Liquid Chromatography-tandem Mass Spectrometry Analysis Research Articles

NP3 MS Workflow: An Open-Source Software System to Empower Natural Product-Based Drug Discovery Using Untargeted Metabolomics.

Natural products (or specialized metabolites) are historically the main source of new drugs. However, the current drug discovery pipelines require miniaturization and speeds that are incompatible with traditional natural product research methods, especially in the early stages of the research. This article introduces the NP3 MS Workflow, a robust open-source software system for liquid chromatography-tandem mass spectrometry (LC-MS/MS) untargeted metabolomic data processing and analysis, designed to rank bioactive natural products directly from complex mixtures of compounds, such as bioactive biota samples. NP3 MS Workflow allows minimal user intervention as well as customization of each step of LC-MS/MS data processing, with diagnostic statistics to allow interpretation and optimization of LC-MS/MS data processing by the user. NP3 MS Workflow adds improved computing of the MS2 spectra in an LC-MS/MS data set and provides tools for automatic [M + H]+ ion deconvolution using fragmentation rules; chemical structural annotation against MS2 databases; and relative quantification of the precursor ions for bioactivity correlation scoring. The software will be presented with case studies and comparisons with equivalent tools currently available. NP3 MS Workflow shows a robust and useful approach to select bioactive natural products from complex mixtures, improving the set of tools available for untargeted metabolomics. It can be easily integrated into natural product-based drug-discovery pipelines and to other fields of research at the interface of chemistry and biology.

Purification, characterization, and identification of a novel bacteriocin produced by Lacticaseibacillus casei KLS1, and its antimicrobial mechanism against Staphylococcus aureus

Staphylococcus aureus (S. aureus) and its biofilm were recognized as one of the major threats to food safety and human health. Bacteriocins produced by Lacticaseibacillus species have been demonstrated to inhibit the growth of foodborne pathogenic bacteria and their biofilm formation. Herein, a novel bacteriocin KLS1 from Lacticaseibacillus casei KLS1 was extracted by ethyl acetate and purified using an AKTA Pure 25 protein chromatography purification system. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses revealed that the molecular mass of bacteriocin KLSI was 3786.91 Da and the amino acid sequence was DTSASIASNKSETNDLLKQIEAANTEVINLNKQID. Bacteriocin KLS1 was stable at pH 2.0∼6.0, sensitive to proteases, and showed excellent thermal stability. Furthermore, bacteriocin KLS1 exhibited broad-spectrum antimicrobial activity against both Gram-positive and Gram-negative bacteria, even fungi. The crystal violet staining assay indicated that bacteriocin KLS1 significantly reduced the relative percentage of S. aureus biofilm (P < 0.05). Meanwhile, bacteriocin KLS1 was found to significantly decrease the metabolic activity of S. aureus by Cell Counting Kit-8 assay (P < 0.05). In addition, scanning electron microscopy and confocal laser scanning microscope showed that bacteriocin KLS1 disrupted the structure of S. aureus biofilm and cell membrane integrity, leading to cell deformation and leakage of contents. These results suggested that bacteriocin KLS1 might have the potential to serve as a biological preservative in the food industry.

4D label-free proteomics analysis of oxygen-induced retinopathy with or without anti-VEGF treatment

Oxygen-induced retinopathy (OIR) animal model is widely used for retinopathy of prematurity (ROP) researches. The purpose of this study was to identify proteins and related pathways of OIR with or without anti-vascular endothelial growth factor (VEGF) treatment, for use as biomarkers in diagnosing and treating ROP. Nine samples were subjected to proteomic analysis. Retina specimens were collected from 3 OIR mice, 3 OIR mice with anti-VEGF treatment and 3 normal mice (control group). Liquid chromatography-tandem mass spectrometry analysis was performed using the 4D label-free technique. Statistically significant differentially expressed proteins, gene ontology (GO) terms, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway representations, InterPro (IPR) and protein interactions were analyzed. In total, 4585 unique proteins were identified as differentially expressed proteins (DEPs). Enrichment analysis of the GO and KEGG indicated functional clusters related to peptide biosynthetic and metabolic process, cellular macromolecule biosynthetic process and nucleic acid binding in OIR group. For anti-VEGF treatment group, DEPs were clustered in DNA replication, PI3K/Akt signaling pathway and Jak/STAT signaling pathway. Proteomic profiling is useful for the exploration of molecular mechanisms of OIR and mechanisms of anti-VEGF treatment. These findings may be useful for identification of novel biomarkers for ROP pathogenesis and treatment.

Glycosylation of recombinant adeno-associated virus serotype 6

Glycosylation of biopharmaceuticals can affect their safety and efficacy. Glycans can occur on recombinant adeno-associated viruses (rAAVs) that are used for gene therapy; however, the types of glycan that attach to rAAVs are controversial. Here, we conducted lectin microarray analyses on six rAAVs serotype 6 (rAAV6) preparations that were produced differently. We demonstrate that O-glycans considered to be attached to rAAV6 were recognized by Agaricus bisporus agglutinin (ABA) and that N-glycans were detected in rAAV6 purified without affinity-chromatography. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis showed that the N-glycans detected in rAAV6 were derived from host cell proteins. A combination of ABA-based fractionation and LC-MS/MS revealed that rAAV6 was O-glycosylated with the mucin-type glycans, O-GalNAc (Tn-antigen) and mono- and di-sialylated Galβ1-3GalNAc (T-antigen) at S156, T162, T194, and T201 in viral protein (VP) 2, and with O-GlcNAc at T242 in VP3. The mucin-type O-glycosylated rAAV6 particles were 0.1%–1% of total particles. Further physicochemical and biological analyses revealed that mucin-type O-glycosylated rAAV6 had a lower ratio of VP1 to VP2/VP3, resulting in lower transduction efficiency both in vitro and in vivo compared with rAAV6 without mucin-type O-glycans. This report details conclusive evidence of rAAV glycosylation and its impact on rAAV-based therapeutics.

Lipid matrix-specific pretreatment method for enhancing the extractability and allergenicity maintenance of bovine milk allergens in ELISA detection

The presence of various components in the food matrix makes allergen detection difficult and inaccurate, and pretreatment is an innovative breakthrough point. Food matrices were categorised based on their composition. Subsequently, a pretreatment method was established using a combination of ultrasound-assisted n-hexane degreasing and weakly alkaline extraction systems to enhance the detection accuracy of bovine milk allergens. Results showed that more allergens were obtained with less structural destruction, as demonstrated using immunological quantification and spectral analysis. Concurrently, allergenicity preservation was confirmed through liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis, a KU812 cell degranulation model, and western blotting. The method exhibited good accuracy (bias, 8.47%), repeatability (RSDr, 1.52%), and stability (RSDR, 5.65%). In foods with high lipid content, such as chocolate, the allergen content was 2.29-fold higher than that of commercial kits. Laser confocal scanning microscopy (LCSM) and scanning electron microscopy (SEM) analyses revealed a significant decrease in fat content after post-pretreatment using our method. In addition, colloidal stability surpassed that achieved using commercial kits, as indicated through the PSA and zeta potential results. The results demonstrated the superiority of the extractability and allergenicity maintenance of lipid matrix-specific pretreatment methods for improving the accuracy of ELISA based allergen detection in real food.

Chemoselectivity Strategy Based on B-Label Integrated with Tailored COF for Targeted Metabolomic Analysis of Short-Chain Fatty Acids by UHPLC-MS/MS.

Chemoselective extraction strategy is an emerging and powerful means for targeted metabolomics analysis, which allows for the selective identification of biomarkers. Short-chain fatty acids (SCFAs) as functional metabolites for many diseases pose challenges in qualitative and quantitative analyses due to their high polarity and uneven abundance. In our study, we proposed the B-labeled method for the derivatization of SCFAs using easily available 3-aminobenzeneboronic acid as the derivatization reagent, which enables the introduction of recognition unit (boric acid groups). To analyze the B-labeled targeted metabolites accurately, cis-diol-based covalent organic framework (COF) was designed to specifically capture and release target compounds by pH-response borate affinity principle. The COF synthesized by the one-step Schiff base reaction possessed a large surface area (215.77 m2/g), excellent adsorption capacity (774.9 μmol/g), good selectivity, and strong regeneration ability (20 times). Combined with ultrahigh-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) analysis, our results indicated that the detection sensitivities of SCFAs increased by 1.2-2500 folds compared with unlabeled method, and the retention time and isomer separation were improved. Using this strategy, we determined twenty-six SCFAs in the serum and urine of rats in four groups about osteoporosis and identified important biomarkers related to the tricarboxylic acid cycle and fatty acid metabolism pathways. In summary, UHPLC-MS/MS based on B-labeled derivatization with tailored COF strategy shows its high selectivity, excellent sensitivity, and good chromatographic behavior and has remarkable application prospect in targeted metabolomics study of biospecimens.

Ultra-Performance Liquid Chromatography-Tandem Mass Spectrometry Analysis of Urinary Oligosaccharides and Glycoamino Acids for the Diagnosis of Mucopolysaccharidosis and Glycoproteinosis.

Mucopolysaccharidosis (MPS) and glycoproteinosis are 2 groups of heterogenous lysosomal storage disorders (LSDs) caused by defective degradation of glycosaminoglycans (GAGs) and glycoproteins, respectively. Oligosaccharides and glycoamino acids have been recognized as biomarkers for MPS and glycoproteinosis. Given that both groups of LSDs have overlapping clinical features, a multiplexed assay capable of unambiguous subtyping is desired for accurate diagnosis, and potentially for severity stratification and treatment monitoring. Urinary oligosaccharides were derivatized with 3-methyl-1-phenyl-2-pyrazoline-5-one (PMP) and analyzed by ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) together with the underivatized glycoamino acids. Novel biomarkers were identified with a semi-targeted approach with precursor mass scanning, the fragmentation pattern (if applicable), and the biochemical basis of the condition. A UPLC-MS/MS analysis with improved chromatographic separation was developed. Novel biomarkers for MPS-IIIA, IIIB, IIIC, and VII were identified and validated. A total of 28 oligosaccharides, 2 glycoamino acids, and 2 ratios were selected as key diagnostic biomarkers. Validation studies including linearity, lower limit of quantitation (LLOQ), and precision were carried out with the assay performance meeting the required criteria. Age-specific reference ranges were collected. In the 76 untreated patients, unambiguous diagnosis was achieved with 100% sensitivity and specificity. Additionally, the levels of disease-specific biomarkers were substantially reduced in the treated patients. A multiplexed UPLC-MS/MS assay for urinary oligosaccharides and glycoamino acids measurement was developed and validated. The assay is suitable for the accurate diagnosis and subtyping of MPS and glycoproteinosis, and potentially for severity stratification and monitoring response to treatment.

Functionalizing tandem mass tags for streamlining click-based quantitative chemoproteomics

Mapping the ligandability or potential druggability of all proteins in the human proteome is a central goal of mass spectrometry-based covalent chemoproteomics. Achieving this ambitious objective requires high throughput and high coverage sample preparation and liquid chromatography-tandem mass spectrometry analysis for hundreds to thousands of reactive compounds and chemical probes. Conducting chemoproteomic screens at this scale benefits from technical innovations that achieve increased sample throughput. Here we realize this vision by establishing the silane-based cleavable linkers for isotopically-labeled proteomics-tandem mass tag (sCIP-TMT) proteomic platform, which is distinguished by early sample pooling that increases sample preparation throughput. sCIP-TMT pairs a custom click-compatible sCIP capture reagent that is readily functionalized in high yield with commercially available TMT reagents. Synthesis and benchmarking of a 10-plex set of sCIP-TMT reveal a substantial decrease in sample preparation time together with high coverage and high accuracy quantification. By screening a focused set of four cysteine-reactive electrophiles, we demonstrate the utility of sCIP-TMT for chemoproteomic target hunting, identifying 789 total liganded cysteines. Distinguished by its compatibility with established enrichment and quantification protocols, we expect sCIP-TMT will readily translate to a wide range of covalent chemoproteomic applications.

Concentrations of per- and polyfluoroalkyl substances in vegetables from Sydney and Newcastle, Australia.

This study investigated per- and polyfluoroalkyl substances (PFASs) in 53 fruit and vegetable samples collected from a local wholesale and retail market in Sydney and a local supermarket in Newcastle. As there is limited information about PFAS levels in vegetables on the market, this study aimed to fill this gap and assess potential risks for humans through consumption of these vegetables. QuEChERS extraction - a solid-phase extraction method, a portmanteau word formed from 'quick, easy, cheap, effective, rugged and safe' - followed by enhanced matrix removal-lipid cleaning and liquid chromatography-tandem mass spectrometry analysis were used to detect 30 PFASs in vegetables. PFOA was detected in 7 out of the 53 samples, with concentrations of 0.038-1.996 ng g-1 fresh weight; PFOS was detected in 2 samples only, with concentrations ranging from 0.132 to 0.911 ng g-1 fresh weight. PFHxS was not detected in any sample in this study. PFOA and PFOS concentrations measured in vegetables in this study constituted daily intake of 2.03 ng kg-1 body weight (BW) and 1.98 ng kg-1 BW, respectively, according to recommended daily vegetable intake and BW data from the Australian Bureau of Statistics. The most sensitive population group is girls of 4-8 years of age. These estimated exposure levels represent up to 1.3% of the tolerable daily intake for PFOA (160 ng kg-1 BW) and 9.9% for PFOS (20 ng kg-1 BW) according to Food Standards Australia New Zealand. Consumption of the vegetables from the study locations poses a marginal risk to human health. © 2024 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

UPLC-ESI-MS/MS analysis revealed the dynamic changes and conversion mechanism of non-volatile metabolites during green tea fixation

Fixation is crucial for green tea quality; previous studies were conducted on finished teas and focused on the volatile metabolites of green tea. However, non-volatile metabolites’ (NVMs) evolution and formation mechanisms during fixation remain unclear. Here, fixated tea samples were collected at seven different time points during the green tea fixation stage, the dynamic changes and formation mechanisms of NVMs investigated via ultra-performance liquid chromatography-tandem mass spectrometry and enzymatic activity analyses. The results showed that fixation contained enzymatic activity thermal and non-enzymatic thermal stages. Moreover, 1196 NVMs (10 classes) were detected, and significant NVM variations were observed during the "enzymatic activity thermal" fixation stages, with increasing trends in lipids and amino acids, except alkaloids. Furthermore, 160 common differential NVMs were identified. KEGG analysis revealed that unsaturated fatty acid, linoleic acid phenylpropanoid, and flavonoid metabolism pathways were essential during fixation and influenced green tea aroma, taste, and color formation. These results provide a theoretical basis to regulate green tea fixation technology and enrich the chemical theory of green tea processing.

Effect of SO2, glutathione, and glutathione-rich inactive dry yeast on the color, phenolic compounds, ascorbic acid, and antioxidant activity of Roxburgh rose wine.

Conventional methods for inhibiting browning in wine are not suitable for cili (Roxburgh rose) wine, which is naturally rich in ascorbic acid and subject to restrictions on SO2 addition. In this study, the capacity of various additives to suppress the browning of cili wine caused by ascorbic acid degradation was investigated. SO2, pure reduced glutathione (GSH), regular inactive dry yeast (IDY), and IDY with various levels of glutathione enrichment (g-IDY) were separately introduced into cili wine following the completion of alcoholic fermentation. Over a period of 12 months, the color parameters, levels of ascorbic acid, phenolic compounds, antioxidant activity, and GSH content of the aged cili wine were analyzed. Among the investigated additives, g-IDY exhibited the strongest inhibitory effect on browning. Moreover, adding 800mgL-1 g-IDY increased the total reducing power and residual GSH content by factors of 1.52 and 2.44, respectively, with respect to those of the SO2-treated cili wine, thus enhancing its antioxidant capacity. Using ultra-performance liquid chromatography-tandem mass spectrometry analysis, a total of 22 monomeric phenolic compounds were identified. After g-IDY treatment, the contents of 15 easily oxidizable o-diphenols decreased, preventing the depletion of ascorbic acid as an antioxidant. As a result, the levels of ascorbic acid and total phenolics were 1.5-fold and 1.17-fold higher than those in the SO2-treated wine, respectively. This study demonstrates that g-IDY provides a new approach to preventing the browning of wine caused by ascorbic acid degradation. PRACTICAL APPLICATION: Cili wine, characterized by its high ascorbic acid content, can decelerate cellular senescence and bolster immune function, which has contributed to its popularity. Ascorbic acid, a potent antioxidant, can be spiked into white wines to significantly enhance their antioxidative properties. Nevertheless, the high ascorbic acid content in cili wine renders it susceptible to oxidation under both aerobic and anaerobic conditions, which alters the wine's hue from golden to dark brown, thus diminishing its commercial value. Overcoming this browning associated with ascorbic acid degradation is therefore of considerable importance and could facilitate the advancement of the cili industry.

Effect of limited hydrolysis with endopeptidase on bitterness properties of wheat gluten hydrolysates

The application of limited hydrolysis on wheat gluten (WG) has been found to be a highly effective method for improving a wide range of functional properties associated with plant protein. However, the bitter peptides formed during this process have an unpleasant bitterness. To provide a theoretical framework for de-bittering techniques, this study examined the modulation of bitterness intensity in wheat gluten hydrolysates (WGHs) by manipulating enzyme cleavage sites and degree of hydrolysis (DH). It was found that the bitter peptide's release content increased significantly, and the bitterness threshold decreased markedly with increasing DH. Furthermore, the structure-bitterness threshold association of bitter peptides was investigated. The results indicated that peptide segments in molecular weights (MW) from 500 to 1000 exhibited the greatest influence on bitterness threshold compared to peptides with other MWs. The percentage of total hydrophobic amino acid content and position of some hydrophobic amino acids in the amino acid sequence had a significant effect on the bitterness threshold. Finally, 47 peptides were identified by high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) analysis. These peptides were mainly small peptides with less than 13 amino acid residues and MW below 1500 Da, and most of them had Q values higher than 5855 J/mol.

The close association of micronutrients with COVID-19

ObjectivesThe present study was conducted to explore the performance of micronutrients in the prediction and prevention of coronavirus disease 2019 (COVID-19). MethodsThis is an observational case-control study. 149 normal controls (NCs) and 214 COVID-19 patients were included in this study. Fat-soluble and water-soluble vitamins were determined by liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis, and inorganic elements were detected by inductively coupled plasma-mass spectrometry (ICP-MS) analysis. A logistic regression model based on six micronutrients were constructed using DxAI platform. ResultsMany micronutrients were dysregulated in COVID-19 compared to normal control (NC). 25-Hydroxyvitamin D3 [25(OH)D3], magnesium (Mg), copper (Cu), calcium (Ca) and vitamin B6 (pyridoxic acid, PA) were significantly independent risk factors for COVID-19. The logistic regression model consisted of 25(OH)D3, Mg, Cu, Ca, vitamin B5 (VB5) and PA was developed, and displayed a strong discriminative capability to differentiate COVID-19 patients from NC individuals [area under the receiver operating characteristic curve (AUROC) = 0.901]. In addition, the model had great predictive ability in discriminating mild/normal COVID-19 patients from NC individuals (AUROC = 0.883). ConclusionsOur study showed that micronutrients were associated with COVID-19, and our logistic regression model based on six micronutrients has potential in clinical management of COVID-19, and will be useful for prediction of COVID-19 and screening of high-risk population.

Enhancing tomato disease resistance through endogenous antifungal proteins and introduced nematode-targeting dsRNA of biocontrol agent Bacillus velezensis HS-3.

As a type of biological control agent (BCA), Bacillus velezensis possesses the efficacy of inhibiting pathogenic microorganisms, promoting plant growth, and overcoming continuous cropping obstacles (CCOs). However, there is limited reporting on the optimization of the cultivation conditions for such biocontrol agents and their role as double-stranded RNA (dsRNA) delivery vectors. In this study, a Bacillus velezensis strain HS-3 was isolated from the root zone of tomato plants with in vitro anti-Botrytis cinerea activity. The investigation into active compounds revealed that HS-3 predominantly employs proteins with molecular weights greater than 3 kDa for its antifungal activity. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis identified various proteases and chitosanase, further suggesting that HS-3 most likely employs these enzymes to degrade fungal cell walls for its antifungal effect. To optimize the production of extracellular proteins, fermentation parameters for HS-3 were systematically optimized, leading to an optimized medium (OP-M). HS-3 cultured in OP-M demonstrated enhanced capacity to assist tomato plants in withstanding CCOs. However, the presence of excessive nematodes in diseased soil resulted in the disease severity index (DSI) remaining high. An RNA interference mechanism was further introduced to HS-3, targeting the nematode tyrosine phosphatase (TP) gene. Ultimately, HS-3 expressing dsRNA of TP in OP-M effectively assisted tomatoes in mitigating CCOs, reducing DSI to 2.2% and 17.8% of the control after 45 and 90 days of growth, respectively. The advantages of Bacillus velezensis in crop disease management and the mitigation of CCOs become even more pronounced when utilizing both optimized levels of endogenous enzymes and introduced nematode-targeting dsRNA. © 2024 Society of Chemical Industry.

Research on the screening and inhibition mechanism of angiotensin I-converting enzyme (ACE) inhibitory peptides from tuna dark muscle

The rapid screening of angiotensin I-converting enzyme (ACE) inhibitory peptides (ACEIPs) from protein hydrolysates remains a challenge in current researches. The current study presents the development of an efficient affinity medium (AOPAN–ACE) consisting of ACE immobilized on the surface of electrostatically spun polyacrylonitrile nanofibrous membranes for the efficient screening of ACEIPs. The application of this affinity medium followed by liquid chromatography–tandem mass spectrometry analysis resulted in the successful screening and identification of 60 potential ACEIPs from protein hydrolysates of tuna dark muscle. Notably, the application of PeptideRanker, pLM4ACE, and molecular docking approaches resulted in the screening and identification of a novel ACEIP FPPDVA. Furthermore, the peptide FPPDVA was synthesized using the solid-phase method, and its IC50 value on ACE was determined to be 87.11 ± 1.02 μM. Molecular docking analysis suggested that the ACEIP of the peptide FPPDVA is attributable to the formation of hydrogen bonds with the S1 active site (Ala354 and Tyr523) of ACE and metal–ligand bonds with Zn2+. In addition, molecular dynamics simulations revealed that the peptide FPPDVA formed a stable complex with ACE and was consistently localized within the active pocket of ACE over a simulation duration of 100 ns without being displaced from the active site. Lineweaver–Burk analysis further confirmed that the peptide FPPDVA exhibited mixed mode of inhibition against ACE. Overall, the affinity medium developed in the current study is potentially useful for highly efficient screening of ACEIPs, and the novel ACEIP FPPDVA identified herein is a promising functional food ingredient for antihypertensive application.

Abstract 1659: Phosphorylation of cell cycle and apoptosis regulatory protein (CARP)-1 by stress-activated protein kinase P38γ is a novel mechanism of apoptosis signaling by genotoxic chemotherapy

Abstract CARP-1, a perinuclear phospho-protein, regulates cell survival and apoptosis signaling induced by genotoxic drugs. However, kinase(s) phosphorylating CARP-1 and down-stream signal transduction events remain unclear. Here we find that CARP-1 Serine (S)626 and Threonine (T)627 substitution to Alanines (AA) inhibits genotoxic drug-induced apoptosis. CARP-1 T627 is followed by a Proline (P), and this TP motif is conserved in vertebrates. To further elucidate chemotherapy-activated, CARP-1-dependent signaling mechanisms, we UV cross-linked protein extracts from Adriamycin-treated HeLa cervical cancer cells with a CARP-1 (614-638) peptide, and conducted liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses of the peptide-bound protein complexes. This experiment revealed SAPK p38γ interaction with CARP-1 (614-638) peptide. Our studies further revealed that SAPK p38γ phosphorylates CARP-1 T627 in cancer cells treated with genotoxic drugs. CARP-1 T627 phosphorylation was also noted in breast tumors from patients treated with radiation or endocrine therapies. Loss of p38γ abrogates CARP-1 T627 phosphorylation, and results in enhanced survival of breast cancer cells by genotoxic drugs. We conclude that genotoxic drugs activate p38γ-dependent CARP-1 T627 phosphorylation and cell growth inhibition. Citation Format: Jaganathan Venkatesh, Magesh Muthu, Vino T. Cheriyan, Sreeja C. Sekhar, Nuwan C. Acharige, Edi Levi, Hadeel Assad, Mary Kay Pflum, Arun K. Rishi. Phosphorylation of cell cycle and apoptosis regulatory protein (CARP)-1 by stress-activated protein kinase P38γ is a novel mechanism of apoptosis signaling by genotoxic chemotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1659.

TMEM120B strengthens breast cancer cell stemness and accelerates chemotherapy resistance via β1-integrin/FAK-TAZ-mTOR signaling axis by binding to MYH9

BackgroundBreast cancer stem cell (CSC) expansion results in tumor progression and chemoresistance; however, the modulation of CSC pluripotency remains unexplored. Transmembrane protein 120B (TMEM120B) is a newly discovered protein expressed in human tissues, especially in malignant tissues; however, its role in CSC expansion has not been studied. This study aimed to determine the role of TMEM120B in transcriptional coactivator with PDZ-binding motif (TAZ)-mediated CSC expansion and chemotherapy resistance.MethodsBoth bioinformatics analysis and immunohistochemistry assays were performed to examine expression patterns of TMEM120B in lung, breast, gastric, colon, and ovarian cancers. Clinicopathological factors and overall survival were also evaluated. Next, colony formation assay, MTT assay, EdU assay, transwell assay, wound healing assay, flow cytometric analysis, sphere formation assay, western blotting analysis, mouse xenograft model analysis, RNA-sequencing assay, immunofluorescence assay, and reverse transcriptase-polymerase chain reaction were performed to investigate the effect of TMEM120B interaction on proliferation, invasion, stemness, chemotherapy sensitivity, and integrin/FAK/TAZ/mTOR activation. Further, liquid chromatography–tandem mass spectrometry analysis, GST pull-down assay, and immunoprecipitation assays were performed to evaluate the interactions between TMEM120B, myosin heavy chain 9 (MYH9), and CUL9.ResultsTMEM120B expression was elevated in lung, breast, gastric, colon, and ovarian cancers. TMEM120B expression positively correlated with advanced TNM stage, lymph node metastasis, and poor prognosis. Overexpression of TMEM120B promoted breast cancer cell proliferation, invasion, and stemness by activating TAZ-mTOR signaling. TMEM120B directly bound to the coil-coil domain of MYH9, which accelerated the assembly of focal adhesions (FAs) and facilitated the translocation of TAZ. Furthermore, TMEM120B stabilized MYH9 by preventing its degradation by CUL9 in a ubiquitin-dependent manner. Overexpression of TMEM120B enhanced resistance to docetaxel and doxorubicin. Conversely, overexpression of TMEM120B-∆CCD delayed the formation of FAs, suppressed TAZ-mTOR signaling, and abrogated chemotherapy resistance. TMEM120B expression was elevated in breast cancer patients with poor treatment outcomes (Miller/Payne grades 1–2) than in those with better outcomes (Miller/Payne grades 3–5).ConclusionsOur study reveals that TMEM120B bound to and stabilized MYH9 by preventing its degradation. This interaction activated the β1-integrin/FAK-TAZ-mTOR signaling axis, maintaining stemness and accelerating chemotherapy resistance.

Yinhuang buccal tablet alters airway microbiota composition and metabolite profile in healthy humans

Ethnopharmacological relevancePerturbations in airway microbiota composition and disruption of microbe-metabolite interactions have been observed in respiratory infectious diseases (RIDs). The Yinhuang (YH) buccal tablet, as an ancient Chinese medicinal formula, has been traditionally employed for the management of upper RIDs. However, there is a lack of evidence for the effects of YH buccal tablets on upper respiratory tract microbiota and circulating metabolites. Aim of the studyThe aim of this study was to analyze the changes in respiratory microbiota composition and circulating metabolite profile after YH buccal tablets administration. Materials and methodsThroat swab samples and serum samples were collected from 60 healthy subjects for high-throughput 16S ribosomal RNA gene (16S rRNA) sequencing and non-targeted Ultra-high performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) analysis. ResultsAirway microbial composition changed significantly after YH administration. The abundance of Actinomyces and Prevotella_7 increased, while the abundance of potentially pathogenic Pseudomonas and Corynebacterium decreased. A total of 168 significant HMDB taxonomic metabolites were identified in serum samples, of which lipid metabolites accounted for the largest proportion. Correlation analysis showed that circulatory metabolites were significantly correlated with changes in airway microbiota composition. ConclusionsYH buccal tablets can inhibit opportunistic pathogens, increase beneficial microorganisms in the upper respiratory tract, and regulate the body's metabolic pathways. These findings provide insights into the mechanism of action of YH buccal tablets in the treatment and prevention of respiratory diseases.

MAPK20-mediated ATG6 phosphorylation is critical for pollen development in Solanum lycopersicum L.

In flowering plants, male gametogenesis is tightly regulated by numerous genes. Mitogen-activated protein kinase (MAPK) plays a critical role in plant development and stress response, while its role in plant reproductive development is largely unclear. The present study demonstrated MAPK20 phosphorylation of ATG6 to mediate pollen development and germination in tomato (Solanum lycopersicum L.). MAPK20 was preferentially expressed in the stamen of tomato, and mutation of MAPK20 resulted in abnormal pollen grains and inhibited pollen viability and germination. MAPK20 interaction with ATG6 mediated the formation of autophagosomes. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis showed that ATG6 was phosphorylated by MAPK20 at Ser-265. Mutation of ATG6 in wild-type (WT) or in MAPK20 overexpression plants resulted in malformed and inviable pollens. Meanwhile, the number of autophagosomes in mapk20 and atg6 mutants was significantly lower than that of WT plants. Our results suggest that MAPK20-mediated ATG6 phosphorylation and autophagosome formation are critical for pollen development and germination.

Intracellular proteomics and extracellular vesiculomics as a metric of disease recapitulation in 3D-bioprinted aortic valve arrays.

In calcific aortic valve disease (CAVD), mechanosensitive valvular cells respond to fibrosis- and calcification-induced tissue stiffening, further driving pathophysiology. No pharmacotherapeutics are available to treat CAVD because of the paucity of (i) appropriate experimental models that recapitulate this complex environment and (ii) benchmarking novel engineered aortic valve (AV)-model performance. We established a biomaterial-based CAVD model mimicking the biomechanics of the human AV disease-prone fibrosa layer, three-dimensional (3D)-bioprinted into 96-well arrays. Liquid chromatography-tandem mass spectrometry analyses probed the cellular proteome and vesiculome to compare the 3D-bioprinted model versus traditional 2D monoculture, against human CAVD tissue. The 3D-bioprinted model highly recapitulated the CAVD cellular proteome (94% versus 70% of 2D proteins). Integration of cellular and vesicular datasets identified known and unknown proteins ubiquitous to AV calcification. This study explores how 2D versus 3D-bioengineered systems recapitulate unique aspects of human disease, positions multiomics as a technique for the evaluation of high throughput-based bioengineered model systems, and potentiates future drug discovery.