Mass Spectrometry-based Methods Research Articles

Phytochemical characterization and comparative analysis of cycloartane-type triterpenes in Astragalus adsurgens and Astragalus membranaceus.

Astragalus adsurgens, a significant forage plant cultivated in arid regions of northwest China, remains underexplored for its triterpenoid saponins and medicinal properties compared to the extensively studied Astragalus membranaceus. To explore the phytochemical profile of A. adsurgens for its potential application in the medical field, we employed ultra-pressure liquid chromatography coupled with tandem mass spectrometry-based method to identify cycloartane-type triterpenes. Eventually, five new cycloartane-type triterpenoids, adsurgosides A‒D (1‒4) and 3-methyl-3,4-seco-cyclostellanol (5), together with two known analogues cycloastragenol (6) and cyclopycanthogenin (7), were isolated from the roots of A. adsurgens. Their structures were elucidated using 1D and 2D NMR analyses in combination with HRESIMS data. Additionally, a comparative study on the distribution patterns of these compounds revealed qualitative and quantitative variations between A. adsurgens and A. membranaceus. Our findings not only identified an alternative plant for isolating cycloartane-type triterpenoids but also offer new insights into the chemical properties of A. adsurgens.

Using in vivo intact structure for system-wide quantitative analysis of changes in proteins

Mass spectrometry-based methods can provide a global expression profile and structural readout of proteins in complex systems. Preserving the in vivo conformation of proteins in their innate state is challenging during proteomic experiments. Here, we introduce a whole animal in vivo protein footprinting method using perfusion of reagents to add dimethyl labels to exposed lysine residues on intact proteins which provides information about protein conformation. When this approach is used to measure dynamic structural changes during Alzheimer’s disease (AD) progression in a mouse model, we detect 433 proteins that undergo structural changes attributed to AD, independent of aging, across 7 tissues. We identify structural changes of co-expressed proteins and link the communities of these proteins to their biological functions. Our findings show that structural alterations of proteins precede changes in expression, thereby demonstrating the value of in vivo protein conformation measurement. Our method represents a strategy for untangling mechanisms of proteostasis dysfunction caused by protein misfolding. In vivo whole-animal footprinting should have broad applicability for discovering conformational changes in systemic diseases and for the design of therapeutic interventions.

Bioanalytical method development and validation of docetaxel and carvacrol in mice plasma using LC-QqQ-MS/MS.

Present work describes the development of a liquid chromatography tandem mass spectrometry-based bioanalytical method for the reliable simultaneous quantification of docetaxel (DXL) and carvacrol (CVL) in the mice plasma. A rapid and sensitive bioanalytical method was developed and optimized in mice plasma using Paclitaxel as an internal standard. Validation of the bioanalytical method was performed according to the ICH M10 guideline covering the range of 9.62-1923.08 ng/mL in the mice plasma milleu at the low, mid, and high-quality control concentrations of 28.86 ng/mL, 961.54 ng/mL, and 1346.15 ng/mL, respectively for both the analytes. Validation parameters such as accuracy, precision, carryover-test, matrix effect, and reinjection reproducibility were carried out and were found in limits. Stability studies (Benchtop, autosampler, freeze-thaw, and long-term) were performed and found to be within limits. The developed bioanalytical method was found to be suitable for the simultaneous quantification of DXL and CVL in the mice plasma.

Environmental contaminants, sex hormones and SHBG in an elderly population

IntroductionEffects of environmental contaminants (ECs) on endocrine systems have been reported, but few studies assessed associations between ECs and sex hormones (SH) in elderly. Aim of this study was to investigate whether blood concentrations of four classes of ECs were associated with SH concentrations in elderly. MethodsSamples from participants of the cross-sectional population-based Prospective Investigation of the Vasculature in Uppsala Seniors study (PIVUS, 70-year-old men and women, n = 1016) were analyzed using validated mass spectrometry-based methods for SH (testosterone (T), dihydrotestosterone (DHT), estrone and estradiol (E2)); 23 persistent organic pollutants (POPs); 8 perfluoroalkyl substances (PFAS); 4 phthalates and 11 metals. SH binding globulin (SHBG) was analyzed using immunoassay. The measured concentrations were normalized, and the values converted to a z-scale. Linear regression analyses were conducted to assess association between concentration of the SH, SHBG and E2/T (aromatase enzyme index, AEI) with the ECs. Multiple linear regression analyses were performed to model the relationships. ResultsThe strongest associations were observed with the polychlorinated biphenyls (PCBs). In men, the strongest associations with concentrations of SH and SHBG were seen for PCBs containing >5 chlorine, monoethyl phthalate (MEP), Ni and Cd; and in women, with PCBs, MEP, several of the PFAS, Cd, Co, and Ni. Difference in the effect of ECs on AEI between men and women were observed. Area under the ROC curve for the models predicting abnormal values of SH and SHBG >0.75 due to the effects of ECs was observed for T, DHT, and E2 in men, and for E2 and SHBG in women. ConclusionsResults of this study suggest that in elderly subjects, concentrations of many ECs associated with concentrations of SH and SHBG, and AEI. Further studies are needed to confirm the findings and to assess effect of the pollutants on endocrine system function in elderly.

Label-Free Quantitative Proteomics Analysis of COVID-19 Vaccines by Nano LC-HRMS.

A nanoliter liquid chromatography-high resolution mass spectrometry-based method was developed for quantitative proteomics analysis of COVID-19 vaccines. It can be used for simultaneous qualitative and quantitative analysis of target proteins and host cell proteins (HCPs) in vaccine samples. This approach can directly provide protein information at the molecular level. Based on this, the proteomes of 15 batches of COVID-19 inactivated vaccine samples from two companies and 12 batches of COVID-19 recombinant protein vaccine samples from one company were successfully analyzed, which provided a significant amount of valuable information. Samples produced in different batches or by different companies can be systematically contrasted in this way, offering powerful supplements for existing quality standards. This strategy paves the way for profiling proteomics in complex samples and provides a novel perspective on the quality evaluation of bio-macromolecular drugs.

In-Depth Host Cell Protein Analysis and Viral Protein Impurity Monitoring in Adeno-Associated Virus-Based Gene Therapy Products Using Optimized Wide Window Data-Dependent Acquisition Method.

Compared to other protein therapeutics, there is currently limited knowledge about the residual host cell proteins (HCPs) in adeno-associated virus (AAV)-based gene therapy products. This is primarily due to the lack of a robust and sensitive mass spectrometry-based method for HCP analysis in AAV samples. Existing liquid chromatography-mass spectrometry methods used for analyzing HCPs in therapeutic monoclonal antibodies (mAbs) often cannot be directly applied to AAVs, due to some unique characteristics of AAV samples encountered during their development such as limited sample availability/protein concentration and the presence of surfactants. In this study, we have developed a novel workflow for robust and in-depth HCP analysis of AAV samples by combining wide-window data-dependent acquisition for improved low-abundance HCP detection with single-pot, solid-phase-enhanced sample preparation (SP3) for low-input sample preparation. Using this newly developed method, we were able to detect more than 650 HCPs in a commercial AAV1 sample with a high quantitative reproducibility. This represents a greater than 5-fold increase in HCP protein identification compared to an in-solution digestion method followed by traditional data-dependent acquisition. Similar benefits can also be achieved for other AAV serotypes that were produced internally and purified through different processes. The detection limit of this method is as low as 0.06 ng/mL, enabling more comprehensive HCP coverage in AAV samples. Moreover, for the first time, we have identified several process-related viral proteins, such as Rep 78 and E4. These proteins need to be closely monitored during AAV process development as they may present a greater risk for immunogenicity compared to HCPs that are derived from human HEK293 cells.

Optimized liquid chromatography-tandem mass spectrometry protocol for enhanced detection of 45 pesticides in water and soil samples.

The development of analytical screening techniques for pesticides is crucial for preventing and mitigating environmental contamination. Mass spectrometry-based screening methods differ based on the complexity of the sample matrix and the diversity of the target compounds. One of the major challenges is balancing cost reduction in the extraction process with the optimization of analytical results. This protocol introduces a universal and efficient scheme for the qualitative and quantitative schemes for 45 pesticides within a single analytical run. Water samples were extracted using an SPE column, with the pH adjusted to 7. Soil samples were processed using a modified QuEChERS method. The pretreatment for water samples emphasized selecting appropriate SPE columns and optimizing pH, while for soil samples, the focus was on choosing suitable extraction solvents and extraction salt packages. The enriched samples were then analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The method was evaluated for accuracy, precision, detection limits, and matrix effects. The method enabled the simultaneous detection of 45 pesticides within a 15-minute analysis period. SPE recoveries ranged from 56.1% to 118.8%. Instrumental detection limits varied between 0.02 and 1pg, while method detection limits extended from 0.05 to 18.47 ng/lin soil and water matrices. The approach was successfully applied to water and soil samples, with the pesticide concentration ranging from 0.1ng/L to 38 μg/L. The protocol substantially enhances the characterization and quantification of 45 pesticides in environmental samples, achieving a remarkable reduction in detection limits by an order of magnitude compared to previous research. This method enables the simultaneous detection of pesticides in both water and soil matrices using a single system, addressing the challenges of using separate systems for different environmental media. Furthermore, this protocol provides a crucial theoretical foundation for managing and safeguarding against pesticide pollution.

GRable Version 1.0: A Software Tool for Site-Specific Glycoform Analysis With Improved MS1-Based Glycopeptide Detection With Parallel Clustering and Confidence Evaluation With MS2 Information

High-throughput intact glycopeptide analysis is crucial for elucidating the physiological and pathological status of the glycans attached to each glycoprotein. Mass spectrometry-based glycoproteomic methods are challenging because of the diversity and heterogeneity of glycan structures. Therefore, we developed an MS1-based site-specific glycoform analysis method named "Glycan heterogeneity-based Relational IDentification of Glycopeptide signals on Elution profile (Glyco-RIDGE)" for a more comprehensive analysis. This method detects glycopeptide signals as a cluster based on the mass and chromatographic properties of glycopeptides and then searches for each combination of core peptides and glycan compositions by matching their mass and retention time differences. Here, we developed a novel browser-based software named GRable for semi-automated Glyco-RIDGE analysis with significant improvements in glycopeptide detection algorithms, including "parallel clustering." This unique function improved the comprehensiveness of glycopeptide detection and allowed the analysis to focus on specific glycan structures, such as pauci-mannose. The other notable improvement is evaluating the "confidence level" of the GRable results, especially using MS2 information. This function facilitated reduced misassignment of the core peptide and glycan composition and improved the interpretation of the results. Additional improved points of the algorithms are "correction function" for accurate monoisotopic peak picking; one-to-one correspondence of clusters and core peptides even for multiply sialylated glycopeptides; and "inter-cluster analysis" function for understanding the reason for detected but unmatched clusters. The significance of these improvements was demonstrated using purified and crude glycoprotein samples, showing that GRable allowed site-specific glycoform analysis of intact sialylated glycoproteins on a large-scale and in-depth. Therefore, this software will help us analyze the status and changes in glycans to obtain biological and clinical insights into protein glycosylation by complementing the comprehensiveness of MS2-based glycoproteomics. GRable can be freely run online using a web browser via the GlyCosmos Portal (https://glycosmos.org/grable).

NeoMS: Mass Spectrometry-based Method for Uncovering Mutated MHC-I Neoantigens.

Major Histocompatibility Complex (MHC) molecules play a critical role in the immune system by presenting peptides on the cell surface for recognition by T-cells. Tumor cells often produce MHC peptides with amino acid mutations, known as neoantigens, which evade T-cell recognition, leading to rapid tumor growth. In immunotherapies such as TCR-T and CAR-T, identifying these mutated MHC peptide sequences is crucial. Current mass spectrometry-based peptide identification methods primarily rely on database searching, which fails to detect mutated peptides not present in human databases. In this paper, we propose a novel workflow called NeoMS, designed to efficiently identify both non-mutated and mutated MHC-I peptides from mass spectrometry data. NeoMS utilizes a tagging algorithm to generate an expanded sequence database that includes potential mutated proteins for each sample. Furthermore, it employs a machine learning-based scoring function for each peptide-spectrum match (PSM) to maximize search sensitivity. Finally, a rigorous target-decoy approach is implemented to control the false discovery rates (FDR) of the peptides with and without mutations separately. Experimental results for regular peptides demonstrate that NeoMS outperforms four benchmark methods. For mutated peptides, NeoMS successfully identifies hundreds of high-quality mutated peptides in a melanoma-associated sample, with their validity confirmed by further studies.

Plasma lipidomics in early APP/PS1 female mouse model and its relationship with brain: Is it affected by the estrous cycle?

BackgroundAlzheimer's disease (AD) is the most prevalent dementia, showing higher incidence in women. Besides, lipids play an essential role in brain, and they could be dysregulated in neurodegeneration. Specifically, impaired plasma lipid levels could predict early AD diagnosis. This work aims to identify the main plasma lipids altered in early AD female mouse model and evaluate their relationship with brain lipidome. Also, the possible involvement of the estrous cycle in lipid metabolism has been evaluated.MethodsPlasma samples of wild-type (n = 10) and APP/PS1 (n = 10) female mice of 5 months of age were collected, processed, and analysed using a lipidomic mass spectrometry-based method. A statistical analysis involving univariate and multivariate approaches was performed to identify significant lipid differences related to AD between groups. Also, cytology tests were conducted to confirm estrous cycle phases.ResultsThree hundred thirty lipids were detected in plasma, 18 of them showed significant differences between groups; specifically, some triacylglycerols, cholesteryl esters, lysophosphatidylcholines, phosphatidylcholines, and ether-linked phosphatidylcholines, increased in early AD; while other phosphatidylcholines, phosphatidylethanolamines, ceramides, and ether-linked phosphatidylethanolamines decreased in early AD. A multivariate approach was developed from some lipid variables, showing high diagnostic indexes (70% sensitivity, 90% specificity, 80% accuracy). From brain and plasma lipidome, some significant correlations were observed, mainly in the glycerophospholipid family. Also, some differences were found in both plasma and brain lipids, according to the estrous cycle phase.ConclusionsTherefore, lipid alterations can be identified in plasma at early AD stages in mice females, with a relationship with brain lipid metabolism for most of the lipid subfamilies, suggesting some lipids as potential AD biomarkers. In addition, the estrous cycle monitoring could be relevant in female studies.

Mass Spectrometry-based Profiling of Single-cell Histone Post-translational Modifications to Dissect Chromatin Heterogeneity.

Single-cell proteomics confidently quantifies cellular heterogeneity, yet precise quantification of post-translational modifications, such as those deposited on histone proteins, has remained elusive. Here, we developed a robust mass spectrometry-based method for the unbiased analysis of single-cell histone post-translational modifications (schPTM). schPTM identifies both single and combinatorial histone post-translational modifications (68 peptidoforms in total), which includes nearly all frequently studied histone post-translational modifications with comparable reproducibility to traditional bulk experiments. As a proof of concept, we treated cells with sodium butyrate, a histone deacetylase inhibitor, and demonstrated that our method can i) distinguish between treated and non-treated cells, ii) identify sub-populations of cells with heterogeneous response to the treatment, and iii) reveal differential co-regulation of histone post-translational modifications in the context of drug treatment. The schPTM method enables comprehensive investigation of chromatin heterogeneity at single-cell resolution and provides further understanding of the histone code.

A DNA-peptide probe coupled mass spectrometry-based method for the detection of LncRNA in hepatocyte and serum samples

Liver cancer, a prominent contributor to cancer-related deaths, necessitates timely identification for successful intervention. In recent years, long non-coding RNAs (lncRNAs) have gained attention as potential biomarkers for liver cancer, and accurate quantification of lncRNA is essential for early diagnosis of liver cancer. However, existing methods for lncRNA detection rely on amplification and labeling techniques, resulting in semi-quantitative or qualitative outcomes. DNA-peptide technology offers a promising alternative. It has successfully translated nucleic acid quantification into peptide quantification, particularly in the context of miRNA analysis. However, the intricate structure of long-chain lncRNAs presents a challenge not encountered with miRNAs, making the design and acquisition of specific DNA-peptide probes for direct quantification more difficult. In this study, a strategy for lncRNA quantification was developed using a DNA-peptide probe coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based quasi-targeted proteomics. The inherent structural complexity of long-chain lncRNAs was overcome by designing DNA-peptide probes based on their unique sequence segments, enabling direct quantification without the need for amplification. Highly upregulated in liver cancer (HULC) was identified as a target lncRNA through bioinformatics analysis using GEO2R online software. Subsequently, the target lncRNA (i.e., HULC), which had been biotinylated and bound to streptavidin agarose beforehand, was hybridized with the probe. Following trypsin digestion, the reporter peptide was released and quantified using LC-MS/MS. Finally, this method was applied to analyze HULC levels in liver cancer cell lines and serum samples, enabling quantitative assessment and early diagnosis. The results demonstrated that liver cancer diagnostics could be enhanced through the integration of mass spectrometry and DNA-peptide probe technology for lncRNA quantification.

A new generation of nanobody research tools using improved mass spectrometry-based discovery methods

Single domain antibodies (“nanobodies”) derived from the variable region of camelid heavy-chain only antibody variants have proven to be widely useful tools for research, as well as therapeutic and diagnostic applications. In addition to traditional display techniques, methods to generate nanobodies using direct detection by mass spectrometry and DNA sequencing have been highly effective. However, certain technical challenges have limited widespread application. We have optimized a new pipeline for this approach that greatly improves screening sensitivity, depth of antibody coverage, antigen compatibility, and overall hit rate and affinity. We have applied this improved methodology to generate significantly higher affinity nanobody repertoires against widely used targets in biological research – i.e., GFP, tdTomato, GST, and mouse, rabbit, and goat IgG. We have characterized these reagents in affinity isolations and tissue immunofluorescence microscopy, identifying those that are optimal for these particularly demanding applications, and engineering dimeric constructs for ultra-high affinity. This study thus provides new nanobody tools directly applicable to a wide variety of research problems, and improved techniques enabling future nanobody development against diverse targets.

A MEPS-UHPLC-MS/MS analytical platform to detect isoprostanoids and specialized pro-resolving mediators in the urinary extracellular vesicles of mountain ultramarathon runners

Oxylipins are powerful signalling compounds derived from polyunsaturated fatty acids (PUFAs) and involved in regulating the immune system response. A mass spectrometry-based method was developed and validated for the targeted profiling of 52 oxylipins (e.g., isoprostanoids, prostaglandins, epoxy- and hydroxy-fatty acids, specialized pro-resolving mediators) and 4 PUFAs in small urinary extracellular vesicles (uEVs). Ultrasound-assisted extraction using a 50:50 v/v MeOH:H2O mixture ensured optimal analytical performances. Limits of detection ranged between 10 and 400 pg/mL for oxylipins and 0.10–3 ng/mL for PUFAs. Satisfactory recoveries (85–116 %) and good intra- and inter-day precisions (RSD ≤15 %) were obtained for all the analytes. The reliability of the procedure was tested in a real case scenario by monitoring ultramarathon runners during the world Tor des Géants® (TDG) race. Both F2- and E2-isoprostanes were detected in small uEVs of the ultramarathon runners, suggesting the onset of an oxidant insult. 5-F2t-IsoP exhibited significant pre- to post-race variations, thus potentially representing a non-invasive marker of in-vivo lipid peroxidation. The presence of specialized pro-resolving mediators suggests the activation of pro-resolution signalling cascade resolving inflammation. These outcomes may help manage post-exercise recovery and improve training.

Development of a cyclic ion mobility spectrometry-mass spectrometry-based collision cross-section database of permethylated human milk oligosaccharides.

Human milk oligosaccharides (HMOs) are an important class of biomolecules responsible for the healthy development of the brain-gut axis of infants. Unfortunately, their accurate characterization is largely precluded due to a variety of reasons - there are over 200 possible HMO structures whereas only 10s of these are available as authentic analytical standards. Furthermore, their isomeric heterogeneity stemming from their many possible glycosidic linkage positions and corresponding α/β anomericities further complicates their analyses. While liquid chromatography coupled to tandem mass spectrometry remains the gold standard for HMO analyses, it often times cannot resolve all possible isomeric species and thus warrants the development of other orthogonal approaches. High-resolution ion mobility spectrometry coupled to mass spectrometry has emerged as a rapid alternative to condensed-phase separations but largely has remained limited to qualitative information related to the resolution of isomers. In this work, we have assessed the use of permethylation to improve both the resolution and sensitivity of HMO analyses with cyclic ion mobility separations coupled with mass spectrometry. In addition to this, we have developed the first-ever high-resolution collision cross-section database for permethylated HMOs using our previously established calibration protocol. We envision that this internal reference database generated from high-resolution cyclic ion mobility spectrometry-mass spectrometry will greatly aid in the accurate characterization of HMOs and provide a valuable, orthogonal, approach to existing liquid chromatography-tandem mass spectrometry-based methods.

An analytical method using salting-out assisted liquid-liquid extraction to quantify ceftriaxone from micro volumes of human serum.

Ceftriaxone (CTRX) is a commonly used cephalosporin antibiotic. It is suggested that monitoring plasma/serum concentrations is helpful for its safe use. This study aimed to develop and validate an analytical method for measuring CTRX concentrations in human serum according to International Conference on Harmonization guideline M10. Ten microliters of serum sample was purified using a salting-out assisted liquid-liquid extraction procedure with magnesium sulfate. The upper layer was then diluted threefold and analyzed using a liquid chromatography-tandem mass spectrometry-based method with a total run time of 12 min. The linear calibration curve was obtained over the concentration range 5-500 μg/ml. The within-run accuracy varied from 0.2 to 6.5%, and the precision was ≤8.0%. The between-run accuracy and precision ranged from 0.7% to 5.6% and ≤6.4%, respectively. Significant carryover was resolved by injecting four blanks after high-concentration CTRX samples. The recovery rates from spiked serum at low and high concentrations were 44.4 and 43.4%, respectively. Other factors, including selectivity, matrix effects, stability, dilution integrity and reinjection reproducibility also met the acceptance criteria. Serum concentrations in 14 samples obtained from two participants receiving 2 g/day of CTRX were successfully determined using this method.

Thiamine status and genes encoding intestinal thiamine transporters and transcription factors in obese subjects

Background and aimsThe inconsistent data on thiamine status in obese subjects necessitates an examination of genes associated with intestinal absorption of thiamine. We aimed to reveal thiamine status in obese subjects and examine the expression of SLC19A2/3 genes encoding thiamine transporters and Sp1 transcription factor. Methods and resultsThirty-five adult obese subjects and 11 healthy controls were included in this cross-sectional study. Small intestine epithelial cells were used for quantitative RT-PCR analysis of the gene expression. The daily thiamine and energy intake were assessed with a food frequency questionnaire. Thiamine phosphate esters were hydrolyzed to free thiamine, and liquid chromatography with a tandem mass spectrometry-based method was used to measure total thiamine in whole blood. Daily energy intake according to body weight and daily carbohydrate intake were not significantly different between groups after adjustment for sex. Although daily thiamine intake was significantly lower in the obesity group (p = 0.015), obese subjects had significantly higher whole blood thiamine levels than controls (44.96 ± 14.6 ng/mL and 33.05 ± 8.6 ng/mL, p = 0.002). There was a significant positive correlation between whole blood thiamine and BMI (r = 0.342, p = 0.020). SLC19A2 gene expression was lower in those with BMI ≥35 kg/m2 (p = 0.036). A significant positive correlation was found between SLC19A2 expression and whole blood thiamine level (r = 0.310, p = 0.038). ConclusionA possible association between intestinal thiamine intake and total thiamine in whole blood was determined. The transcriptional changes of genes encoding the high-affinity membrane thiamine transporters, especially SLC19A2, probably play a role in this relationship.

A Comprehensive Review of Innovative Paradigms in Microbial Detection and Antimicrobial Resistance: Beyond Traditional Cultural Methods.

Microbial detection and antimicrobial resistance (AMR) surveillance are critical components of public health efforts to combat infectious diseases and preserve the efficacy of antimicrobial agents. While foundational in microbial identification, traditional cultural methods are often laborious, time-consuming, and limited in their ability to detect AMR markers. In response to these challenges, innovative paradigms have emerged, leveraging advances in molecular biology, genomics, proteomics, nanotechnology, and bioinformatics. This comprehensive review provides an overview of innovative approaches beyond traditional cultural methods for microbial detection and AMR surveillance. Molecular-based techniques such as polymerase chain reaction (PCR) and next-generation sequencing (NGS) offer enhanced sensitivity and specificity, enabling the rapid identification of microbial pathogens and AMR determinants. Mass spectrometry-based methods provide rapid and accurate detection of microbial biomarkers, including matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and biosensor technologies. Nanotechnology approaches, such as nanoparticle-based assays and nanopore sequencing, offer novel platforms for sensitive and label-free detection of pathogens and AMR markers. Embracing these innovative paradigms holds immense promise for improving disease diagnosis, antibiotic stewardship, and AMR containment efforts. However, challenges such as cost, standardization, and integration with existing healthcare systems must be addressed to realize the full potential of these technologies. By fostering interdisciplinary collaboration and innovation, we can strengthen our ability to detect, monitor, and combat AMR, safeguarding public health for generations.

#983 Identification of gut microbiome signatures associated with albuminuria in diabetes mellitus

Abstract Background and Aims Diabetes is a growing global problem with serious complications, including kidney impairment and cardiovascular morbidity and mortality. Monitoring albuminuria, which is associated with these complications, is crucial in optimal diabetes management. Recent research suggests a link between the gut microbiome, plasma metabolites and albuminuria development in diabetes patients, highlighting the need for further investigation using deep metagenomic sequencing. Method We investigated the relationship between 1002 gut microbial species, 1308 metabolites and albuminuria in 752 participants with diabetes from the Swedish CArdioPulmonary BioImage Study. To determine the relative abundance of species, we employed deep shotgun metagenomic sequencing of fecal samples. Plasma metabolites were analyzed using mass spectrometry-based methods. Results Shannon diversity index was inversely associated with albuminuria after adjusting for confounding factors (Fig. 1). Our multivariable-adjusted models revealed seven metagenomic species that were associated with albuminuria (Fig. 2). Furthermore, employing a global metabolomics approach, we identified phenyl sulfate, among 98 annotated metabolites (Fig. 3), as linked to the species Clostridium sp. AT4 and Eggerthella lenta. Notably, phenyl sulfate is involved in tyrosine metabolism, and we also observed an association between the gut metabolic module of Tyrosine degradation II and albuminuria. Conclusion In the present study, we identified seven gut microbial species linked to albuminuria and established a connection between these species and phenyl sulfate, which previously has been associated with podocyte damage and the development of albuminuria. These findings provided additional evidence of the impact of microbial species and contribute to our understanding of the complex relationship between the gut microbiome, plasma metabolites, and albuminuria in patients with diabetes.

Plasticity of the Arabidopsis leaf lipidome and proteome in response to pathogen infection and heat stress.

Plants must cope with a variety of stressors during their life cycle, and the adaptive responses to these environmental cues involve all cellular organelles. Among them, comparatively little is known about the contribution of cytosolic lipid droplets (LDs) and their core set of neutral lipids and associated surface proteins to the rewiring of cellular processes in response to stress. Here, we analyzed the changes that occur in the lipidome and proteome of Arabidopsis (Arabidopsis thaliana) leaves after pathogen infection with Botrytis cinerea or Pseudomonas syringae, or after heat stress. Analyses were carried out in wild-type plants and the oil-rich double mutant trigalactosyldiacylglycerol1-1 sugar dependent 1-4 (tgd1-1 sdp1-4) that allowed for an allied study of the LD proteome in stressed leaves. Using liquid chromatography-tandem mass spectrometry-based methods, we showed that a hyperaccumulation of the primary LD core lipid triacylglycerol is a general response to stress and that acyl chain and sterol composition are remodeled during cellular adaptation. Likewise, comparative analysis of the LD protein composition in stress-treated leaves highlighted the plasticity of the LD proteome as part of the general stress response. We further identified at least two additional LD-associated proteins, whose localization to LDs in leaves was confirmed by confocal microscopy of fluorescent protein fusions. Taken together, these results highlight LDs as dynamic contributors to the cellular adaptation processes that underlie how plants respond to environmental stress.