Liquid Chromatography-coupled Tandem Mass Spectrometry Research Articles

Derangement in Nicotinamide Adenine Dinucleotide Metabolism is Observed During Acute Kidney Injury Among Male Agricultural Workers at Risk for Mesoamerican Nephropathy

IntroductionMesoamerican Nephropathy (MeN) is a chronic kidney disease (CKD) which may be caused by recurrent acute kidney injury (AKI). We investigated urinary quinolinate to tryptophan ratio (Q/T), a validated marker of nicotinamide adenine dinucleotide (NAD+) biosynthesis elevated during ischemic and inflammatory AKI, in a sugarcane worker population with high rates of MeN in Nicaragua. MethodsAmong 693 male sugarcane workers studied, we identified 45 who developed AKI during the harvest season. We matched them 1:1 based on age and job category with two comparison groups: (1) “no kidney injury,” active sugarcane workers with serum creatinine <1.1mg/dL; and (2) “CKD,” individuals no longer working in sugarcane due to their CKD, who had additional 1:1 matching for serum creatinine. We measured urine metabolites using liquid chromatography-coupled tandem mass spectrometry, and compared Q/T and other metabolic features between the AKI and comparison groups. ResultsUrine Q/T was significantly higher in workers with AKI than in those with no kidney injury (median [IQR] 0.104 [0.074-0.167] vs 0.060 [0.045-0.091], P < 0.0001) and marginally higher than in workers with CKD (0.086 (0.063-0.142), P = 0.059). Urine levels of the NAD+ precursor nicotinamide were lower in the AKI group than in comparison groups. ConclusionWorkers at risk for MeN who develop AKI demonstrate features of impaired NAD+ biosynthesis, providing new insights into the metabolic mechanisms of injury in this population. Therapeutic use of oral nicotinamide, which may ameliorate NAD+ biosynthetic derangement and fortify against kidney injury, should be investigated to prevent AKI in this setting.

Abstract 5138: Proteomic analyses of the urothelial cancer landscape reveal highly distinct prognostic and predictive subtypes

Abstract Introduction: Urothelial cancer (UC) is a challenging disease with a wide tumor-biological spectrum. Most molecular classifications cover only muscle-invasive bladder cancer and are transcriptome-based, relating only indirectly to the therapeutically relevant and more stable protein level. Also, the recent introduction of antibody-drug conjugates (ADCs) requires quantitative data about the tumor specificity of their target proteins. We turned to the proteome to address these questions. Methods: We performed deep proteomic profiling of a comprehensive cohort by optimized tandem mass tag-labelled liquid chromatography-coupled tandem mass spectrometry. Data acquisition was validated internally with immunoblotting and externally by bioinformatic reclassification within existing, filtered transcriptomic data. After bioinformatics, the top cluster defining proteins were quantified immunohistochemically under real-world conditions. Protein profiles were individualized and separately evaluated with drug repurposing libraries. Cell viability assays were performed for a panel of twelve UC cell lines to validate these predictions in vitro. Results: We analyzed 434 samples with 242 tumors and 192 paired normal mucosae, covering all stages of UC. 9542 proteins were quantified and revealed five distinct proteomic subtypes. These were validated internally and externally, showing relevant survival stratification also in the TCGA dataset. The proteomic subtypes were independent from pathological groups with relevant stratification of progression- free and overall survival (low vs. high-risk: median 103 vs. 27 months). Tumor specificity of all proteins was highly heterogeneous across stages and subtypes. As an example, the ADC target NECTIN4 was generally overexpressed mainly in non-muscle-invasive UC. Drug repurposing revealed several new candidate drugs, each specific to different proteomic subtypes. In vitro data showed increased sensitivity by subtype in line with four out of seven representative predictions. Conclusions: Proteomic subtypes add independent prognostic information and carry predictive value for several newly identified adjuvant drug candidates. The actual tumor specificity of biomarkers and ADC targets is highly dependent on stage and subtype and calls for individualized patient-specific predictive testing. Citation Format: Franz Friedrich Dressler, Falk Diedrichs, Deema Sabtan, Sofie Hinrichs, Paulina Mackedanz, Mareile Schlotfeldt, Christoph Krisp, Martin Hennig, Hartmut Schlueter, Ulrich Wetterauer, Roman Zubarev, David Horst, Sven Perner, Philipp Wolf, Ákos Végvári. Proteomic analyses of the urothelial cancer landscape reveal highly distinct prognostic and predictive subtypes [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 5138.

Comparative analysis of hippocampal extracellular space uncovers widely altered peptidome upon epileptic seizure in urethane-anaesthetized rats

BackgroundThe brain extracellular fluid (ECF), composed of secreted neurotransmitters, metabolites, peptides, and proteins, may reflect brain processes. Analysis of brain ECF may provide new potential markers for synaptic activity or brain damage and reveal additional information on pathological alterations. Epileptic seizure induction is an acute and harsh intervention in brain functions, and it can activate extra- and intracellular proteases, which implies an altered brain secretome. Thus, we applied a 4-aminopyridine (4-AP) epilepsy model to study the hippocampal ECF peptidome alterations upon treatment in rats.MethodsWe performed in vivo microdialysis in the hippocampus for 3–3 h of control and 4-AP treatment phase in parallel with electrophysiology measurement. Then, we analyzed the microdialysate peptidome of control and treated samples from the same subject by liquid chromatography-coupled tandem mass spectrometry. We analyzed electrophysiological and peptidomic alterations upon epileptic seizure induction by two-tailed, paired t-test.ResultsWe detected 2540 peptides in microdialysate samples by mass spectrometry analysis; and 866 peptides—derived from 229 proteins—were found in more than half of the samples. In addition, the abundance of 322 peptides significantly altered upon epileptic seizure induction. Several proteins of significantly altered peptides are neuropeptides (Chgb) or have synapse- or brain-related functions such as the regulation of synaptic vesicle cycle (Atp6v1a, Napa), astrocyte morphology (Vim), and glutamate homeostasis (Slc3a2).ConclusionsWe have detected several consequences of epileptic seizures at the peptidomic level, as altered peptide abundances of proteins that regulate epilepsy-related cellular processes. Thus, our results indicate that analyzing brain ECF by in vivo microdialysis and omics techniques is useful for monitoring brain processes, and it can be an alternative method in the discovery and analysis of CNS disease markers besides peripheral fluid analysis.

Integrative physiological and metabolic traits reveal the mechanisms of chamomile flowers in response to nicotine stress

BackgroundChamomile (Matricaria recutita L.) is an important economic crop after tobacco (Nicotiana tabacum L.) cultivation. The nicotine released into the soil during tobacco cultivation has an impact on various aspects of chamomile growth, including plant height, flowering period, flower yield, and flower quality. We aimed to examine the effects of physiological and metabolic response of chamomile under different concentrations of nicotine stress.ResultsThe study revealed that chamomile growth was positively influenced by nicotine concentrations of 1.0 μg/g (N-1) and 10.0 μg/g (N-10). However, higher nicotine concentrations of 100.0 μg/g (N-100) and 500.0 μg/g (N-500) were found to induce stress as the highest levels of antioxidant enzyme activities and malondialdehyde (MDA) levels were observed under this treatment. In addition, it was observed that nicotine was transported from the roots to other organs during the entire growth period of chamomile and the nicotine levels reached saturation under N-100 treatment. A total of 1096 metabolites were detected by ultra-high-performance liquid chromatography-coupled tandem mass spectrometry (UHPLC–MS/MS) analysis, and 48 differentially expressed metabolites (DEMs) were identified among the groups via widely targeted metabolomics studies. The response of chamomile flowers to nicotine stress is associated with the presence of flavonoids, phenolic acids, organic acids, and other substances. Metabolic regulation under nicotine stress primarily involves processes, such as aminoacyl-tRNA biosynthesis, ABC (ATP-binding cassette) transporter activity, glyoxylate and dicarboxylate metabolism and pyrimidine metabolism.ConclusionsThis report presents the first findings on how nicotine affects the metabolism of chamomile. It also provides a comprehensive understanding of how crops can resist nicotine stress from a metabolic perspective.Graphical

Non-neuronal acetylcholine is causal for cardioprotection by hypoxic preconditioning in adult rat cardiomyocytes

Abstract Introduction Brief episodes of non-lethal myocardial ischemia/reperfusion preceding more sustained ischemia and reperfusion reduce lethal ischemia/reperfusion injury. The underlying protective signaling mechanisms of such ischemic preconditioning are unclear in their details. Among other protective mediators, neuronal acetylcholine (ACh) and its signaling through cholinergic receptors is involved in protection by ischemic preconditioning. Recently, a non-neuronal cardiac cholinergic system (NNCCS) has been identified, suggesting that a nervous system-independent, cardiomyocyte-derived acetylcholine signaling with signal amplification by auto- and paracrine cholinergic receptor activation could also participate in ischemic preconditioning. Aim We aimed to examine the role of NNCCS-derived ACh as a mediator of ischemic preconditioning. We therefore, in a reductionist approach, used isolated adult cardiomyocytes with hypoxic preconditioning (HPC). Methods Adult ventricular rat cardiomyocytes were isolated (from n=9 hearts), and HPC was induced by one cycle of 10 min hypoxia / 20 min reoxygenation. Thirty min normoxia served as control. Cardiomyocytes were then exposed to 30 min sustained hypoxia / 5 min reoxygenation (H/R), or a 35 min time control (TC). Cardiomyocyte viability was quantified before and after H/R or TC, respectively, by trypan blue staining. In a subgroup of experiments (cardiomyocytes from n=6 hearts) in the presence of physostigmine (0.2 mmol/L), intracellular ACh was quantified before and after HPC or normoxia and after sustained hypoxia and reoxygenation or TC, respectively, via liquid chromatography-coupled tandem mass spectrometry. Experiments on cardiomyocyte viability (from n=9 hearts) were repeated with the addition of cholinergic receptor antagonists (nicotinic: hexamethonium [1 µmol/L], muscarinic: atropine [0.1 µmol/L]) a) during the first 30 min with HPC or normoxia, b) during H/R or TC (30-65 min), or c) throughout the total 65 min protocol. Results The viability of cardiomyocytes subjected to H/R was better preserved with HPC than without (Figure A), and intracellular ACh was increased during hypoxia after prior HPC (Figure B). Cholinergic receptor antagonists during HPC did not change HPC´s protection (Figure A). However, the combination of both antagonists during sustained hypoxia abrogated HPC´s protection (Figure A), whereas nicotinic or muscarinic cholinergic receptor antagonists alone did not. Cholinergic receptor antagonists throughout the total 65 min also abrogated HPC´s protection (Figure A). Conclusion: The NNCCS is activated by HPC and causal for HPC´s protection. HPC increases intracellular acetylcholine, and cardiomyocyte protection is mediated via both nicotinic and muscarinic cholinergic receptors, suggesting an auto- and paracrine signal amplification on the cardiomyocyte level.Figure

Lipid metabolism reprogramming roles in mantel cell lymphoma growth and survival

Introduction: Metabolic reprogramming is a hallmark of cancer progression. However, there are few studies in mantle cell lymphoma (MCL). Protein arginine methyltransferase 5 (PRMT5), catalyzes monomethylation and symmetric demethylation of arginine residues on histone and nonhistone proteins and participates in tumor progression. This study aimed to investigate the mechanism of PRMT5-induced lipid reprogramming in MCL. Method: Lymph node, bone marrow biopsy, peripheral blood specimens and MCL cell lines were utilized as models. Liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS)-based analysis was performed to measure the steady-state level of metabolites. GSE93291 dataset and immunohistochemistry (IHC) staining were utilized to determine the relationship between expression levels of PRMT5 and patient outcome. CRISPR/Cas9 editing was employed to engineer the loss-of-function models of PRMT5 and other key genes involved in lipid metabolism. Result: Non-targeted LC-MS/MS analysis showed that lipid metabolites were rich in MCL cell lines (Figure 1A and 1B). Through systematic analysis of the relationship between lipid metabolism-related genes and MCL prognosis in GSE93291, PRMT5, SREBP1, SRENP2, FASN and MYC were found to be associated with the overall survival (OS) of MCL patients (Figure 1F–1J), which suggested that lipid metabolism reprogramming may be involved in the development of MCL. IHC staining of PRMT5 in 105 MCL tissues confirmed that elevated PRMT5 expression was significantly associated with poor progression free survival (PFS) (P = 0.039) and OS (P < 0.001) in MCL patients (Figure 1D and 1E). Multivariate Cox regression analysis showed that high PRMT5 expression was an independent prognostic indicator of OS (P = 0.003). Gene transcriptome sequencing showed downregulation of the PRMT5 caused the reduced expression of SREBP1/SREBP2 and FASN and change the expression of lipid metabolite (Figure 1K). PRMT5, SREBP1/SREBP2 and FASN depletion significantly impaired outgrowth and increased apoptosis of MCL cells. In primary tumor samples, MYC protein levels were significantly correlated with PRMT5 protein levels (P < 0.001). PRMT5 knockout blocked MYC mRNA and protein expression, suggesting a requisite role of PRMT5 in MYC transcription regulation. Further molecular biological methods were used to verify that PRMT5 could participate in lipid metabolism reprogramming through MYC by changing the expression levels of SREBP1/SREBP2 and FASN (Figure 1L). Keywords: Aggressive B-cell non-Hodgkin lymphoma, Diagnostic and Prognostic Biomarkers, Metabolism No conflicts of interests pertinent to the abstract.

CTPS1 acts as a prognostic biomarker and therapeutic target in mantle cell lymphoma

Introduction: Mantle cell lymphoma (MCL) represents 6 to 8% of non-Hodgkin’s lymphoma with generally poor prognosis. Cytidine triphosphate synthase 1 (CTPS1) is a critical regulatory enzyme in cytidine metabolism, catalyzing the rate-limiting step in de novo CTP synthesis. Herein, we aim to investigate the clinical significance and functional mechanisms of CTPS1 in MCL patients. Methods: Lymph node, bone marrow biopsy, peripheral blood specimens and MCL cell lines were utilized as models. Liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS)-based analysis was performed to measure the steady-state level of metabolites. GSE93291 dataset and immunohistochemistry (IHC) staining were utilized to determine the relationship between expression levels of CTPS1 and patient outcome. CRISPR/Cas9 editing was employed to engineer the loss-of-function models of CTPS1 and other key enzymes involved in CTP synthesis. Results: Metabolic Profiling revealed dramatically aberrant cellular abundance of metabolic intermediates in the CTP synthesis pathway (Figure 1A). For GSE93291 analysis, a nucleotide metabolism related prognostic model was established by bioinformatic analysis and CTPS1 was screened out by highest regression coefficient (Figure 1B). IHC staining of CTPS1 in 105 MCL tissues confirmed that elevated CTPS1 expression was significantly associated with poor PFS (P = 0.038) and OS (P = 0.001) in MCL patients (Figure 1C-D). Multivariate Cox regression analysis showed that high CTPS1 expression was an independent prognostic indicator of both PFS and OS. CTPS1 depletion significantly impaired outgrowth and increased apoptosis of MCL cells, suggesting that CTPS1 is the major isozyme important for MCL survival (Figure 1E-F). In primary tumor samples, MYC protein levels were significantly correlated with CTPS1 protein levels (P < 0.001, R = 0.638). MYC knockout blocked CTPS1 mRNA and protein expression prior to induction of cell death, suggesting a requisite role of MYC in CTPS1 transcription regulation (Figure 1G). Remarkably, TP53 aberrant and ibrutinib-resistant MCL cells rely on cytidine metabolism (Figure 1H). Genetic or chemical inhibition (3-deazauridine) of CTPS1 reversed poor responsiveness of MCL cell lines to ibrutinib (Figure 1I). Cytidine level was significantly increased in TP53-deficient MCL cells and the effect of CTPS1 inhibition was independent of TP53 status (Figure 1K). Gene set enrichment analysis of RNA-sequencing revealed that CTPS1 inhibition induced DNA damage and apoptosis. Moreover, CTPS1 inhibition caused cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) activation, which triggered innate immune pathway, leading to cells growth inhibition (Figure 1L). Keywords: Aggressive B-cell non-Hodgkin lymphoma, Diagnostic and Prognostic Biomarkers, Metabolism No conflicts of interests pertinent to the abstract.

Isolation and Characteristics of Extracellular Vesicles Produced by Probiotics: Yeast Saccharomyces boulardii CNCM I-745 and Bacterium Streptococcus salivarius K12

Numerous probiotic microorganisms have repeatedly been shown to produce nanometer-sized structures named extracellular vesicles (EVs). Recently, it has been suggested that similarly to whole microbial cells, EVs produced by probiotics may also demonstrate health benefits to the host, while their application does not involve the risk of infection caused by live microorganisms. In this work, we isolated EVs from two probiotic species originating from different taxonomic domains — yeast Saccharomyces boulardii CNCM I-745 and bacterium Streptococcus salivarius K12. The diameters of S. boulardii EVs were about 142 nm and for S. salivarius EVs about 123 nm. For S. boulardii EVs, 1641 proteins and for S. salivarius EVs, 466 proteins were identified with a liquid chromatography-coupled tandem mass spectrometry and then functionally classified. In both microbial species, metabolic proteins significantly contributed to the cargo of EVs comprising 25% and 26% of all identified vesicular proteins for fungi and bacteria, respectively. Moreover, enzymes associated with cell wall rearrangement, including enzymatically active glucanases, were also identified in EVs. Furthermore, probiotic EVs were shown to influence host cells and stimulate the production of IL-1β and IL-8 by the human monocytic cell line THP-1, and, at the same time, did not cause any remarkable reduction in the survival rate of Galleria mellonella larvae in this invertebrate model commonly used to evaluate microbial EV toxicity. These observations suggest that the EVs produced by the investigated probiotic microorganisms may be promising structures for future use in pro-health applications.

Weighted Gene Co-Expression Network Analysis and Support Vector Machine Learning in the Proteomic Profiling of Cerebrospinal Fluid from Extraventricular Drainage in Child Medulloblastoma.

Medulloblastoma (MB) is the most common pediatric malignant central nervous system tumor. Overall survival in MB depends on treatment tuning. There is aneed for biomarkers of residual disease and recurrence. We analyzed the proteome of waste cerebrospinal fluid (CSF) from extraventricular drainage (EVD) from six children bearing various subtypes of MB and six controls needing EVD insertion for unrelated causes. Samples included total CSF, microvesicles, exosomes, and proteins captured by combinatorial peptide ligand library (CPLL). Liquid chromatography-coupled tandem mass spectrometry proteomics identified 3560 proteins in CSF from control and MB patients, 2412 (67.7%) of which were overlapping, and 346 (9.7%) and 805 (22.6%) were exclusive. Multidimensional scaling analysis discriminated samples. The weighted gene co-expression network analysis (WGCNA) identified those modules functionally associated with the samples. A ranked core of 192 proteins allowed distinguishing between control and MB samples. Machine learning highlighted long-chain fatty acid transport protein 4 (SLC27A4) and laminin B-type (LMNB1) as proteins that maximized the discrimination between control and MB samples. Machine learning WGCNA and support vector machine learning were able to distinguish between MB versus non-tumor/hemorrhagic controls. The two potential protein biomarkers for the discrimination between control and MB may guide therapy and predict recurrences, improving the MB patients’ quality of life.

Modulating Lysine Crotonylation in Cardiomyocytes Improves Myocardial Outcomes.

Ischemic heart disease is a major global public health challenge, and its functional outcomes remain poor. Lysine crotonylation (Kcr) was recently identified as a post-translational histone modification that robustly indicates active promoters. However, the role of Kcr in myocardial injury is unknown. In this study, we aimed to clarify the pathophysiological significance of Kcr in cardiac injury and explore the underlying mechanism. We investigated the dynamic change of both the Kcr sites and protein level in left ventricular tissues at 2 time points following sham or cardiac ischemia-reperfusion injury, followed by liquid chromatography-coupled tandem mass tag mass spectrometry. After validation of the enriched protein Kcr by immunoprecipitation and Western blot, the function and mechanism of specific Kcr sites were further investigated in vitro and in vivo by gain- or loss-of-function mutations targeting Kcr sites of selected proteins. We found that cardiac ischemia-reperfusion injury triggers preferential Kcr of proteins required for cardiomyocyte contractility, including mitochondrial and cytoskeleton proteins, which occurs largely independently of protein-level changes in the same proteins. Those exhibiting Kcr changes were associated not only with disruption of cardiomyocyte mitochondrial, sarcomere architecture, and gap junction but also with cardiomyocyte autophagy and apoptosis. Modulating site-specific Kcr of selected mitochondrial protein IDH3a (isocitrate dehydrogenase 3 [NAD+] alpha) at K199 and cytoskeletal protein TPM1 (tropomyosin alpha-1 chain) at K28/29 or enhancing general Kcr via sodium crotonate provision not only protects cardiomyocyte from apoptosis by inhibiting BNIP3 (Bcl-2 adenovirus E18 19-kDa-interacting protein 3)-mediated mitophagy or cytoskeleton structure rearrangement but also preserves postinjury myocardial function by inhibiting fibrosis and apoptosis. Our results indicate that Kcr modulation is a key response of cardiomyocytes to ischemia-reperfusion injury and may represent a novel therapeutic target in the context of ischemic heart disease.

Abstract 2008: The oncogenic fusion protein DNAJB1-PRKACA can be actively targeted by peptide-based immunotherapy in fibrolamellar hepatocellular carcinoma

Abstract Fibrolamellar hepatocellular carcinoma (FL-HCC) is a rare tumor disease, which affects children and adolescents without history of primary liver disease. Beside surgical resection established treatment options are lacking for FL-HCC. Recently, the DNAJB1-PRKACA fusion transcript was identified as the oncogenic driver of tumor pathogenesis in 100% of FL-HCC patients. Here, we investigated the role of the DNAJB1-PRKACA fusion protein as a source for immunogenic neoepitopes and showed first immunotherapeutic application of these antigens in a FL-HCC patient.HLA class I- and class II-presented neoantigens derived from the DNAJB1-PRKACA fusion protein were predicted in silico using NetMHCpan 4.1 and SYFPEITHI 1.0, or NetMHCIIpan 4.0, respectively. With this workflow nine binding cores of nine amino acid length for a total of 1290 different HLA class II alleles, as well as 13 HLA class I ligands for the 20 most frequent HLA class I allotypes (European population, iedb.org) were identified. Cellular processing and HLA presentation of DNAJB1-PRKACA-derived peptides was proven by liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) of DNAJB1-PRKACA-transduced HCC cell lines. Immunogenicity of DNAJB1-PRKACA-derived peptides was assessed for the HLA class II peptide (PII-1) and the HLA-A*24 peptide (PA*24) by in vitro priming experiments which showed an induction of multifunctional peptide-specific CD4+ and CD8+ T cells, respectively, with expression of CD107a, IFNγ, and TNF upon peptide-pulsing. Furthermore, PA*24-specific T cells showed antigen-specific lysis of autologous peptide-loaded target cells and single-cell next-generation sequencing (10x Genomics) of PA*24-specific CD8+ T cells further enabled the identification of DNAJB1-PRKACA-reactive T cell receptors. Based on these preclinical data we applied a peptide vaccine, consisting of three HLA class I ligands (PA*02, PB*44, and PC*05) and PII-1 spanning the DNAJB1-PRKACA fusion region, to a 15-year old patient with histologically confirmed FL-HCC, who experienced multiple tumor relapses after early liver transplant due to unresectable FL-HCC not responsive to chemotherapy. After two vaccinations in vivo induction of multifunctional CD4+ T cells targeting PII-1 and PB*44 was observed by IFNγ ELISPOT. Single-cell RNA sequencing of vaccine-induced CD4+ T cells revealed distinct gene expression clusters of T cell activation and high TCR clonality. DNAJB1-PRKACA-specific T cells persisted in peripheral blood and were accompanied by relapse free survival of the patient until now, more than one year post vaccination. These findings identified the DNAJB1-PRKACA fusion transcript as novel prime source for broadly applicable neoepitopes and corresponding TCRs and provide first evidence for their application in cancer immunotherapy of FL-HCC. Citation Format: Jens Bauer, Natalie Köhler, Yacine Maringer, Philip Bucher, Tatjana Bilich, Melissa Zwick, Severin Dicks, Annika Nelde, Marissa Dubbelaar, Jonas Scheid, Marcel Wacker, Jonas J. Heitmann, Sarah Schroeder, Jonas Rieth, Monika Denk, Marion Richter, Reinhild Klein, Irina Bonzheim, Julia Luibrand, Ursula Holzer, Martin Ebinger, Ines B. Brecht, Michael Bitzer, Melanie Boerries, Helmut R. Salih, Hans-Georg Rammensee, Stephan Hailfinger, Juliane S. Walz. The oncogenic fusion protein DNAJB1-PRKACA can be actively targeted by peptide-based immunotherapy in fibrolamellar hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2008.

Rapid LC–MS/MS detection of different carbapenemase types in carbapenemase-producing Enterobacterales

Klebsiella pneumoniae carbapenemase (KPC)-2, metallo-beta-lactamases (MBL), and oxacillinase (OXA)-48-like carbapenemases are considered the most important carbapenemases. In vitro studies have demonstrated that the carbapenemase activity of KPC-2 and MBL can be inhibited by 3-aminophenylboronic acid and ethylenediaminetetraacetic acid (EDTA), respectively. Understanding the carbapenemase types expressed in carbapenem-resistant Enterobacterales (CRE) is of great significance to clinical therapies. Liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) is fast, stable, and specific; and is considered the gold standard method for measuring small molecules. In this study, we developed carbapenemase inhibition tests combined with LC-MS/MS to rapidly identify carbapenemase types. A total of 295 clinical isolates were examined, including 212 KPC-2 producers, 29 MBL producers, 15 OXA-48-like producers, 3 KPC-2 + OXA-232 producers, and 36 carbapenem-sensitive strains. We used LC-MS/MS to determine the carbapenemase types by measuring the ratio of the hydrolyzed meropenem peak areas in the presence and absence of different inhibitors. The sensitivity and specificity of LC-MS/MS in detecting single KPC-2 producers were 97.64% and 100.00%, respectively, and 96.55% and 100.00% for MBL producers, respectively. In addition, the sensitivity and specificity of LC-MS/MS in detecting single OXA-48-like producers were both 100.00% when extending incubation time up to 2.5h. LC-MS/MS showed excellent agreement in detecting carbapenemase types using the modified carbapenem inactivation (mCIM)/EDTA-carbapenem inactivation assay (eCIM) (kappa = 0.93 for serine carbapenemases and kappa = 0.98 for MBL carbapenemases). In this study, LC-MS/MS demonstrated excellent detection of different carbapenemase types, showing potential reliability in future clinical applications.

Nigericin and Geldanamycin Are Phytotoxic Specialized Metabolites Produced by the Plant Pathogen Streptomyces sp. 11-1-2.

ABSTRACTStreptomyces bacteria are a key source of microbial specialized metabolites with useful applications in medicine and agriculture. In addition, some species are important plant pathogens and cause diseases such as potato scab, which reduces the quality and market value of affected potato crops. Most scab-associated Streptomyces spp. produce the phytotoxic metabolite thaxtomin A as the principal pathogenicity factor. However, recent reports have described scab-causing strains that do not produce thaxtomin A, but instead produce other phytotoxins that are thought to contribute to plant host infection and symptom development. Streptomyces sp. 11-1-2 is a highly pathogenic strain that was originally isolated from a scab symptomatic potato tuber in Newfoundland, Canada. The strain secretes one or more phytotoxic compounds of unknown identity, and it is hypothesized that these compounds serve as virulence factors for this organism. We analyzed the genome sequence of Streptomyces sp. 11-1-2 and found biosynthetic gene clusters for producing the known herbicidal compounds nigericin and geldanamycin. Phytotoxic culture extracts were analyzed using liquid chromatography-coupled tandem mass spectrometry and molecular networking, and this confirmed the production of both compounds by Streptomyces sp. 11-1-2 along with other, potentially related metabolites. The biosynthesis of both metabolites was found to be suppressed by the addition of N-acetylglucosamine to the culture medium, and pure nigericin and geldanamycin were able to exhibit phytotoxic effects against both radish seedlings and potato tuber tissue. Furthermore, the coadministration of the two compounds produced greater phytotoxic effects against potato tuber tissue than administration of each compound alone.IMPORTANCE Plant pathogens use a variety of mechanisms, including the production of phytotoxic specialized metabolites, to establish an infection of host tissue. Although thaxtomin A is considered the key phytotoxin involved in the development of potato scab disease, there is increasing evidence that other phytotoxins can play a role in disease development in some instances. In this study, we show that the highly pathogenic Streptomyces sp. 11-1-2 is capable of producing nigericin and geldanamycin, which individually and combined can cause significant damage to potato tuber tissue and radish seedlings. Our results suggest that the pathogenic phenotype of Streptomyces sp. 11-1-2 is due in part to the production of these specialized metabolites. As the biological activity of nigericin and geldanamycin is vastly different from the proposed activity of thaxtomin A against plants, the secretion of these compounds may represent a novel mechanism of plant pathogenicity exhibited by some Streptomyces species.

Comparative proteome analysis identified CD44 as a possible serum marker for docetaxel resistance in castration-resistant prostate cancer.

Baseline or acquired resistance to docetaxel (DOC) represents a significant risk for patients with metastatic prostate cancer (PC). In the last years, novel therapy regimens have been approved providing reasonable alternatives for DOC‐resistant patients making prediction of DOC resistance of great clinical importance. We aimed to identify serum biomarkers, which are able to select patients who will not benefit from DOC treatment. DOC‐resistant PC3‐DR and DU145‐DR sublines and their sensitive parental cell lines (DU145, PC3) were comparatively analyzed using liquid chromatography‐coupled tandem mass spectrometry (LC‐MS/MS). Results were filtered using bioinformatics approaches to identify promising serum biomarkers. Serum levels of five proteins were determined in serum samples of 66 DOC‐treated metastatic castration‐resistant PC patients (mCRPC) using ELISA. Results were correlated with clinicopathological and survival data. CD44 was subjected to further functional cell culture analyses. We found at least 177 two‐fold significantly overexpressed proteins in DOC‐resistant cell lines. Our bioinformatics method suggested 11/177 proteins to be secreted into the serum. We determined serum levels of five (CD44, MET, GSN, IL13RA2 and LNPEP) proteins in serum samples of DOC‐treated patients and found high CD44 serum levels to be independently associated with poor overall survival (p = 0.001). In accordance, silencing of CD44 in DU145‐DR cells resulted in re‐sensitization to DOC. In conclusion, high serum CD44 levels may help identify DOC‐resistant patients and may thereby help optimize clinical decision‐making regarding type and timing of therapy for mCRPC patients. In addition, our in vitro results imply the possible functional involvement of CD44 in DOC resistance.

Characterisation of the Mouse Cerebellar Proteome in the GFAP-IL6 Model of Chronic Neuroinflammation

GFAP-IL6 transgenic mice are characterised by astroglial and microglial activation predominantly in the cerebellum, hallmarks of many neuroinflammatory conditions. However, information available regarding the proteome profile associated with IL-6 overexpression in the mouse brain is limited. This study investigated the cerebellum proteome using a top-down proteomics approach using 2-dimensional gel electrophoresis followed by liquid chromatography-coupled tandem mass spectrometry and correlated these data with motor deficits using the elevated beam walking and accelerod tests. In a detailed proteomic analysis, a total of 67 differentially expressed proteoforms including 47 cytosolic and 20 membrane-bound proteoforms were identified. Bioinformatics and literature mining analyses revealed that these proteins were associated with three distinct classes: metabolic and neurodegenerative processes as well as protein aggregation. TheGFAP-IL6 mice exhibited impaired motor skills in the elevated beam walking test measured by their average scores of 'number of footslips' and 'time to traverse' values. Correlation of theproteoforms' expression levels with themotor testscores showed a significantpositive correlation to peroxiredoxin-6 and negative correlation to alpha-internexin and mitochondrial cristae subunit Mic19. These findings suggest that the observed changes in theproteoform levels caused by IL-6 overexpression might contribute to themotor function deficits.

HGG-03. THE GLYCOSPHINGOLIPIDS METABOLISM IS A NOVEL TARGET IN H3K27M-MUTANT DIFFUSE MIDLINE GLIOMA

H3K27M-mutant diffuse midline glioma (H3K27M-mutant DMG) is a rare malignant brain tumour entity in children and adults with a median overall survival of around 12 months. Genomic and proteomic analysis may help to identify new target structures, however not all relevant targets are covered by these analyses. Glycosphingolipids and particularly gangliosides play a major role in brain development and have been involved in the pathology of brain tumours. The conversion of ceramide to glucosylceramide via glucosylceramide synthase (GCS) is one of the first steps in the synthesis of glycosphingolipids. Therefore, targeting GCS will inhibit their synthesis. Here we analysed the glycosphingolipids composition and tested GCS inhibitors in an in vitro model of H3K27M-mutant DMG. Methods: H3K27M-mutant DMG primary cells were established from needle biopsies of two paediatric patients and characterised by immunohistochemistry. Glycosphingolipids were analysed by thin layer chromatography, liquid chromatography-coupled tandem mass spectrometry and flow cytometry. The effect of the GCS inhibitor eliglustat on the cell proliferation was examined. Results. The primary cells maintained the features of the tumour of origin, including the H3K27M mutation. Neutral glycosphingolipids with 1 to 4 monosaccharides and the ganglioside GD2 were expressed at high concentration. Eliglustat completely abrogated the proliferation of the H3K27M-mutant DMG primary cells. Conclusions. The glycosphingolipids oncometabolism represents a novel target in H3K27M-mutant DMG. The GCS inhibitors eliglusat and miglustat are already used to treat paediatric patients with the lysosomal storage disorders Niemann Pick’s and Gaucher′s disease and miglustat can cross the blood-brain barrier. Thus, our finding may accelerate the access of H3K27M-mutant DMG patients to novel innovative clinical studies based on the inhibition of the glycosphingolipids metabolism.

The Non‐Neuronal Cholinergic System is Causal for Cardioprotection by Hypoxic Preconditioning in Isolated Adult Rat Cardiomyocytes

Introduction Brief episodes of non-lethal myocardial ischemia/reperfusion preceding more sustained ischemia reduce lethal ischemia/reperfusion injury in all species tested so far, including humans. Although this phenomenon is known for more than 3 decades, the underlying signaling mechanisms are unclear in their details. Among various cardioprotective mediators, neuronal acetylcholine (ACh) and its signaling through cholinergic receptors is certainly involved. However, a non-neuronal cardiac cholinergic system (NNCCS) has been recently identified, suggesting a nervous system-independent, cardiomyocyte-derived ACh signaling with signal amplification by autocrine cholinergic receptor activation. Aim We aimed to examine the role of NNCCS-derived ACh as a mediator of cardioprotection. We therefore in a reductionist approach used isolated adult cardiomyocytes with hypoxic preconditioning (HPC). Methods Hearts from male Lewis rats were harvested, and adult ventricular cardiomyocytes were isolated. In suspended cardiomyocytes HPC was induced by one cycle of 10 min brief hypoxia and 20 min reoxygenation. Thirty min normoxia served as control. Afterwards, cardiomyocytes were exposed to 30 min sustained hypoxia and 5 min reoxygenation (H/R) or to 35 min normoxia as time control (TC). Cardiomyocyte viability was quantified before and after H/R or TC, respectively, as the percent fraction of rod-shaped, unstained (0.5% trypan blue) cells over all cells. In parallel experiments, physostigmine (0.2 mmol/L) was added to cardiomyocyte suspensions to block the ubiquitous ACh esterase. Intracellular ACh was quantified with and without HPC via liquid chromatography-coupled tandem mass spectrometry. In subsets, the nicotinic cholinergic receptor antagonists hexamethonium (1.0 µmol/L) and α-bungarotoxine (0.1 µmol/L) or the muscarinic cholinergic receptor antagonist atropine (0.1 µmol/L) were added to cardiomyocyte suspensions with and without HPC, respectively, and exposure to H/R or TC, respectively, afterwards. Again, cardiomyocyte viability was quantified. Results With HPC, the viability of cardiomyocytes subjected to H/R was better preserved than without (24±1% vs. 7±1%, figure A). Also, intracellular ACh was slightly (n.s.) increased after sustained hypoxia (6±2 pmol/mg protein), but significantly with HPC (13±3 pmol/mg protein) in comparison to baseline (3±1 pmol/mg protein) or TC (3±1 pmol/mg protein, figure B). However, this increase was only detectable in the presence of physostigmine (figure B). Addition of nicotinic and muscarinic cholinergic receptor antagonists attenuated the protection by HPC to the same extent (hexamethonium: 12±2%, α-bungarotoxine: 11±1%, atropine: 10±1%, figure A). Conclusion The NNCCS is activated by HPC and causal for HPC´s protection. HPC increases intracellular ACh, and cardiomyocyte protection is mediated via both nicotinic and muscarinic cholinergic receptors, suggesting an autocrine signal amplification on the cardiomyocyte level.

Genomic and Metabolomic Analysis of the Potato Common Scab Pathogen Streptomyces scabiei.

Streptomyces scabiei is a key causative agent of common scab disease, which causes significant economic losses to potato growers worldwide. This organism produces several phytotoxins that are known or suspected to contribute to host–pathogen interactions and disease development; however, the full metabolic potential of S. scabiei has not been previously investigated. In this study, we used a combined metabolomic and genomic approach to investigate the metabolites that are produced by S. scabiei. The genome sequence was analyzed using antiSMASH and DeepBGC to identify specialized metabolite biosynthetic gene clusters. Using untargeted liquid chromatography-coupled tandem mass spectrometry (LC-MS2), the metabolic profile of S. scabiei was compared after cultivation on three different growth media. MS2 data were analyzed using Feature-Based Molecular Networking and hierarchical clustering in BioDendro. Metabolites were annotated by performing a Global Natural Products Social Molecular Networking (GNPS) spectral library search or using Network Annotation Propagation, SIRIUS, MetWork, or Competitive Fragmentation Modeling for Metabolite Identification. Using this approach, we were able to putatively identify new analogues of known metabolites as well as molecules that were not previously known to be produced by S. scabiei. To our knowledge, this study represents the first global analysis of specialized metabolites that are produced by this important plant pathogen.

Extension of Diagnostic Fragmentation Filtering for Automated Discovery in DNA Adductomics.

Development of high-resolution/accurate mass liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) methodology enables the characterization of covalently modified DNA induced by interaction with genotoxic agents in complex biological samples. Constant neutral loss monitoring of 2'-deoxyribose or the nucleobases using data-dependent acquisition represents a powerful approach for the unbiased detection of DNA modifications (adducts). The lack of available bioinformatics tools necessitates manual processing of acquired spectral data and hampers high throughput application of these techniques. To address this limitation, we present an automated workflow for the detection and curation of putative DNA adducts by using diagnostic fragmentation filtering of LC-MS/MS experiments within the open-source software MZmine. The workflow utilizes a new feature detection algorithm, DFBuilder, which employs diagnostic fragmentation filtering using a user-defined list of fragmentation patterns to reproducibly generate feature lists for precursor ions of interest. The DFBuilder feature detection approach readily fits into a complete small-molecule discovery workflow and drastically reduces the processing time associated with analyzing DNA adductomics results. We validate our workflow using a mixture of authentic DNA adduct standards and demonstrate the effectiveness of our approach by reproducing and expanding the results of a previously published study of colibactin-induced DNA adducts. The reported workflow serves as a technique to assess the diagnostic potential of novel fragmentation pattern combinations for the unbiased detection of chemical classes of interest.

Potential biomarkers of childhood brain tumor identified by proteomics of cerebrospinal fluid from extraventricular drainage (EVD)

Brain tumors are the most common solid tumors in childhood. There is the need for biomarkers of residual disease, therapy response and recurrence. Cerebrospinal fluid (CSF) is a source of brain tumor biomarkers. We analyzed the proteome of waste CSF from extraventricular drainage (EVD) from 29 children bearing different brain tumors and 17 controls needing EVD insertion for unrelated causes. 1598 and 1526 proteins were identified by liquid chromatography-coupled tandem mass spectrometry proteomics in CSF control and brain tumor patients, respectively, 263 and 191 proteins being exclusive of either condition. Bioinformatic analysis revealed promising protein biomarkers for the discrimination between control and tumor (TATA-binding protein-associated factor 15 and S100 protein B). Moreover, Thymosin beta-4 (TMSB4X) and CD109, and 14.3.3 and HSP90 alpha could discriminate among other brain tumors and low-grade gliomas plus glyoneuronal tumors/pilocytic astrocytoma, or embryonal tumors/medulloblastoma. Biomarkers were validated by ELISA assay. Our method was able to distinguish among brain tumor vs non-tumor/hemorrhagic conditions (controls) and to differentiate two large classes of brain tumors. Further prospective studies may assess whether the biomarkers proposed by our discovery approach can be identified in other bodily fluids, therefore less invasively, and are useful to guide therapy and predict recurrences.