Publications by authors named "Peter J Oefner"

177 Publications

Lactonization of the Oncometabolite D-2-Hydroxyglutarate Produces a Novel Endogenous Metabolite.

Cancers (Basel) 2021 Apr 7;13(8). Epub 2021 Apr 7.

Institute of Functional Genomics, University of Regensburg, 93053 Regensburg, Germany.

In recent years, onco-metabolites like D-2-hydroxyglutarate, which is produced in isocitrate dehydrogenase-mutated tumors, have gained increasing interest. Here, we report a metabolite in human specimens that is closely related to 2-hydroxyglutarate: the intramolecular ester of 2-hydroxyglutarate, 2-hydroxyglutarate-γ-lactone. Using C-L-glutamine tracer analysis, we showed that 2-hydroxyglutarate is the endogenous precursor of 2-hydroxyglutarate-lactone and that there is a high exchange between these two metabolites. Lactone formation does not depend on mutated isocitrate dehydrogenase, but its formation is most probably linked to transport processes across the cell membrane and favored at low environmental pH. Furthermore, human macrophages showed not only striking differences in uptake of 2-hydroxyglutarate and its lactone but also in the enantiospecific hydrolysis of the latter. Consequently, 2-hydroxyglutarate-lactone may play a critical role in the modulation of the tumor microenvironment.
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http://dx.doi.org/10.3390/cancers13081756DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8067704PMC
April 2021

A serum microRNA sequence reveals fragile X protein pathology in amyotrophic lateral sclerosis.

Brain 2021 May;144(4):1214-1229

Department of Neurology, Ulm University, Ulm, Germany.

Knowledge about converging disease mechanisms in the heterogeneous syndrome amyotrophic lateral sclerosis (ALS) is rare, but may lead to therapies effective in most ALS cases. Previously, we identified serum microRNAs downregulated in familial ALS, the majority of sporadic ALS patients, but also in presymptomatic mutation carriers. A 5-nucleotide sequence motif (GDCGG; D = G, A or U) was strongly enriched in these ALS-related microRNAs. We hypothesized that deregulation of protein(s) binding predominantly to this consensus motif was responsible for the ALS-linked microRNA fingerprint. Using microRNA pull-down assays combined with mass spectrometry followed by extensive biochemical validation, all members of the fragile X protein family, FMR1, FXR1 and FXR2, were identified to directly and predominantly interact with GDCGG microRNAs through their structurally disordered RGG/RG domains. Preferential association of this protein family with ALS-related microRNAs was confirmed by in vitro binding studies on a transcriptome-wide scale. Immunohistochemistry of lumbar spinal cord revealed aberrant expression level and aggregation of FXR1 and FXR2 in C9orf72- and FUS-linked familial ALS, but also patients with sporadic ALS. Further analysis of ALS autopsies and induced pluripotent stem cell-derived motor neurons with FUS mutations showed co-aggregation of FXR1 with FUS. Hence, our translational approach was able to take advantage of blood microRNAs to reveal CNS pathology, and suggests an involvement of the fragile X-related proteins in familial and sporadic ALS already at a presymptomatic stage. The findings may uncover disease mechanisms relevant to many patients with ALS. They furthermore underscore the systemic, extra-CNS aspect of ALS.
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http://dx.doi.org/10.1093/brain/awab018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8105042PMC
May 2021

Urine Metabolite Levels, Adverse Kidney Outcomes, and Mortality in CKD Patients: A Metabolome-wide Association Study.

Am J Kidney Dis 2021 Apr 8. Epub 2021 Apr 8.

Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Hugstetter Str. 49, 79106 Freiburg, Germany. Electronic address:

Rationale & Objective: Mechanisms underlying the variable course of disease progression in patients with chronic kidney disease (CKD) are incompletely understood. The aim of this study was to identify novel biomarkers of adverse kidney outcomes and overall mortality, which may offer insights into pathophysiological mechanisms.

Study Design: Metabolome-wide association study.

Setting & Participants: 5,087 CKD patients enrolled in the observational German Chronic Kidney Disease study.

Exposure(s): Measurements of 1,487 metabolites in urine.

Outcome(s): Endpoints of interest were time to kidney failure (KF), a combined endpoint of KF and acute kidney injury (KF+AKI), and overall mortality.

Analytical Approach: Statistical analysis was based on a discovery-replication design (ratio 2:1) and multivariable adjusted Cox regression models.

Results: After a median follow-up of 4 years, 362 patients died, 241 experienced KF, and 382 KF+AKI. Overall, we identified 55 urine metabolites whose levels were significantly associated with adverse kidney outcomes and/or mortality. Higher levels of C-glycosyltryptophan were consistently associated with all three main endpoints (KF: hazard ratio 1.43, 95% confidence interval [1.27;1.61], KF+AKI: 1.40 [1.27;1.55], death: 1.47 [1.33;1.63]). Metabolites belonging to the phosphatidylcholine pathway showed significant enrichment. Members of this pathway contributed to the improvement of the prediction performance for KF observed when multiple metabolites were added to the well-established kidney failure risk equation.

Limitations: Findings among CKD patients of European ancestry may not be generalizable to the general population.

Conclusions: Our comprehensive screen of the association between urine metabolite levels and adverse kidney outcomes and mortality identifies metabolite that predict KF and represents a valuable resource for future studies of biomarkers of CKD progression.
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http://dx.doi.org/10.1053/j.ajkd.2021.01.018DOI Listing
April 2021

Cytokine-specific autoantibodies shape the gut microbiome in autoimmune polyendocrine syndrome type 1.

J Allergy Clin Immunol 2021 Apr 2. Epub 2021 Apr 2.

Broad Institute of MIT and Harvard, Cambridge, Mass; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Mass; Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Mass; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Mass. Electronic address:

Background: Gastrointestinal dysfunction is a frequent and disabling manifestation of autoimmune polyendocrine syndrome type 1 (APS-1), a rare monogenic multiorgan autoimmune disease caused by the loss of central AIRE-controlled immune tolerance.

Objectives: This study aimed to understand the role of the gut microbiome in APS-1 symptoms and potentially alleviate common gastrointestinal symptoms by probiotic intervention.

Methods: This study characterized the fecal microbiomes of 28 patients with APS-1 and searched for associations with gastrointestinal symptoms, circulating anti-cytokine autoantibodies, and tryptophan-related metabolites. Additionally, daily doses of the probiotic Lactobacillus rhamnosus GG were administered for 3 months.

Results: Of 581 metagenomic operational taxonomic units (mOTUs) characterized in total, 14 were significantly associated with patients with APS-1 compared with healthy controls, with 6 mOTUs depleted and 8 enriched in patients with APS-1. Four overabundant mOTUs were significantly associated with severity of constipation. Phylogenetically conserved microbial associations with autoantibodies against cytokines were observed. After the 3-month intervention with the probiotic L rhamnosus GG, a subset of gastrointestinal symptoms were alleviated. L rhamnosus GG abundance was increased postintervention and corresponded with decreased abundances of Alistipes onderdonkii and Collinsella aerofaciens, 2 species positively associated with severity of diarrhea in patients with APS-1.

Conclusions: The APS-1 microbiome correlates with several APS-1 symptoms, some of which are alleviated after a 3-month L rhamnosus GG intervention. Autoantibodies against cytokines appear to shape the gut microbiome by positively correlating with a taxonomically consistent group of bacteria.
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http://dx.doi.org/10.1016/j.jaci.2021.03.025DOI Listing
April 2021

Mitochondrial arginase-2 is essential for IL-10 metabolic reprogramming of inflammatory macrophages.

Nat Commun 2021 03 5;12(1):1460. Epub 2021 Mar 5.

School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin 2, Ireland.

Mitochondria are important regulators of macrophage polarisation. Here, we show that arginase-2 (Arg2) is a microRNA-155 (miR-155) and interleukin-10 (IL-10) regulated protein localized at the mitochondria in inflammatory macrophages, and is critical for IL-10-induced modulation of mitochondrial dynamics and oxidative respiration. Mechanistically, the catalytic activity and presence of Arg2 at the mitochondria is crucial for oxidative phosphorylation. We further show that Arg2 mediates this process by increasing the activity of complex II (succinate dehydrogenase). Moreover, Arg2 is essential for IL-10-mediated downregulation of the inflammatory mediators succinate, hypoxia inducible factor 1α (HIF-1α) and IL-1β in vitro. Accordingly, HIF-1α and IL-1β are highly expressed in an LPS-induced in vivo model of acute inflammation using Arg2 mice. These findings shed light on a new arm of IL-10-mediated metabolic regulation, working to resolve the inflammatory status of the cell.
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http://dx.doi.org/10.1038/s41467-021-21617-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7936006PMC
March 2021

Rare genetic variants affecting urine metabolite levels link population variation to inborn errors of metabolism.

Nat Commun 2021 02 11;12(1):964. Epub 2021 Feb 11.

Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany.

Metabolite levels in urine may provide insights into genetic mechanisms shaping their related pathways. We therefore investigate the cumulative contribution of rare, exonic genetic variants on urine levels of 1487 metabolites and 53,714 metabolite ratios among 4864 GCKD study participants. Here we report the detection of 128 significant associations involving 30 unique genes, 16 of which are known to underlie inborn errors of metabolism. The 30 genes are strongly enriched for shared expression in liver and kidney (odds ratio = 65, p-FDR = 3e-7), with hepatocytes and proximal tubule cells as driving cell types. Use of UK Biobank whole-exome sequencing data links genes to diseases connected to the identified metabolites. In silico constraint-based modeling of gene knockouts in a virtual whole-body, organ-resolved metabolic human correctly predicts the observed direction of metabolite changes, highlighting the potential of linking population genetics to modeling. Our study implicates candidate variants and genes for inborn errors of metabolism.
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http://dx.doi.org/10.1038/s41467-020-20877-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7878905PMC
February 2021

Associations between urinary 3-indoxyl sulfate, a gut microbiome-derived biomarker, and patient outcomes after intensive care unit admission.

J Crit Care 2021 Jun 21;63:15-21. Epub 2021 Jan 21.

Department of Medicine, Division of Digestive and Liver Diseases, Columbia University Medical Center, New York, NY, USA. Electronic address:

Purpose: 3-indoxyl sulfate (3-IS) is an indole metabolism byproduct produced by commensal gut bacteria and excreted in the urine; low urinary 3-IS has been associated with increased mortality in bone marrow transplant recipients. This study investigated urinary 3-IS and patient outcomes in the ICU.

Materials And Methods: Prospective study that collected urine samples, rectal swabs, and clinical data on 78 adult ICU patients at admission and again 72 h later. Urine was analyzed for 3-IS by mass spectrometry.

Results: Median urinary 3-IS levels were 17.1 μmol/mmol creatinine (IQR 9.5 to 26.2) at admission and 15.6 (IQR 4.2 to 30.7) 72 h later. 22% of patients had low 3-IS (≤6.9 μmol/mmol) on ICU admission and 28% after 72 h. Low 3-IS at 72 h was associated with fewer ICU-free days (22.5 low versus 26 high, p = 0.03) and with death during one year of follow-up (36% low versus 9% high 3-IS, p < 0.01); there was no detectable difference in 30-day mortality (18% low versus 5% high, p = 0.07).

Conclusions: Low urinary 3-IS level 72 h after ICU admission was associated with fewer ICU-free days and with increased one-year but not 30-day mortality. Further studies should investigate urinary 3-IS as an ICU biomarker.
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http://dx.doi.org/10.1016/j.jcrc.2021.01.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8084995PMC
June 2021

Shear Force Processing of Lipoaspirates for Stem Cell Enrichment Does Not Affect Secretome of Human Cells Detected by Mass Spectrometry In Vitro.

Plast Reconstr Surg 2020 12;146(6):749e-758e

From the Department of Plastic, Hand, and Reconstructive Surgery, University Hospital Regensburg; the Faculty of Mechanical Engineering, Ostbayerische Technische Hochschule Regensburg; and the Institute of Functional Genomics, University of Regensburg.

Background: Lipofilling is one of the most often performed surgical procedures in plastic and reconstructive surgery. Lipoaspirates provide a ready source of stem cells and secreted factors that contribute to neoangiogenesis and fat graft survival. However, the regulations about the enrichment of these beneficial cells and factors are ambiguous. In this study, the authors tested whether a combination of centrifugation and homogenization allowed the enrichment of viable stem cells in lipoaspirates through the selective removal of tumescent solution, blood, and released lipids without significantly affecting the cell secretome.

Methods: Human lipoaspirate was harvested from six different patients using water jet-assisted liposuction. Lipoaspirate was homogenized by first centrifugation (3584 rpm for 2 minutes), shear strain (10 times intersyringe processing), and second centrifugation (3584 rpm for 2 minutes). Stem cell enrichment was shown by cell counting after stem cell isolation. Lipoaspirate from different processing steps (unprocessed, after first centrifugation, after homogenization, after second centrifugation) was incubated in serum-free cell culture medium for mass spectrometric analysis of secreted proteins.

Results: Lipoaspirate homogenization leads to a significant 2.6 ± 1.75-fold enrichment attributable to volume reduction without reducing the viability of the stem cells. Protein composition of the secretome did not change significantly after tissue homogenization. Considering the enrichment effects, there were no significant differences in the protein concentration of the 83 proteins found in all processing steps.

Conclusions: Stem cells can be enriched mechanically without significantly affecting the composition of secreted proteins. Shear-assisted enrichment of lipoaspirate constitutes no substantial manipulation of the cells' secretome.
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http://dx.doi.org/10.1097/PRS.0000000000007343DOI Listing
December 2020

Non-Invasive Prediction of Mutation in Patients with Glioma WHO II/III/IV Based on F-18-FET PET-Guided In Vivo H-Magnetic Resonance Spectroscopy and Machine Learning.

Cancers (Basel) 2020 Nov 17;12(11). Epub 2020 Nov 17.

Department of Neurology and Wilhelm Sander-NeuroOncology Unit, Regensburg University Hospital, 93053 Regensburg, Germany.

( mutation is an important prognostic factor and a potential therapeutic target in glioma. Immunohistological and molecular diagnosis of mutation status is invasive. To avoid tumor biopsy, dedicated spectroscopic techniques have been proposed to detect D-2-hydroxyglutarate (2-HG), the main metabolite of , directly in vivo. However, these methods are technically challenging and not broadly available. Therefore, we explored the use of machine learning for the non-invasive, inexpensive and fast diagnosis of status in standard H-magnetic resonance spectroscopy (H-MRS). To this end, 30 of 34 consecutive patients with known or suspected glioma WHO grade II-IV were subjected to metabolic positron emission tomography (PET) imaging with O-(2-F-fluoroethyl)-L-tyrosine (F-FET) for optimized voxel placement in H-MRS. Routine H-magnetic resonance (H-MR) spectra of tumor and contralateral healthy brain regions were acquired on a 3 Tesla magnetic resonance (3T-MR) scanner, prior to surgical tumor resection and molecular analysis of status. Since 2-HG spectral signals were too overlapped for reliable discrimination of mutated () and wild-type () glioma, we used a nested cross-validation approach, whereby we trained a linear support vector machine (SVM) on the complete spectral information of the H-MRS data to predict status. Using this approach, we predicted status with an accuracy of 88.2%, a sensitivity of 95.5% (95% CI, 77.2-99.9%) and a specificity of 75.0% (95% CI, 42.9-94.5%), respectively. The area under the curve (AUC) amounted to 0.83. Subsequent ex vivo H-nuclear magnetic resonance (H-NMR) measurements performed on metabolite extracts of resected tumor material (eight specimens) revealed myo-inositol (M-ins) and glycine (Gly) to be the major discriminators of status. We conclude that our approach allows a reliable, non-invasive, fast and cost-effective prediction of status in a standard clinical setting.
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http://dx.doi.org/10.3390/cancers12113406DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7698334PMC
November 2020

Robust Metabolite Quantification from J-Compensated 2D H-C-HSQC Experiments.

Metabolites 2020 Nov 7;10(11). Epub 2020 Nov 7.

Institute of Functional Genomics, University of Regensburg, 93053 Regensburg, Germany.

The spectral resolution of 2D 1H-13C heteronuclear single quantum coherence (1H-13C-HSQC) nuclear magnetic resonance (NMR) spectra facilitates both metabolite identification and quantification in nuclear magnetic resonance-based metabolomics. However, quantification is complicated by variations in magnetization transfer, which among others originate mainly from scalar coupling differences. Methods that compensate for variation in scalar coupling include the generation of calibration factors for individual signals or the use of additional pulse sequence schemes such as quantitative HSQC (Q-HSQC) that suppress the -dependence by modulating the polarization transfer delays of HSQC or, additionally, employ a pure-shift homodecoupling approach in the 1H dimension, such as Quantitative, Perfected and Pure Shifted HSQC (QUIPU-HSQC). To test the quantitative accuracy of these three methods, employing a 600 MHz NMR spectrometer equipped with a helium cooled cryoprobe, a Latin-square design that covered the physiological concentration ranges of 10 metabolites was used. The results show the suitability of all three methods for the quantification of highly abundant metabolites. However, the substantially increased residual water signal observed in QUIPU-HSQC spectra impeded the quantification of low abundant metabolites located near the residual water signal, thus limiting its utility in high-throughput metabolite fingerprinting studies.
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http://dx.doi.org/10.3390/metabo10110449DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7695005PMC
November 2020

De novo polyamine synthesis supports metabolic and functional responses in activated murine NK cells.

Eur J Immunol 2021 01 9;51(1):91-102. Epub 2020 Nov 9.

School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland.

Cellular metabolism is dynamically regulated in NK cells and strongly influences their responses. Metabolic dysfunction is linked to defective NK cell responses in diseases such as obesity and cancer. The transcription factors, sterol regulatory element binding protein (SREBP) and cMyc, are crucial for controlling NK cell metabolic and functional responses, though the mechanisms involved are not fully understood. This study reveals a new role for SREBP in NK cells in supporting de novo polyamine synthesis through facilitating elevated cMyc expression. Polyamines have diverse roles and their de novo synthesis is required for NK cell glycolytic and oxidative metabolism and to support optimal NK cell effector functions. When NK cells with impaired SREBP activity were supplemented with exogenous polyamines, NK cell metabolic defects were not rescued but these NK cells displayed significant improvement in some effector functions. One role for polyamines is in the control of protein translation where spermidine supports the posttranslational hypusination of translation factor eIF5a. Pharmacological inhibition of hypusination also impacts upon NK cell metabolism and effector function. Considering recent evidence that cholesterol-rich tumor microenvironments inhibit SREBP activation and drive lymphocyte dysfunction, this study provides key mechanistic insight into this tumor-evasion strategy.
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http://dx.doi.org/10.1002/eji.202048784DOI Listing
January 2021

Activation of Epidermal Growth Factor Receptor Sensitizes Glioblastoma Cells to Hypoxia-Induced Cell Death.

Cancers (Basel) 2020 Aug 3;12(8). Epub 2020 Aug 3.

Dr. Senckenberg Institute of Neurooncology, University Hospital Frankfurt, Goethe University, 60528 Frankfurt am Main, Germany.

Background: The epidermal growth factor receptor (EGFR) signaling pathway is genetically activated in approximately 50% of glioblastomas (GBs). Its inhibition has been explored clinically but produced disappointing results, potentially due to metabolic effects that protect GB cells against nutrient deprivation and hypoxia. Here, we hypothesized that EGFR activation could disable metabolic adaptation and define a GB cell population sensitive to starvation.

Methods: Using genetically engineered GB cells to model different types of EGFR activation, we analyzed changes in metabolism and cell survival under conditions of the tumor microenvironment.

Results: We found that expression of mutant EGFR as well as EGF stimulation of EGFR-overexpressing cells impaired physiological adaptation to starvation and rendered cells sensitive to hypoxia-induced cell death. This was preceded by adenosine triphosphate (ATP) depletion and an increase in glycolysis. Furthermore, EGFR mutant cells had higher levels of mitochondrial superoxides potentially due to decreased metabolic flux into the serine synthesis pathway which was associated with a decrease in the NADPH/NADP+ ratio.

Conclusions: The finding that EGFR activation renders GB cells susceptible to starvation could help to identify a subgroup of patients more likely to benefit from starvation-inducing therapies.
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http://dx.doi.org/10.3390/cancers12082144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7464192PMC
August 2020

Arginase impedes the resolution of colitis by altering the microbiome and metabolome.

J Clin Invest 2020 11;130(11):5703-5720

Mikrobiologisches Institut, Klinische Mikrobiologie, Immunologie und Hygiene.

Arginase 1 (Arg1), which converts l-arginine into ornithine and urea, exerts pleiotropic immunoregulatory effects. However, the function of Arg1 in inflammatory bowel disease (IBD) remains poorly characterized. Here, we found that Arg1 expression correlated with the degree of inflammation in intestinal tissues from IBD patients. In mice, Arg1 was upregulated in an IL-4/IL-13- and intestinal microbiota-dependent manner. Tie2-Cre Arg1fl/fl mice lacking Arg1 in hematopoietic and endothelial cells recovered faster from colitis than Arg1-expressing (Arg1fl/fl) littermates. This correlated with decreased vessel density, compositional changes in intestinal microbiota, diminished infiltration by myeloid cells, and an accumulation of intraluminal polyamines that promote epithelial healing. The proresolving effect of Arg1 deletion was reduced by an l-arginine-free diet, but rescued by simultaneous deletion of other l-arginine-metabolizing enzymes, such as Arg2 or Nos2, demonstrating that protection from colitis requires l-arginine. Fecal microbiota transfers from Tie2-Cre Arg1fl/fl mice into WT recipients ameliorated intestinal inflammation, while transfers from WT littermates into Arg1-deficient mice prevented an advanced recovery from colitis. Thus, an increased availability of l-arginine as well as altered intestinal microbiota and metabolic products accounts for the accelerated resolution from colitis in the absence of Arg1. Consequently, l-arginine metabolism may serve as a target for clinical intervention in IBD patients.
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http://dx.doi.org/10.1172/JCI126923DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7598089PMC
November 2020

Optimized Protocol for the In Situ Derivatization of Glutathione with -Ethylmaleimide in Cultured Cells and the Simultaneous Determination of Glutathione/Glutathione Disulfide Ratio by HPLC-UV-QTOF-MS.

Metabolites 2020 Jul 17;10(7). Epub 2020 Jul 17.

Institute of Functional Genomics, University of Regensburg, Am BioPark 9, 93053 Regensburg, Germany.

Glutathione (GSH) and glutathione disulfide (GSSG) are commonly used to assess the oxidative status of a biological system. Various protocols are available for the analysis of GSH and GSSG in biomedical specimens. In this study, we present an optimized protocol for the in situ derivatization of GSH with -ethylmaleimide (NEM) to prevent GSH autooxidation, and thus to preserve the GSH/GSSG ratio during sample preparation. The protocol comprises the incubation of cells in NEM containing phosphate buffered saline (PBS), followed by metabolite extraction with 80% methanol. Further, to preserve the use of QTOF-MS, which may lack the linear dynamic range required for the simultaneous quantification of GSH and GSSG in non-targeted metabolomics, we combined liquid chromatographic separation with the online monitoring of UV absorbance of GS-NEM at 210 nm and the detection of GSSG and its corresponding stable isotope-labeled internal standard by QTOF-MS operated with a 10 Da Q1 window. The limit of detection (LOD) for GS-NEM was 7.81 µM and the linear range extended from 15.63 µM to 1000 µM with a squared correlation coefficient of 0.9997. The LOD for GSSG was 0.001 µM, and the lower limit of quantification (LLOQ) was 0.01 µM, with the linear ( = 0.9994) range extending up to 10 µM. The method showed high repeatability with intra-run and inter-run coefficients of variation of 3.48% and 2.51% for GS-NEM, and 3.11% and 3.66% for GSSG, respectively. Mean recoveries of three different spike-in levels (low, medium, high) of GSSG and GS-NEM were above 92%. Finally, the method was applied to the determination of changes in the GSH/GSSG ratio either in response to oxidative stress in cells lacking one or both monocarboxylate transporters and , or in adaptation to the NADPH (nicotinamide adenine dinucleotide phosphate) consuming production of D-2-hydroxyglutarate in cells carrying mutations in the isocitrate dehydrogenase genes and
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http://dx.doi.org/10.3390/metabo10070292DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7407321PMC
July 2020

Acquired resistance to DZNep-mediated apoptosis is associated with copy number gains of AHCY in a B-cell lymphoma model.

BMC Cancer 2020 May 14;20(1):427. Epub 2020 May 14.

Department of Experimental Hematopathology, Institute of Pathology, Charité Medical University, Berlin, Charitéplatz 1, 10117, Berlin, Germany.

Background: Enhancer of zeste homolog 2 (EZH2) is considered an important driver of tumor development and progression by its histone modifying capabilities. Inhibition of EZH2 activity is thought to be a potent treatment option for eligible cancer patients with an aberrant EZH2 expression profile, thus the indirect EZH2 inhibitor 3-Deazaneplanocin A (DZNep) is currently under evaluation for its clinical utility. Although DZNep blocks proliferation and induces apoptosis in different tumor types including lymphomas, acquired resistance to DZNep may limit its clinical application.

Methods: To investigate possible mechanisms of acquired DZNep resistance in B-cell lymphomas, we generated a DZNep-resistant clone from a previously DZNep-sensitive B-cell lymphoma cell line by long-term treatment with increasing concentrations of DZNep (ranging from 200 to 2000 nM) and compared the molecular profiles of resistant and wild-type clones. This comparison was done using molecular techniques such as flow cytometry, copy number variation assay (OncoScan and TaqMan assays), fluorescence in situ hybridization, Western blot, immunohistochemistry and metabolomics analysis.

Results: Whole exome sequencing did not indicate the acquisition of biologically meaningful single nucleotide variants. Analysis of copy number alterations, however, demonstrated among other acquired imbalances an amplification (about 30 times) of the S-adenosyl-L-homocysteine hydrolase (AHCY) gene in the resistant clone. AHCY is a direct target of DZNep and is critically involved in the biological methylation process, where it catalyzes the reversible hydrolysis of S-adenosyl-L-homocysteine to L-homocysteine and adenosine. The amplification of the AHCY gene is paralleled by strong overexpression of AHCY at both the transcriptional and protein level, and persists upon culturing the resistant clone in a DZNep-free medium.

Conclusions: This study reveals one possible molecular mechanism how B-cell lymphomas can acquire resistance to DZNep, and proposes AHCY as a potential biomarker for investigation during the administration of EZH2-targeted therapy with DZNep.
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http://dx.doi.org/10.1186/s12885-020-06937-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7227222PMC
May 2020

Platform independent protein-based cell-of-origin subtyping of diffuse large B-cell lymphoma in formalin-fixed paraffin-embedded tissue.

Sci Rep 2020 05 12;10(1):7876. Epub 2020 May 12.

Chair and Institute of Functional Genomics, University of Regensburg, 93053, Regensburg, Germany.

Diffuse large B-cell lymphoma (DLBCL) is commonly classified by gene expression profiling according to its cell of origin (COO) into activated B-cell (ABC)-like and germinal center B-cell (GCB)-like subgroups. Here we report the application of label-free nano-liquid chromatography - Sequential Window Acquisition of all THeoretical fragment-ion spectra - mass spectrometry (nanoLC-SWATH-MS) to the COO classification of DLBCL in formalin-fixed paraffin-embedded (FFPE) tissue. To generate a protein signature capable of predicting Affymetrix-based GCB scores, the summed log-transformed fragment ion intensities of 780 proteins quantified in a training set of 42 DLBCL cases were used as independent variables in a penalized zero-sum elastic net regression model with variable selection. The eight-protein signature obtained showed an excellent correlation (r = 0.873) between predicted and true GCB scores and yielded only 9 (21.4%) minor discrepancies between the three classifications: ABC, GCB, and unclassified. The robustness of the model was validated successfully in two independent cohorts of 42 and 31 DLBCL cases, the latter cohort comprising only patients aged >75 years, with Pearson correlation coefficients of 0.846 and 0.815, respectively, between predicted and NanoString nCounter based GCB scores. We further show that the 8-protein signature is directly transferable to both a triple quadrupole and a Q Exactive quadrupole-Orbitrap mass spectrometer, thus obviating the need for proprietary instrumentation and reagents. This method may therefore be used for robust and competitive classification of DLBCLs on the protein level.
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http://dx.doi.org/10.1038/s41598-020-64212-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7217957PMC
May 2020

DTD: An R Package for Digital Tissue Deconvolution.

J Comput Biol 2020 03 29;27(3):386-389. Epub 2020 Jan 29.

Department of Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Regensburg, Germany.

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http://dx.doi.org/10.1089/cmb.2019.0469DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7074920PMC
March 2020

Loss-Function Learning for Digital Tissue Deconvolution.

J Comput Biol 2020 03 29;27(3):342-355. Epub 2020 Jan 29.

Department of Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Regensburg, Germany.

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http://dx.doi.org/10.1089/cmb.2019.0462DOI Listing
March 2020

Genetic studies of urinary metabolites illuminate mechanisms of detoxification and excretion in humans.

Nat Genet 2020 02 20;52(2):167-176. Epub 2020 Jan 20.

Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany.

The kidneys integrate information from continuous systemic processes related to the absorption, distribution, metabolism and excretion (ADME) of metabolites. To identify underlying molecular mechanisms, we performed genome-wide association studies of the urinary concentrations of 1,172 metabolites among 1,627 patients with reduced kidney function. The 240 unique metabolite-locus associations (metabolite quantitative trait loci, mQTLs) that were identified and replicated highlight novel candidate substrates for transport proteins. The identified genes are enriched in ADME-relevant tissues and cell types, and they reveal novel candidates for biotransformation and detoxification reactions. Fine mapping of mQTLs and integration with single-cell gene expression permitted the prioritization of causal genes, functional variants and target cell types. The combination of mQTLs with genetic and health information from 450,000 UK Biobank participants illuminated metabolic mediators, and hence, novel urinary biomarkers of disease risk. This comprehensive resource of genetic targets and their substrates is informative for ADME processes in humans and is relevant to basic science, clinical medicine and pharmaceutical research.
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http://dx.doi.org/10.1038/s41588-019-0567-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7484970PMC
February 2020

High CD206 levels in Hodgkin lymphoma-educated macrophages are linked to matrix-remodeling and lymphoma dissemination.

Mol Oncol 2020 03 28;14(3):571-589. Epub 2020 Jan 28.

Clinic of Hematology and Medical Oncology, University Medical Centre Göttingen, Germany.

Macrophages (Mφ) are abundantly present in the tumor microenvironment and may predict outcome in solid tumors and defined lymphoma subtypes. Mφ heterogeneity, the mechanisms of their recruitment, and their differentiation into lymphoma-promoting, alternatively activated M2-like phenotypes are still not fully understood. Therefore, further functional studies are required to understand biological mechanisms associated with human tumor-associated Mφ (TAM). Here, we show that the global mRNA expression and protein abundance of human Mφ differentiated in Hodgkin lymphoma (HL)-conditioned medium (CM) differ from those of Mφ educated by conditioned media from diffuse large B-cell lymphoma (DLBCL) cells or, classically, by macrophage colony-stimulating factor (M-CSF). Conditioned media from HL cells support TAM differentiation through upregulation of surface antigens such as CD40, CD163, CD206, and PD-L1. In particular, RNA and cell surface protein expression of mannose receptor 1 (MRC1)/CD206 significantly exceed the levels induced by classical M-CSF stimulation in M2-like Mφ; this is regulated by interleukin 13 to a large extent. Functionally, high CD206 enhances mannose-dependent endocytosis and uptake of type I collagen. Together with high matrix metalloprotease9 secretion, HL-TAMs appear to be active modulators of the tumor matrix. Preclinical in ovo models show that co-cultures of HL cells with monocytes or Mφ support dissemination of lymphoma cells via lymphatic vessels, while tumor size and vessel destruction are decreased in comparison with lymphoma-only tumors. Immunohistology of human HL tissues reveals a fraction of cases feature large numbers of CD206-positive cells, with high MRC1 expression being characteristic of HL-stage IV. In summary, the lymphoma-TAM interaction contributes to matrix-remodeling and lymphoma cell dissemination.
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http://dx.doi.org/10.1002/1878-0261.12616DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7053241PMC
March 2020

LEF1 supports metastatic brain colonization by regulating glutathione metabolism and increasing ROS resistance in breast cancer.

Int J Cancer 2020 06 11;146(11):3170-3183. Epub 2019 Nov 11.

Institute of Pathology, University of Regensburg, Regensburg, Germany.

More than half of all brain metastases show infiltrating rather than displacing growth at the macro-metastasis/organ parenchyma interface (MMPI), a finding associated with shorter survival. The lymphoid enhancer-binding factor-1 (LEF1) is an epithelial-mesenchymal transition (EMT) transcription factor that is commonly overexpressed in brain-colonizing cancer cells. Here, we overexpressed LEF1 in an in vivo breast cancer brain colonization model. It shortened survival, albeit without engaging EMT at the MMPI. By differential proteome analysis, we identified a novel function of LEF1 as a regulator of the glutathione (GSH) system, the principal cellular redox buffer. LEF1 overexpression also conferred resistance against therapeutic GSH depletion during brain colonization and improved management of intracellular ROS. We conclude that besides EMT, LEF1 facilitates metastasis by improving the antioxidative capacity of epithelial breast cancer cells, in particular during colonization of the brain parenchyma.
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http://dx.doi.org/10.1002/ijc.32742DOI Listing
June 2020

Restricting Glycolysis Preserves T Cell Effector Functions and Augments Checkpoint Therapy.

Cell Rep 2019 10;29(1):135-150.e9

Department of Chemistry, The Scripps Research Institute, Scripps-Florida, Jupiter, FL, USA.

Tumor-derived lactic acid inhibits T and natural killer (NK) cell function and, thereby, tumor immunosurveillance. Here, we report that melanoma patients with high expression of glycolysis-related genes show a worse progression free survival upon anti-PD1 treatment. The non-steroidal anti-inflammatory drug (NSAID) diclofenac lowers lactate secretion of tumor cells and improves anti-PD1-induced T cell killing in vitro. Surprisingly, diclofenac, but not other NSAIDs, turns out to be a potent inhibitor of the lactate transporters monocarboxylate transporter 1 and 4 and diminishes lactate efflux. Notably, T cell activation, viability, and effector functions are preserved under diclofenac treatment and in a low glucose environment in vitro. Diclofenac, but not aspirin, delays tumor growth and improves the efficacy of checkpoint therapy in vivo. Moreover, genetic suppression of glycolysis in tumor cells strongly improves checkpoint therapy. These findings support the rationale for targeting glycolysis in patients with high glycolytic tumors together with checkpoint inhibitors in clinical trials.
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http://dx.doi.org/10.1016/j.celrep.2019.08.068DOI Listing
October 2019

A multi-source data integration approach reveals novel associations between metabolites and renal outcomes in the German Chronic Kidney Disease study.

Sci Rep 2019 09 27;9(1):13954. Epub 2019 Sep 27.

Institute for Functional Genomics, University of Regensburg, Am Biopark 9, 93053, Regensburg, Germany.

Omics data facilitate the gain of novel insights into the pathophysiology of diseases and, consequently, their diagnosis, treatment, and prevention. To this end, omics data are integrated with other data types, e.g., clinical, phenotypic, and demographic parameters of categorical or continuous nature. We exemplify this data integration issue for a chronic kidney disease (CKD) study, comprising complex clinical, demographic, and one-dimensional H nuclear magnetic resonance metabolic variables. Routine analysis screens for associations of single metabolic features with clinical parameters while accounting for confounders typically chosen by expert knowledge. This knowledge can be incomplete or unavailable. We introduce a framework for data integration that intrinsically adjusts for confounding variables. We give its mathematical and algorithmic foundation, provide a state-of-the-art implementation, and evaluate its performance by sanity checks and predictive performance assessment on independent test data. Particularly, we show that discovered associations remain significant after variable adjustment based on expert knowledge. In contrast, we illustrate that associations discovered in routine univariate screening approaches can be biased by incorrect or incomplete expert knowledge. Our data integration approach reveals important associations between CKD comorbidities and metabolites, including novel associations of the plasma metabolite trimethylamine-N-oxide with cardiac arrhythmia and infarction in CKD stage 3 patients.
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http://dx.doi.org/10.1038/s41598-019-50346-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6764972PMC
September 2019

Quantification and C-Tracer analysis of total reduced glutathione by HPLC-QTOFMS/MS.

Anal Chim Acta 2019 Nov 3;1080:127-137. Epub 2019 Jul 3.

Institute of Functional Genomics, University of Regensburg, Am BioPark 9, 93053, Regensburg, Germany. Electronic address:

Glutathione is an essential intra- and extracellular antioxidant. The level of glutathione in the body is highly related to different disease states and is a useful indicator of disease risk and oxidative stress status. We have developed a sensitive, selective, and comprehensive LC-MS/MS method for the absolute quantification and C-tracer analysis of total glutathione using dithiothreitol for the reduction of glutathione disulfide. The limit of detection (LOD) was 0.01 μM, while the lower limit of quantification (LLOQ) was 0.78 μM, with the linear (R = 0.9997) range extending up to 100 μM. The intra-run and inter-run coefficients of variation of 2.49% and 2.04%, respectively, attest to high repeatability. Mean (±SD) recoveries of three different concentrations (low, medium, high) of GSH spiked into aliquots of HCT116 cells prior to cell extraction were 108.9% (±2.1), 100.8% (±8.3), and 99.9% (±7.1), respectively. Finally, using a 20 Da wide Q1 window in MRM mode, we were able to detect and relatively quantify all isotopic labeling states of GSH extracted from HCT116 cells fed with either C-labeled glucose or glutamine.
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http://dx.doi.org/10.1016/j.aca.2019.07.001DOI Listing
November 2019

Amino Acid Analysis in Physiological Samples by GC-MS with Propyl Chloroformate Derivatization and iTRAQ-LC-MS/MS.

Methods Mol Biol 2019 ;2030:173-190

Institute of Functional Genomics, University of Regensburg, Regensburg, Germany.

Two mass spectrometry-based methods for the quantitative analysis of free amino acids are described. The first method uses propyl chloroformate/propanol derivatization and gas chromatography-quadrupole mass spectrometry (GC-qMS) analysis in a single-ion monitoring mode. Derivatization is carried out directly in the aqueous samples, thereby allowing automation of the entire procedure, including addition of reagents, extraction, and injection into the GC-MS. The method delivers the quantification of 26 amino acids. The iTRAQ method employs the labeling of amino acids with isobaric iTRAQ tags. The tags contain two different cleavable reporter ions, one for the sample and one for the standard, which are detected by fragmentation in a tandem mass spectrometer (MS/MS). Reversed-phase liquid chromatography (RP-LC) of the labeled amino acids is performed prior to mass spectrometric analysis to separate isobaric amino acids. The commercial iTRAQ kit allows for the analysis of 42 physiological amino acids with a respective isotope-labeled standard for each of these 42 amino acids.
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http://dx.doi.org/10.1007/978-1-4939-9639-1_14DOI Listing
April 2020

Topical Diclofenac Reprograms Metabolism and Immune Cell Infiltration in Actinic Keratosis.

Front Oncol 2019 3;9:605. Epub 2019 Jul 3.

Department of Dermatology, University Hospital Regensburg, Regensburg, Germany.

Melanoma and squamous cell carcinoma of the skin are characterized by an altered glucose metabolism, but little is known about metabolic changes in precancerous skin lesions such as actinic keratosis (AK). Here, we studied the central carbon metabolism and immune cell infiltrate of actinic keratosis lesions before, under, and 4 weeks after treatment with topical diclofenac (Solaraze®). This study was designed as a prospective, randomized, controlled, monocentric investigation (ClinicalTrials.gov Identifier: NCT01935531). Myeloid and T cell infiltration was analyzed in skin biopsies from 28 patients by immunohistochemistry. Furthermore, immune cell activation was determined via quantitative real-time PCR (γ, IL-10, β). Glucose, amino acid and Krebs' cycle metabolism was studied by mass spectrometry prior, during and after treatment with topical diclofenac. Biopsies from sun-exposed, untreated, healthy skin served as controls. Increased lactate and decreased glucose levels suggested accelerated glycolysis in pre-treatment AK. Further, levels of Krebs' cycle intermediates other than citrate and amino acids were elevated. Analysis of the immune infiltrate revealed less epidermal CD1a+ cells but increased frequencies of dermal CD8+ T cells in AK. Treatment with diclofenac reduced lactate and amino acid levels in AK, especially in responding lesions, and induced an infiltration of dermal CD8+ T cells accompanied by high γ mRNA expression, suggesting improved T cell function. Our study clearly demonstrated that not only cancers but also pre-malignant skin lesions, like AK, exhibit profound changes in metabolism, correlating with an altered immune infiltrate. Diclofenac normalizes metabolism, immune cell infiltration and function in AK lesions, suggesting a novel mechanism of action.
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http://dx.doi.org/10.3389/fonc.2019.00605DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6619385PMC
July 2019

Degradation of D-2-hydroxyglutarate in the presence of isocitrate dehydrogenase mutations.

Sci Rep 2019 05 15;9(1):7436. Epub 2019 May 15.

Institute of Functional Genomics, University of Regensburg, Am BioPark 9, 93053, Regensburg, Germany.

D-2-Hydroxyglutarate (D-2-HG) is regarded as an oncometabolite. It is found at elevated levels in certain malignancies such as acute myeloid leukaemia and glioma. It is produced by a mutated isocitrate dehydrogenase IDH1/2, a low-affinity/high-capacity enzyme. Its degradation, in contrast, is catalysed by the high-affinity/low-capacity enzyme D-2-hydroxyglutarate dehydrogenase (D2HDH). So far, it has not been proven experimentally that the accumulation of D-2-HG in IDH mutant cells is the result of its insufficient degradation by D2HDH. Therefore, we developed an LC-MS/MS-based enzyme activity assay that measures the temporal drop in substrate and compared this to the expression of D2HDH protein as measured by Western blot. Our data clearly indicate, that the maximum D-2-HG degradation rate by D2HDH is reached in vivo, as v is low in comparison to production of D-2-HG by mutant IDH1/2. The latter seems to be limited only by substrate availability. Further, incubation of IDH wild type cells for up to 48 hours with 5 mM D-2-HG did not result in a significant increase in either D2HDH protein abundance or enzyme activity.
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http://dx.doi.org/10.1038/s41598-019-43891-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6520482PMC
May 2019

Identification of ADGRE5 as discriminating MYC target between Burkitt lymphoma and diffuse large B-cell lymphoma.

BMC Cancer 2019 Apr 5;19(1):322. Epub 2019 Apr 5.

Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, D-10117, Berlin, Germany.

Background: MYC is a heterogeneously expressed transcription factor that plays a multifunctional role in many biological processes such as cell proliferation and differentiation. It is also associated with many types of cancer including the malignant lymphomas. There are two types of aggressive B-cell lymphoma, namely Burkitt lymphoma (BL) and a subgroup of diffuse large cell lymphoma (DLBCL), which both carry MYC translocations and overexpress MYC but both differ significantly in their clinical outcome. In DLBCL, MYC translocations are associated with an aggressive behavior and poor outcome, whereas MYC-positive BL show a superior outcome.

Methods: To shed light on this phenomenon, we investigated the different modes of actions of MYC in aggressive B-cell lymphoma cell lines subdivided into three groups: (i) MYC-positive BL, (ii) DLBCL with MYC translocation (DLBCLpos) and (iii) DLBCL without MYC translocation (DLBCLneg) for control. In order to identify genome-wide MYC-DNA binding sites a chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq) was performed. In addition, ChIP-Seq for H3K4me3 was used for determination of genomic regions accessible for transcriptional activity. These data were supplemented with gene expression data derived from RNA-Seq.

Results: Bioinformatics integration of all data sets revealed different MYC-binding patterns and transcriptional profiles in MYC-positive BL and DLBCL cell lines indicating different functional roles of MYC for gene regulation in aggressive B-cell lymphomas. Based on this multi-omics analysis we identified ADGRE5 (alias CD97) - a member of the EGF-TM7 subfamily of adhesion G protein-coupled receptors - as a MYC target gene, which is specifically expressed in BL but not in DLBCL regardless of MYC translocation.

Conclusion: Our study describes a diverse genome-wide MYC-DNA binding pattern in BL and DLBCL cell lines with and without MYC translocations. Furthermore, we identified ADREG5 as a MYC target gene able to discriminate between BL and DLBCL irrespectively of the presence of MYC breaks in DLBCL. Since ADGRE5 plays an important role in tumor cell formation, metastasis and invasion, it might also be instrumental to better understand the different pathobiology of BL and DLBCL and help to explain discrepant clinical characteristics of BL and DLBCL.
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http://dx.doi.org/10.1186/s12885-019-5537-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6451309PMC
April 2019

Limitation of TCA Cycle Intermediates Represents an Oxygen-Independent Nutritional Antibacterial Effector Mechanism of Macrophages.

Cell Rep 2019 03;26(13):3502-3510.e6

Mikrobiologisches Institut, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, 91054 Erlangen, Germany. Electronic address:

In hypoxic and inflamed tissues, oxygen (O)-dependent antimicrobial defenses are impaired due to a shortage of O. To gain insight into the mechanisms that control bacterial infection under hypoxic conditions, we infected macrophages with the obligate intracellular pathogen Coxiella burnetii, the causative agent of Q fever. Our experiments revealed that hypoxia impeded C. burnetii replication in a hypoxia-inducible factor (HIF) 1α-dependent manner. Mechanistically, under hypoxia, HIF1α impaired the activity of STAT3, which in turn reduced the intracellular level of TCA cycle intermediates, including citrate, and impeded C. burnetii replication in macrophages. However, bacterial viability was maintained, allowing the persistence of C. burnetii, which is a prerequisite for the development of chronic Q fever. This knowledge will open future research avenues on the pathogenesis of chronic Q fever. In addition, the regulation of TCA cycle metabolites by HIF1α represents a previously unappreciated mechanism of host defense against intracellular pathogens.
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http://dx.doi.org/10.1016/j.celrep.2019.02.103DOI Listing
March 2019

A Novel Metabolic Signature To Predict the Requirement of Dialysis or Renal Transplantation in Patients with Chronic Kidney Disease.

J Proteome Res 2019 04 12;18(4):1796-1805. Epub 2019 Mar 12.

Institute of Genetic Epidemiology, Department of Biometry, Epidemiology, and Medical Bioinformatics, Faculty of Medicine and Medical Center , University of Freiburg , Freiburg 79106 , Germany.

Identification of chronic kidney disease patients at risk of progressing to end-stage renal disease (ESRD) is essential for treatment decision-making and clinical trial design. Here, we explored whether proton nuclear magnetic resonance (NMR) spectroscopy of blood plasma improves the currently best performing kidney failure risk equation, the so-called Tangri score. Our study cohort comprised 4640 participants from the German Chronic Kidney Disease (GCKD) study, of whom 185 (3.99%) progressed over a mean observation time of 3.70 ± 0.88 years to ESRD requiring either dialysis or transplantation. The original four-variable Tangri risk equation yielded a C statistic of 0.863 (95% CI, 0.831-0.900). Upon inclusion of NMR features by state-of-the-art machine learning methods, the C statistic improved to 0.875 (95% CI, 0.850-0.911), thereby outperforming the Tangri score in 94 out of 100 subsampling rounds. Of the 24 NMR features included in the model, creatinine, high-density lipoprotein, valine, acetyl groups of glycoproteins, and Ca-EDTA carried the highest weights. In conclusion, proton NMR-based plasma fingerprinting improved markedly the detection of patients at risk of developing ESRD, thus enabling enhanced patient treatment.
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http://dx.doi.org/10.1021/acs.jproteome.8b00983DOI Listing
April 2019