A multi-technique study of altered granitic rock from the Krunkelbach Valley uranium deposit, Southern Germany

Herein, a multi-technique study was performed to reveal the elemental speciation and microphase composition in altered granitic rock collected from the Krunkelbach Valley uranium (U) deposit area near an abandoned U mine, Black Forest, Southern Germany.Comment: RSC Advances (2020

A Proteomic View of an Important Human Pathogen – Towards the Quantification of the Entire Staphylococcus aureus Proteome

The genome sequence is the “blue-print of life,” but proteomics provides the link to the actual physiology of living cells. Because of their low complexity bacteria are excellent model systems to identify the entire protein assembly of a living organism. Here we show that the majority of proteins expressed in growing and non-growing cells of the human pathogen Staphylococcus aureus can be identified and even quantified by a metabolic labeling proteomic approach. S. aureus has been selected as model for this proteomic study, because it poses a major risk to our health care system by combining high pathogenicity with an increasing frequency of multiple antibiotic resistance, thus requiring the development of new anti-staphylococcal therapy strategies. Since such strategies will likely have to target extracellular and surface-exposed virulence factors as well as staphylococcal survival and adaptation capabilities, we decided to combine four subproteomic fractions: cytosolic proteins, membrane-bound proteins, cell surface-associated and extracellular proteins, to comprehensively cover the entire proteome of S. aureus. This quantitative proteomics approach integrating data ranging from gene expression to subcellular localization in growing and non-growing cells is a proof of principle for whole-cell physiological proteomics that can now be extended to address physiological questions in infection-relevant settings. Importantly, with more than 1700 identified proteins (and 1450 quantified proteins) corresponding to a coverage of about three-quarters of the expressed proteins, our model study represents the most comprehensive quantification of a bacterial proteome reported to date. It thus paves the way towards a new level in understanding of cell physiology and pathophysiology of S. aureus and related pathogenic bacteria, opening new avenues for infection-related research on this crucial pathogen

Phenotypic and molecular insights into CASK-related disorders in males

Background: Heterozygous loss-of-function mutations in the X-linked CASK gene cause progressive microcephaly with pontine and cerebellar hypoplasia (MICPCH) and severe intellectual disability (ID) in females. Different CASK mutations have also been reported in males. The associated phenotypes range from nonsyndromic ID to Ohtahara syndrome with cerebellar hypoplasia. However, the phenotypic spectrum in males has not been systematically evaluated to date. Methods: We identified a CASK alteration in 8 novel unrelated male patients by targeted Sanger sequencing, copy number analysis (MLPA and/or FISH) and array CGH. CASK transcripts were investigated by RT-PCR followed by sequencing. Immunoblotting was used to detect CASK protein in patient-derived cells. The clinical phenotype and natural history of the 8 patients and 28 CASK-mutation positive males reported previously were reviewed and correlated with available molecular data. Results: CASK alterations include one nonsense mutation, one 5-bp deletion, one mutation of the start codon, and five partial gene deletions and duplications; seven were de novo, including three somatic mosaicisms, and one was familial. In three subjects, specific mRNA junction fragments indicated in tandem duplication of CASK exons disrupting the integrity of the gene. The 5-bp deletion resulted in multiple aberrant CASK mRNAs. In fibroblasts from patients with a CASK loss-of-function mutation, no CASK protein could be detected. Individuals who are mosaic for a severe CASK mutation or carry a hypomorphic mutation still showed detectable amount of protein. Conclusions: Based on eight novel patients and all CASK-mutation positive males reported previously three phenotypic groups can be distinguished that represent a clinical continuum: (i) MICPCH with severe epileptic encephalopathy caused by hemizygous loss-of-function mutations, (ii) MICPCH associated with inactivating alterations in the mosaic state or a partly penetrant mutation, and (iii) syndromic/nonsyndromic mild to severe ID with or without nystagmus caused by CASK missense and splice mutations that leave the CASK protein intact but likely alter its function or reduce the amount of normal protein. Our findings facilitate focused testing of the CASK gene and interpreting sequence variants identified by next-generation sequencing in cases with a phenotype resembling either of the three groups

PuraStat in gastrointestinal bleeding: results of a prospective multicentre observational pilot study

Background: A recently developed haemostatic peptide gel for endoscopic application has been introduced to improve the management of gastrointestinal bleeding. The aim of this pilot study was to evaluate the feasibility, safety, efficacy and indication profiles of PuraStat in a clinical setting. Methods: In this prospective observational multicentre pilot study, patients with acute non-variceal gastrointestinal bleeding (upper and lower) were included. Primary and secondary application of PuraStat was evaluated. Haemoglobin, prothrombin time, platelets and transfusion behaviour were documented before and after haemostasis. The efficacy of PuraStat was assessed during the procedure, at 3 days and 1 week after application. Results: 111 patients with acute gastrointestinal bleeding were recruited into the study. 70 percent (78/111) of the patients had upper gastrointestinal bleeding and 30% (33/111) had lower gastrointestinal bleeding. After primary application of PuraStat, initial haemostatic success was achieved in 94% of patients (74/79, 95% CI 88-99%), and in 75% of the patients when used as a secondary haemostatic product, following failure of established techniques (24/32, 95% CI 59-91%). The therapeutic success rates (absence of rebleeding) after 3 and 7 days were 91% and 87% after primary use, and 87% and 81% in all study patients. Overall rebleeding rate at 30 day follow-up was 16% (18/111). In the 5 patients who finally required surgery (4.5%), PuraStat allowed temporary haemostasis and stabilisation. Conclusions: PuraStat expanded the therapeutic toolbox available for an effective treatment of gastrointestinal bleeding sources. It could be safely applied and administered without complications as a primary or secondary therapy. PuraStat may additionally serve as a bridge to surgery in order to achieve temporary haemostasis in case of refractory severe bleeding, possibly playing a role in preventing immediate emergency surgery

The histone demethylase LSD1/KDM1A promotes the DNA damage response

Histone demethylation is known to regulate transcription, but its role in other processes is largely unknown. We report a role for the histone demethylase LSD1/KDM1A in the DNA damage response (DDR). We show that LSD1 is recruited directly to sites of DNA damage. H3K4 dimethylation, a major substrate for LSD1, is reduced at sites of DNA damage in an LSD1-dependent manner. The E3 ubiquitin ligase RNF168 physically interacts with LSD1 and we find this interaction to be important for LSD1 recruitment to DNA damage sites. Although loss of LSD1 did not affect the initial formation of pH2A.X foci, 53BP1 and BRCA1 complex recruitment were reduced upon LSD1 knockdown. Mechanistically, this was likely a result of compromised histone ubiquitylation preferentially in late S/G2. Consistent with a role in the DDR, knockdown of LSD1 resulted in moderate hypersensitivity to γ-irradiation and increased homologous recombination. Our findings uncover a direct role for LSD1 in the DDR and place LSD1 downstream of RNF168 in the DDR pathway

Entwicklung und Anwendung von Massenspektrometrie-basierten Methoden zur Identifizierung und Quantifizierung von Zelloberflächen-assoziierten Proteinen des humanpathogenen Bakteriums Staphylococcus aureus

Das humanpathogene Bakterium Staphylococcus aureus kann verschiedene, zum Teil lebensbedrohliche Erkrankungen wie Hautinfektionen (Furunkel, Karbunkel), Lungen-entzündung, Osteomyelitis (Knochenmarksentzündung), Endokarditis (Entzündung der Herzinnenhaut) und Sepsis auslösen. Dabei gehört S. aureus zu den häufigsten Erregern von Krankenhausinfektionen, sogenannten Nosokomialinfektionen. Deren Behandlung mittels Antibiotika stellt aufgrund von multiplen Antibiotikaresistenzen von S. aureus eine immer größere Heraus¬forderung dar, da dieser fähig ist, sich rapide an verändernde Umweltbedingungen anzu¬passen. Die Interaktion des pathogenen Bakteriums mit seiner Umwelt und seinem Wirt ist insbesondere durch den Proteinbestand, der auf der Zelloberfläche exponiert ist, bestimmt. S. aureus exprimiert ein Arsenal an Zellober-flächen-gebundenen Virulenzfaktoren, die zur Kolonisierung und Infektion von humanem Gewebe führen. Ziel dieser Arbeit war die Entwicklung und Anwendung von Massen¬spektrometrie-basierten Methoden zur Identifizierung und Quantifizierung der Zellober¬flächen¬-assoziierten Proteine von S. aureus. Dabei ist es gelungen, durch die Gel-freien und GeLC-MS/MS-basierten Methoden Biotinylierung und Trypsin-Behandlung 77% aller be-kannten Oberflächenproteine und zwei Drittel aller nach außen ragenden Membran-veran-kerten Lipoproteine von S. aureus zugänglich zu machen. Bei der Biotinylierung handelt es sich um eine Methode, bei der die Oberflächenproteine von intakten Zellen mit einem membranimpermeablen Reagenz markiert und anschließend über Affinitäts¬chroma-tographie aufgereinigt werden. Dagegen erfolgt bei der Trypsin-Behandlung die proteo-lytische Abspaltung der Oberflächen-exponierten Protein¬domänen. Erstmalig ist durch Markierung der Proteine mit stabilen Isotopen, dem sogenannten 14N/15N-metabolischen Labeling, auch eine relative Quantifizierung der Oberflächenproteine von S. aureus möglich. Bei der Analyse des Oberflächenproteoms von wachsenden und nicht-wachsenden S. aureus Zellen konnten mittels Biotinylierung 146 Oberflächenproteine identifiziert werden. Durch relative Quantifizierung wurde gezeigt, dass Zelloberflächen-assoziierte Adhäsine von S. aureus, wie der Fibrinogen-bindende clumping Faktor B, vorzugsweise während des Wachstums exprimiert werden, während nicht-wachsende Zellen erhöhte Mengen an clumping Faktor A aufweisen. Desweiteren war die Menge an immunodominanten Antigen B auf der Zelloberfläche in der stationären Phase mehr als 10-fach erhöht. Bei dieser Arbeit wurde erstmalig das Gesamt¬proteom des Methicillin-resistenten Staphylococcus aureus COL, bestehend aus cytosolischem, extra¬zellulärem, Membran- und Oberflächenproteom, um¬fassend identifiziert und quantifiziert (Becher et al., 2009). Um die Pathogenität von S. aureus näher zu erforschen, wurde das Oberflächenproteom des Wildtyps mit dem einer sigB-Mutante verglichen. Der alternative Sigma-Faktor SigmaB kontrolliert ein großes Regulon bestehend aus etwa 300 Genen, von denen viele in die Virulenz von S. aureus involviert sind. Durch Kombination von 14N/15N-metabolischen Labeling, Biotinylierung und GeLC-MS/MS konnten 98 Oberflächen-proteine quantifiziert werden. Von den 49 Proteinen, die in der sigB-Mutante verändert vorlagen, waren 21 schon als SigmaB-abhängig oder durch SigmaB beeinflusst bekannt. In dieser Arbeit konnten weitere 28 Oberflächenproteine erstmalig als SigmaB-abhängig beschrieben werden. Die Gruppe der Zelloberflächen-assoziierten Proteine und Virulenz-faktoren, die durch SigmaB beeinflusst werden, wurde so erweitert (Hempel et al., 2010). Durch Trypsin-Behandlung wurden insgesamt 63 Oberflächen¬proteine beim Vergleich vier verschiedener S. aureus Stämme identifiziert. Hierbei konnte gezeigt werden, dass das Oberflächenproteom verschiedener S. aureus Stämme extrem variabel ist. Weniger als 10% der identifizierten Oberflächenproteine aller vier Stämme stimmten überein (Dreisbach et al., 2010). Eine optimale Analyse der Oberflächen¬proteine von S. aureus wird durch eine Kombination von Biotinylierung und Trypsin-Behandlung erreicht. Es konnte gezeigt werden, dass Sortase-Substrate insbesondere durch Trypsin zugänglich sind, während Lipoproteine optimal durch Biotinylierung analysiert werden können. Das Protokoll zur Trypsin-Behandlung wurde modifiziert, stark vereinfacht und ist auch zur Quantifizierung von Oberflächen¬proteinen geeignet. Durch Kombi¬nation beider Methoden mit 14N/15N-metabolischen Labeling konnten 221 Oberflächen¬proteine identifiziert und 158 quantifiziert werden. Hierbei wurde S. aureus unter Eisenmangel-bedingungen untersucht. In den Körperflüssigkeiten von Säugetieren herrschen Eisenmangelbedingungen, und diese fungieren als wichtiges Wirtssignal für die Bakterien um Virulenzproteine zu exprimieren. Unter diesen infektionsrelevanten in vitro Bedingungen wurden insbesondere Zelloberflächenproteine wie die eisenabhängigen Häm-bindenden Proteine IsdA, IsdB, IsdC und IsdD, sowie lipidver¬ankerte Eisen-bindende Proteine stark induziert gefunden (Hempel et al., unpublished).The human pathogenic bacterium Staphylococcus aureus causes a wide variety of in part life-threatening diseases such as skin infections (furunculosis), pneumonia, osteomyelitis, endocarditis and sepsis. Thereby S. aureus belongs to the most prevalent pathogenic agents of nosocomial infections. Antibiotic treatment becomes more challenging because of an increasing frequency of multiple antibiotic resistances, as S. aureus is capable of adapting to rapidly changing environmental conditions. The interaction of this pathogenic bacterium with its environment and its host is specifically based on the protein set presented on the surface of the bacterial cell. S. aureus expresses an arsenal of cell surface-associated virulence factors leading to colonization and infection of human tissue. The aim of this work was the development and implementation of mass spectrometry-based approaches for identification and quantification of cell surface-associated proteins of the human pathogenic bacterium Staphylococcus aureus. Thereby access to 77% of all known cell surface-associated proteins and two thirds of all external exposed membrane-anchored lipoproteins was enabled by the gel-free and GeLC-MS/MS-based methods named biotinylation and trypsin-shaving. Biotinylation implies the labeling of cell surface-associated proteins of intact staphylococcal cells by a membrane impermeable biotinylation reagent and subsequent enrichment by affinity-chromatography. In contrast trypsin-shaving is the proteolytical digestion of all cell surface-exposed protein domains. In addition, a relative quantification of the surface-associated proteins by labeling of the proteins with stable isotopes, the 14N/15N-metabolic labeling, was enabled for the first time. Analysis of the surface-associated proteome of growing and non-growing S. aureus cells by biotinylation led to the identification of 146 surface proteins. It could be shown by relative protein quantification, that cell surface adhesins of S. aureus, as the fibrinogen-binding protein clumping factor B, were preferentially synthesized during growth, whereas clumping factor A is expressed in higher amounts on the surface of non-growing cells. Remarkably, the immunodominant antigen IsaB was present in a more than tenfold increased amount on the surface of cells in stationary phase. This work was the first comprehensive identification and quantification of the entire methicillin-resistent Staphylococcus aureus COL proteome, comprising cytosolic, extracellular, membrane und surface-associated proteome, to date (Becher et al., 2009). To address the important question of S. aureus pathogenicity, the influence of the alternative sigma factor SigmaB on the expression of cell surface-associated proteins was analyzed. Therefore, the S. aureus wild-type strain COL was compared to its isogenic sigB-mutant. SigmaB controls a large regulon in S. aureus, comprising about 300 genes, among them many with a function in virulence. By combination of 14N/15N- metabolic labeling, biotinylation, and GeLC-MS/MS 98 surface-associated proteins could be quantified. Fourty nine surface-associated proteins were modulated by SigmaB, including 21 proteins already known to be SigB-dependent or SigB-influenced. This work revealed further 28 surface-associated proteins not previously reported as SigB-dependent or -influenced, expanding the group of surface-associated proteins and virulence factors modulated by SigmaB (Hempel et al., 2010). Trypsin-shaving led to a total of 63 identified surface-associated proteins by comparing four different S. aureus strains. It could be shown, that the cell surface proteome of different S. aureus strains is extremely heterogenous. The overlap between the surface-associated proteins of the four different strains was below 10% (Dreisbach et al., 2010). An optimal analysis of surface-associated proteins of S. aureus is achieved by combination of biotinylation and trypsin-shaving. Whereas Sortase-Substrates were preferentially analysed by trypsin shaving, the biotinylation is a powerful tool for the analysis of lipoproteins. The trypsin-shaving protocol was modified, simplified and is applicable for quantification of surface proteins. By combination of both methods with 14N/15N-metabolic labeling 221 surface-associated proteins could be identified and 158 quantified. Here S. aureus was analysed under iron limitation. The iron-limited conditions in mammalian body fluids serve as a major environmental signal to the bacteria to express virulence determinants. For this infection-relevant situation particularly surface-exposed proteins were strongly induced such as the iron-regulated surface determinant proteins IsdA, IsdB, IsdC and IsdD as well as lipid-anchored iron compound-binding proteins (Hempel et al., unpublished)

A Specific LSD1/KDM1A Isoform Regulates Neuronal Differentiation through H3K9 Demethylation

Lysine-specific demethylase 1 (LSD1) has been reported to repress and activate transcription by mediating histone H3K4me1/2 and H3K9me1/2 demethylation, respectively. The molecular mechanism that underlies this dual substrate specificity has remained unknown. Here we report that an isoform of LSD1, LSD1+8a, does not have the intrinsic capability to demethylate H3K4me2. Instead, LSD1+8a mediates H3K9me2 demethylation in collaboration with supervillin (SVIL), a new LSD1+8a interacting protein. LSD1+8a knockdown increases H3K9me2, but not H3K4me2, levels at its target promoters and compromises neuronal differentiation. Importantly, SVIL co-localizes to LSD1+8a-bound promoters, and its knockdown mimics the impact of LSD1+8a loss, supporting SVIL as a cofactor for LSD1+8a in neuronal cells. These findings provide insight into mechanisms by which LSD1 mediates H3K9me demethylation and highlight alternative splicing as a means by which LSD1 acquires selective substrate specificities (H3K9 versus H3K4) to differentially control specific gene expression programs in neurons

Landscape of Biomarkers and Actionable Gene Alterations in Adenocarcinoma of GEJ and Stomach—A Real World Data Analysis

After several years of negative phase III trials in gastric and esophageal cancer, a significant breakthrough in the treatment of metastatic adenocarcinomas of the gastroesophageal junction (GEJ) and stomach (GC) is now becoming evident with the emerging of precision oncology and implementation of molecular targets in tumor treatment. In addition, new generation studies such as umbrella and basket trials are focused on these molecular targets, which makes an early molecular diagnosis based on IHC/ISH and NGS necessary. The required companion diagnostics of Her2neu overamplification or PD-L1 expression is based on immunohistochemistry (IHC) or additionally in situ hybridization (ISH) in case of an IHC Her2neu score of 2+. However, there are investigator-dependent differences in the assessment of Her2neu amplification and different PD-L1 scoring systems obtained by IHC/ISH. The use of high-throughput technologies such as next-generation sequencing (NGS) holds the potential to standardize the analysis and thus make them more comparable. In the presented study, real-world multigene sequencing data of 72 Caucasian patients diagnosed with metastatic adenocarcinomas of GEJ and stomach were analyzed. In the clinical companion diagnostics, we found ESCAT level I molecular targets in one-third of our patients, which directly determined the therapy. In addition, we found potential targets in 14/72 patients (19.4%) who potentially qualify for precision therapies in corresponding molecular studies. The study highlights the importance of comprehensive molecular profiling for precision treatment of GEJ/GC and indicates that a biomarker evaluation should be performed for all patients with metastatic adenocarcinomas before the initiation of first-line treatment and during second-line or subsequent treatment

A multi-technique study of altered granitic rock from the Krunkelbach Valley uranium deposit, Southern Germany

Herein, a multi-technique study was performed to reveal the elemental speciation and microphase composition in altered granitic rock collected from the Krunkelbach Valley uranium (U) deposit area near an abandoned U mine, Black Forest, Southern Germany. The former Krunkelbach U mine with 1-2 km surrounding area represents a unique natural analogue site with the rich accumulation of secondary U minerals suitable for radionuclide migration studies from a spent nuclear fuel (SNF) repository. Based on a micro-technique analysis using several synchrotron-based techniques such as X-ray fluorescence analysis, X-ray absorption spectroscopy, powder X-ray diffraction and laboratory-based scanning electron microscopy and Raman spectroscopy, the complex mineral assemblage was identified. While on the surface of granite, heavily altered metazeunerite-metatorbernite (Cu(UO2)(2)(AsO4)(2-x)(PO4)(x)center dot 8H(2)O) microcrystals were found together with diluted coatings similar to cuprosklodowskite (Cu(UO2)(2)(SiO3OH)(2)center dot 6H(2)O), in the cavities of the rock predominantly well-preserved microcrystals close to metatorbernite (Cu(UO2)(2)(PO4)(2)center dot 8H(2)O) were identified. The Cu(UO2)(2)(AsO4)(2-x)(PO4)(x)center dot 8H(2)O species exhibit uneven morphology and varies in its elemental composition, depending on the microcrystal part ranging from well-preserved to heavily altered on a scale of similar to 200 mu m. The microcrystal phase alteration could be presumably attributed to the microcrystal morphology, variations in chemical composition, and geochemical conditions at the site. The occurrence of uranyl-arsenate-phosphate and uranyl-silicate mineralisation on the surface of the same rock indicates the signatures of different geochemical conditions that took place after the oxidative weathering of the primary U- and arsenic (As)-bearing ores. The relevance of uranyl minerals to SNF storage and the potential role of uranyl-arsenate mineral species in the mobilization of U and As into the environment is discussed