant cells showed increased levels of Transcription Factor EB (TFEB), a master regulator of lysosomal-autophagy genes, and siRNA mediated knockdown of TFEB decreased invasion in resistant cells. TFEB was found to be mutated in a subset of invasive human breast cancer samples, and overall survival analysis in ER+, lymph node-positive breast cancer showed that increased TFEB expression correlated with decreased survival. Collectively, we show that acquired resistance to abemaciclib leads to increased metastatic potential and increased levels of protumorigenic lysosomal proteins. Therefore, the lysosomal pathway could be a therapeutic target in advanced ER+ breast cancer.

ZDHHC5-mediated NLRP3 palmitoylation promotes NLRP3-NEK7 interaction and inflammasome activation.

The nucleotide-binding domain (NBD), leucine-rich repeat (LRR), and pyrin domain (PYD)-containing protein 3 (NLRP3) inflammasome is a critical mediator of the innate immune response. How NLRP3 responds to stimuli and initiates the assembly of the NLRP3 inflammasome is not fully understood. Here, we found that a cellular metabolite, palmitate, facilitates NLRP3 activation by enhancing its S-palmitoylation, in synergy with lipopolysaccharide stimulation. NLRP3 is post-translationally palmitoylated by zinc-finger and aspartate-histidine-histidine-cysteine 5 (ZDHHC5) at the LRR domain, which promotes NLRP3 inflammasome assembly and activation. Silencing ZDHHC5 blocks NLRP3 oligomerization, NLRP3-NEK7 interaction, and formation of large intracellular ASC aggregates, leading to abrogation of caspase-1 activation, IL-1ß/18 release, and GSDMD cleavage, both in human cells and in mice. ABHD17A depalmitoylates NLRP3, and one human-heritable disease-associated mutation in NLRP3 was found to be associated with defective ABHD17A binding and hyper-palmitoylation. Furthermore, Zdhhc5-/- mice showed defective NLRP3 inflammasome activation in vivo. Taken together, our data reveal an endogenous mechanism of inflammasome assembly and activation and suggest NLRP3 palmitoylation as a potential target for the treatment of NLRP3 inflammasome-driven diseases.

Sodium hexametaphosphate-treated halloysite based solid-phase extraction of biguanides from dietary supplements.

Raw halloysite was purified by using sodium hexametaphosphate and utilized as the solid-phase extraction sorbent for the determination of biguanides from dietary supplements. The purified halloysite was characterized using scanning electron microscopy, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, and X-ray diffraction. The purified halloysite interacted with biguanides through hydrophilic interaction and ion exchange on account of its abundant hydroxyl groups and negative charge. Compared with traditional extraction methods based on hydrophobic interaction and/or ion exchange, the purified halloysite adsorbed more biguanides due to hydrophilicity and ion exchange, with a sample loading volume of up to 100 mL at least. Excellent reproducibility of halloysite purification was achieved, with within-batch (n = 3) and batch-to-batch (n = 3) relative standard deviations in the ranges of 1.5-4.2% and 5.6-8.8%, respectively. Coupled with reversed-phase liquid chromatography-tandem mass spectrometry, a low limit of detection of 0.3 µg kg-1 was obtained. The intra- and inter-day mean recoveries of the biguanides spiked at three levels in dietary supplements were within the ranges of 88.5-107.2% and 86.4-102.0%, respectively. The intra- and inter-day precisions were within the ranges of 1.5-6.4% and 5.4-9.9%, respectively. These results indicated that the developed method is efficient for the determination of trace biguanides in dietary supplements.

Determination of neotame in various foods by high-performance liquid chromatography coupled with ultraviolet and mass spectrometric detection.

A new analytical technique involving protein precipitation, heating, lipid degreasing, and SPE procedures combined with HPLC-UV and HPLC-MS/MS has been developed for the determination of neotame in a variety of food samples. This method is applicable for high-protein, high-lipid, or gum-based solid samples. The limit of detection of the HPLC-UV method was 0.5 µg/mL, while that of the HPLC-MS/MS method was 3.3 ng/mL. The spiked recoveries of neotame in 73 kinds of foods were in the range of 81.1-107.2 % with UV detection. The spiked recoveries obtained by HPLC-MS/MS in 14 kinds of foods ranged from 81.6 % to 105.8 %. This technique was successfully used to determine the contents of neotame in two positive samples, indicating its applicability in food analysis.

Management of take-all disease caused by Gaeumannomyces graminis var. tritici in wheat through Bacillus subtilis strains.

Wheat (Triticum aestivum) is the second largest grain crop worldwide, and one of the three major grain crops produced in China. Take-all disease, caused by Gaeumannomyces graminis var. tritici (Ggt) infection, is a widespread and devastating soil-borne disease that harms wheat production. At present, the prevention and control of wheat take-all depend largely on the application of chemical pesticides. Chemical pesticides, however, not only lead to increased drug resistance of pathogens but also leave significant residues in the soil, causing serious environmental pollution. In this study, we investigated the application of Bacillus subtilis to achieve take-all disease control in wheat while reducing pesticide application. Antagonistic bacteria were screened by plate test, species identification of strains was performed by Gram staining and sequencing of 16s rDNA, secondary metabolite activity of strains was detected by clear circle method, strain compatibility and effect of compounding on Ggt were detected by plate, and the application prospects of specific strains were analyzed by greenhouse and field experiments. We found that five B. subtilis strains, JY122, JY214, ZY133, NW03, Z-14, had significant antagonistic effects against Ggt, and could secrete antimicrobial proteins including amylase, protease, and cellulase. Furthermore, Z-14 and JY214 cultures have also been shown to change the morphology of Ggt mycelium. These results also showed that Z-14, JY214, and their combination can control take-all disease in wheat at a reduced level of pesticide use. In summary, we screened two Bacillus spp. strains, Z-14 and JY214, that could act as antagonists that contribute to the biological control of wheat take-all disease. These findings provide resources and ideas for controlling crop diseases in an environmentally friendly manner.