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The Kinase Chemogenomic Set (KCGS): An open science resource for kinase vulnerability identification
(2019)
We describe the assembly and annotation of a chemogenomic set of protein kinase inhibitors as an open science resource for studying kinase biology. The set only includes inhibitors that show potent kinase inhibition and a narrow spectrum of activity when screened across a large panel of kinase biochemical assays. Currently, the set contains 187 inhibitors that cover 215 human kinases. The kinase chemogenomic set (KCGS) is the most highly annotated set of selective kinase inhibitors available to researchers for use in cell-based screens.
Autophagy is a highly conserved catabolic process through which defective or otherwise harmful cellular components are targeted for degradation via the lysosomal route. Regulatory pathways, involving post-translational modifications such as phosphorylation, play a critical role in controlling this tightly orchestrated process. Here, we demonstrate that TBK1 regulates autophagy by phosphorylating autophagy modifiers LC3C and GABARAP-L2 on surface-exposed serine residues (LC3C S93 and S96; GABARAP-L2 S87 and S88). This phosphorylation event impedes their binding to the processing enzyme ATG4 by destabilizing the complex. Phosphorylated LC3C/GABARAP-L2 cannot be removed from liposomes by ATG4 and are thus protected from ATG4-mediated premature removal from nascent autophagosomes. This ensures a steady coat of lipidated LC3C/GABARAP-L2 throughout the early steps in autophagosome formation and aids in maintaining a unidirectional flow of the autophagosome to the lysosome. Taken together, we present a new regulatory mechanism of autophagy, which influences the conjugation and de-conjugation of LC3C and GABARAP-L2 to autophagosomes by TBK1-mediated phosphorylation.
Das Projekt „Geo-Social Analysis of Physicians' Settlement" (kurz GAP) wurde ins Leben gerufen, um potentielle Lücken in der ambulanten medizinischen Versorgung deutscher Großstädte aufzudecken, insbesondere in Bezug auf den sozioökonomischen Status der in einem Praxisumfeld lebenden Bewohner. In der vorliegenden Studie erfolgte die Untersuchung des Niederlassungsverhaltens von Ärzten und Psychotherapeuten in Berlin-West im Hinblick auf sozioökonomische, demographische und topographische Faktoren.
Das Untersuchungsgebiet Berlin-West wurde in 251 Praxisumfelder untergliedert. Für diese wurden Daten zu Einwohnerzahl, Altersstruktur und Wohnlage sowie Arbeitslosen- und Ausländerquoten zusammengetragen. In vergleichenden Analysen konnten dann die Unterschiede im Niederlassungsverhalten der 20 Fachgebietskategorien hinsichtlich des sozialen Status der Praxisumfelder herausgearbeitet werden. Weitere Auswertungen beinhalteten eine genderspezifische Praxisumfeld-Analyse sowie Analysen nach Praxisform, Fremdsprachenkenntnissen der Ärzte und Psychotherapeuten sowie des Praxis-Jahres-Überschusses als Maß für das ärztliche Einkommen.
Im Rahmen einer Fachgebiet-Sozialindikatoren-Analyse ergab sich weder für die hausärztliche noch für den Großteil der fachärztlichen Versorgung in Berlin-West eine signifikante Bevorzugung von Gebieten mit einem höheren sozialen Status. Lediglich für die Gruppe der Ärztlichen und Psychologischen Psychotherapeuten zeigte sich, dass diese eindeutig vermehrt in Gegenden mit hohem sozialen Status niedergelassen sind. In der Gender-Analyse konnte gezeigt werden, dass Ärztinnen und Psychotherapeutinnen sozial schwächere Gegenden seltener als Niederlassungsstandort wählen. Im Rahmen einer Störfaktoren-Analyse konnten Zentrumsdistanz und Einwohnerdichte als mögliche Einflussfaktoren auf die Standortwahl der Ärzte und Psychotherapeuten ausgeschlossen werden.
Insgesamt zeigen die Ergebnisse, dass über eine Unterteilung der einzelnen Großstädte in mehrere Planungsbereiche – statt sie wie bisher als einen einzelnen großen zu betrachten – nachgedacht werden sollte. Um die medizinischen Bedürfnisse der sozial schlechter gestellten Bevölkerung besser abdecken zu können, wäre die Einführung eines Sozialfaktors, ähnlich dem des bereits existierenden Demographiefaktors (zur Anpassung an die Altersstruktur der Bevölkerung) für die Berechnung des tatsächlichen Ärztebedarfs empfehlenswert. Auf diese Art und Weise könnte zukünftig eine bedarfsgerechtere Planung der Ärzteverteilung erfolgen und somit ein gleichmäßigerer Zugang zu ambulanter vertragsärztlicher Versorgung für alle GKV-Versicherten gewährleistet werden.
The carpal tunnel syndrome (CTS) is a chronic compression of the median nerve in the carpal tunnel, a condition in which the nerve is constricted especially under the flexor retinaculum (FR). The disease predominantly appears between 40 and 83 years of age. Women are significantly more often affected than men. The same applies to overweight people in comparison to normal weight people. Abnormal sensations at night, including paresthesias and dysesthesias, are classical CTS symptoms, predominately involving the middle fingers, later also the thumb. Diagnosis of CTS usually proceeds by motor nerve conduction study (mNCS) and determination of the distal motoric latency (DML). In conformity with electrophysiology, peripheral nerve ultrasonography has also attained an important diagnostic informative value. In principle, there is an open surgical procedure and an endoscopic carpal roof cleavage. The goal of therapy is the complete open division of the flexor retinaculum (FR) in order to relieve the median nerve from compression.
This work examines the morphological alterations of the median nerve at the site of the carpal tunnel after surgical decompression by means of high-resolution neurosonography in the scope of a prospective study. More than 100 patients were examined between October and December 2014 for planned decompressions surgery due to CTS. A total of 81 patients were prospectively included, 5 of which could not take part in the follow-up after six months and were excluded from this evaluation. A medical CTS case history, clinical examination findings, as well as a neurographic result were included. Patients with a relapse operation were not considered in this regard. Apart from a clinical examination and questioning of the patient three and six months after surgery, an electrophysiological examination and a high-resolution sonography of the median nerve were also carried out. Electroneurography and nerve sonography of the median nerve were applied to both hands. A prolonged distal motor latency of the median nerve amounting to 4ms, as well as a slowed nerve conduction velocity below the benchmark value of approx. 45m/s, were classified as pathological findings. In sonography, the largest cross-section area (CSA) of the median nerve was measured by applying transversal slicing to the distal transverse creases of the skin on the palmar surface of the wrist (rasceta) as well as 5cm proximal to the rasceta. The highest CSA values were determined visually. In cases of doubt several transversal slices were made until the highest CSA value could be identified.
The average age at which the disease was contracted amounted to 56.9 years. With one exception, all patients complained of nocturnal brachialgia before surgery (74, 96.2%). As far as neurological symptoms were concerned, 72 patients had paresthesias (93.6%) and 29 patients (37.7%) felt permanent numbness. A thenar atrophy of higher degree was diagnosed in two patients (2.6%). These complaints had improved in the patients surveyed in the scope of postoperative evaluations after three and six months.
Patients with motor deficits had a statistically significantly longer preoperative distal motor latency (10.5 ± 2.8ms vs. 6.5 ± 2.3ms). We observed an improvement of distal motor latency in 98% of the patients three months and six months after surgical decompression, displaying a statistically significant DML decrease from 6.6 ± 2.4ms to 4.8 ± 1.0ms and from 6.6 ± 2.4ms to 4.4 ± 1.0ms, respectively. There was a statistically significant correlation between the decrease of the nerve cross-section area and the decrease of distal motor latency.
At the time of the follow-up examination, three months after surgery, we were able to document a decrease in the CSA value in 80% of the patients. The mean CSA value decreased from 14.7 ± 4.4mm² to 12.4 ± 3.4 mm². Six months after surgical decompression the mean CSA value decreased from 14.3 ± 4.4mm² to 9.6 ± 2.3mm². Patients with a preoperative CSA value of ≥ 12mm² displayed a significantly greater relative reduction of their postoperative CSA value. Concerning all preoperative and postoperative parameters in patients who had undergone either open or endoscopic surgery, none revealed significant differences. Neither could an exploratory analysis (i.e. age, diabetic diseases) reveal any significant correlation between the parameters. Prior to surgery, a flattening of the median nerve or a loss of its fascicular structure (texture) had also been seen to exist in patients, apart from the nerve's larger cross-section area. Nerve sonography is an inexpensive and fast method. It is also extraordinarily reliable in the assessment of the CTS diagnosis and suits the necessary demands. We achieved a good efficiency with our sonographic examinations in the study presented here. New and improved developments show that high-resolution sonography will gain more and more significance in future CTS diagnostics.
Parkinson disease (PD), one of the most common neurodegenerative disorder, is believed to be driven by toxic α-synuclein aggregates eventually resulting in selective loss of vulnerable neuron populations, prominent among them, nigrostriatal dopamine (DA) neurons in the lateral substantia nigra (l-SN). How α-synuclein aggregates initiate a pathophysiological cascade selectively in vulnerable neurons is still unclear. Here, we show that the exposure to low nanomolar concentrations of α-synuclein aggregates (i.e. fibrils) but not its monomeric forms acutely and selectively disrupted the electrical pacemaker function of the DA subpopulation most vulnerable in PD. This implies that only dorsolateral striatum projecting l-SN DA neurons were electrically silenced by α-synuclein aggregates, while the activity of neither neighboring DA neurons in medial SN projecting to dorsomedial striatum nor mesolimbic DA neurons in the ventral tegmental area (VTA) were affected. Moreover, we demonstrate functional K-ATP channels comprised of Kir6.2 subunit in DA neurons to be necessary to mediate this acute pacemaker disruption by α-synuclein aggregates. Our study thus identifies a molecularly defined target that quickly translates the presence of α-synuclein aggregates into an immediate impairment of essential neuronal function. This constitutes a novel candidate process how a protein-aggregation-driven sequence in PD is initiated that might eventually lead to selective neurodegeneration.
The nucleoside analogue nelarabine, the prodrug of arabinosylguanine (AraG), has been known for decades to be effective against acute lymphoblastic leukaemias of T-cell (T-ALL), but not of B-cell (B-ALL) origin. The mechanisms underlying this lineage-specific drug sensitivity have remained elusive. Data from pharmacogenomics studies and from a panel of ALL cell lines revealed an inverse correlation of SAMHD1 expression and nelarabine sensitivity. SAMHD1 can hydrolyse and thus inactivate triphosphorylated nucleoside analogues. Transcriptomic and protein expression profiling of cell lines and patient-derived leukaemic blasts revealed lower SAMHD1 abundance in T-ALL than in B-ALL. Mechanistically, SAMHD1 promoter methylation strongly correlated with suppressed SAMHD1 expression, while T-ALL cells did not display increased global DNA methylation. Targeted SAMHD1 degradation using virus-like particles containing Vpx sensitised B-ALL cells to AraG, while ectopic SAMHD1 expression in SAMHD1-null T-ALL cells induced AraG resistance. SAMHD1 had a larger impact on cytarabine activity than on nelarabine/ AraG activity in acute myeloid leukaemia (AML) cells, but more strongly affected nelarabine/ AraG activity in ALL cells. This indicates a critical role of the cancer entity. In conclusion, lineage-specific differences in SAMHD1 promoter methylation and, in turn, SAMHD1 expression levels determine ALL cell response to nelarabine. SAMHD1 is a potential biomarker for the identification of ALL patients likely to benefit from nelarabine therapy and a therapeutic target to overcome nelarabine resistance.
Cancer microenvironment is now recognized as a critical regulator of all stages of cancer development. Beside the tumor vasculature and tumor-infiltrating immune cells, other stromal cells such as cancer-associated fibroblasts (CAFs) regulate tumor growth. Fibroblasts are ubiquitous cells in connective tissue, where they shape the extracellular matrix (ECM). Fibroblasts are usually quiescent but get activated when tissue homeostasis is disturbed. Then, activated fibroblasts rebuild the ECM and communicate with local cells to participate in wound repair. These repair properties can go awry when being unchecked, which can lead to fibrosis and subsequently cancer development. CAFs can promote cancer development by fostering tumor cell growth, polarizing immune cells to an immunosuppressive phenotype, and crosslinking collagen to enable tumor cell invasion. Molecular mechanisms of CAF activation, thus, need to be understood to target these cells in tumors. Prostanoid prostaglandin E2 (PGE2) is viewed as a pro-tumor lipid mediator as suggested by studies pharmacologically or genetically targeting the enzymes producing PGE2, such as microsomal PGE synthase-1 (mPGES-1) in tumor models. Similar to CAFs, PGE2 drives tumor cell growth and tumor-associated immune suppression. Therefore, I hypothesized that PGE2 may play a role in CAF activation.
This hypothesis was tested in two mouse models of breast cancer (orthotopic grafting model, and polyoma middle T oncogene transgenic model), besides using isolated mammary gland (MG) fibroblasts in vitro. As expected, given the pro-tumor function of PGE2, knocking out mPGES-1 reduced the growth of oncogene-driven and transplanted mammary tumors. Surprisingly, CAF density was markedly increased when mPGES-1 was depleted. Importantly, despite reduced primary tumor growth, I observed enhanced lung metastasis upon mPGES-1depletion. Using MG-derived fibroblasts in vitro furthermore revealed that treatment with PGE2 reduced a TGFβtriggered CAF-like activation state. Importantly, bioinformatics analysis of a human breast cancer patient dataset revealed a negative correlation of a PGE2 production signature with fibroblast marker genes. In a next step I investigated if the increased CAF infiltrate was connected to the reduced tumor growth upon depletion of PGE2. To unravel this, I first asked through which E prostanoid (EP) receptor PGE2 signals in fibroblasts. MG fibroblasts mainly expressed EP3, and EP3 KO fibroblasts showed a hyper-proliferative and activated phenotype, indicating EP3 as the main PGE2 receptor in MG fibroblasts. Co-injecting of EP3 KO MG fibroblasts and tumor cells in WT mice suppressed tumor growth, whereas co-injection of WT fibroblasts with tumor cell in mPGES-1 KO mice increased tumor growth. These data indicate that PGE2 restricts CAF levels through EP3, which supports tumor growth. Whole transcriptome mRNAsequencing of WT and mPGES-1 KO FACS-sorted CAFs combined with immunohistochemical data suggested a role of p38 mitogen-activated protein kinase (MAPK) in the modulation of fibroblast activation by PGE2.
In summary, I showed in two breast cancer models that mPGES-1 depletion delays breast cancer progression, which is probably driven by the EP3-PGE2 signaling axis in host stroma. PGE2 appears to be a potent anti-fibroblast activation agent in tumors via EP3 and downstream p38 MAPK signaling. This study therefore hits the dogmatic perception of the general pro-tumor nature of PGE2; showing that PGE2 might be a double-edged mediator that can promote tumor growth at the primary site by restricting CAF expansion, which may in turn hinder infiltration of tumor cells to a secondary site.
Over the last decade, cases of metabolic syndrome and type II diabetes have increased exponentially. Exercise and ω-3 polyunsaturated fatty acid (PUFA)-enriched diets are usually prescribed but no therapy is effectively able to restore the impaired glucose metabolism, hypertension, and atherogenic dyslipidemia encountered by diabetic patients. PUFAs are metabolized by different enzymes into bioactive metabolites with anti- or pro-inflammatory activity. One important class of PUFA metabolizing enzymes are the cytochrome P450 (CYP) enzymes that can generate a series of bioactive products, many of which have been attributed protective/anti-inflammatory and insulin-sensitizing effects in animal models. PUFA epoxides are, however, further metabolized by the soluble epoxide hydrolase (sEH) to fatty acid diols. The biological actions of the latter are less well understood but while low concentrations may be biologically important, higher concentrations of diols derived from linoleic acid and docosahexaenoic acid have been linked with inflammation. One potential application for sEH inhibitors is in the treatment of diabetic retinopathy where sEH expression and activity is elevated as are levels of a diol of docosahexaenoic acid that can induce the destabilization of the retina vasculature.
Infektionen durch multiresistente Erreger führen jährlich zum Tod von ca. 33.000 Menschen in Europa.192 Insbesondere ist eine weltweite Zunahme von multiresistenten Gram-negativen Bakterien zu verzeichnen.193 Im Rahmen dieser Arbeit wurden zwei Projekte bezüglich der Resistenzmechanismen gegenüber Beta-Laktam-Antibiotika bei Gram-negativen Bakterien bearbeitet.
Das Gammaproteobakterium Psychrobacter sanguinis PS2578 wurde im März 2015 von einem Neonaten isoliert und verursachte eine early onset Neugeboreneninfektion. Aufgrund der insuffizienten Datenlage bezüglich Diagnostik, Antibiotikaresistenz und Pathogenität von Psychrobacter spp. wurden diese Aspekte weiter evaluiert. P. sanguinis zeigte geringes Wachstum auf Blutagar und keinerlei Wachstum in Standardnährmedien. Als optimales Nährmedium erwies sich das Spezialmedium BHI mit 10% Fetalem Kälberserum, wobei eine Abhängigkeit des Wachstums von FCS beobachtet wurde. Die Virulenz des klinischen Isolats sowie des Referenzstamms P. sanguinis DSM 23635 war in einem in vivo Infektionsmodell vergleichbar mit klinischen Escherichia coli und Klebsiella pneumoniae Isolaten sowie dem phylogenetisch nahe verwandten Acinetobacter calcoaceticus DSM 30006. Demnach ist die Spezies P. sanguinis moderat virulent und als humanpathogen anzusehen. Als molekulares Äquivalent der phänotypischen Penicillinresistenz wurde die Carbenicillinase CARB-8 (RTG-3) identifiziert, wodurch die These gestützt wird, dass der Genus Psychrobacter spp. ein mögliches Genreservoir von Carbenicillinasen darstellt.3 Im Rahmen dieser Arbeit konnte das Genom der Spezies erstmals komplett sequenziert werden. Es beinhaltete ein Chromosom von 2.946.289 bp, ein größeres Plasmid von 49.981 bp und ein kleineres Plasmid von 11.576 bp, welches blaCARB-8 kodierte.
Der Nachweis von Carbapenem-resistenten Gammaproteobacteria hat sich von 2010 zu 2017 in Deutschland mehr als verzehnfacht. Dabei ist OXA-48 die häufigste Carbapenemase in Europa und tritt vor allem bei den Spezies K. pneumoniae und E. coli auf.75 In dieser Arbeit wurden 62 klinische Stämme hinsichtlich ihres Plasmidtyps und ihres Verwandtschaftsgrads untersucht.
In der Klonalitätsanalyse gehörten 25 (n=44) K. pneumoniae derselben klonalen Linie an. Hiervon wurden 22 (n=25) Isolate in den Jahren 2010 und 2011 isoliert, was einen klonalen Ausbruch vermuten lässt.158 Bei der Spezies E. coli (n=8) waren lediglich zwei Stämme klonal verwandt. Insgesamt indizierten diese Ergebnisse eine hohe Diversität der klinischen Isolate. Die Plasmidtypisierung hingegen zeigte, dass 95% der Stämme (n=62) ein IncL Plasmid aufwiesen. Basierend auf den Selektionskriterien Klonalität und Plasmidtyp wurden 21 Stämme für weitere Analysen mittels Multilocus-Sequenz-Typisierung und Transkonjugation ausgewählt. Es konnten sehr hohe Konjugationsfrequenzen von 7,51 x 10-1 im Intraspezies- und von 8,15 x 10-1 im Intergenus- HGT für das blaOXA-48 IncL Plasmid in vitro ermittelt werden. Unter Verwendung von Galleria mellonella Larven als in vivo Transkonjugationsmodell wurde eine Transkonjugationsfrequenz von nahezu 100% detektiert. Daher lässt sich vermuten, dass der HGT von Antibiotikaresistenzgenen im Darm eines Patienten eine sehr viel höhere Effizienz aufweisen könnte, als bisher basierend auf in vitro generierten Daten angenommen. Dies impliziert, dass die globale Verbreitung von OXA-48 auf dem effizienten horizontalen Gentransfers eines einzigen IncL Plasmids beruht und nicht auf der Expansion einer bestimmten klonalen Linie.