Super-enhancer hypermutation alters oncogene expression in B cell lymphoma.

Diffuse large B cell lymphoma (DLBCL) is the most common B cell non-Hodgkin lymphoma and remains incurable in around 40% of patients. Efforts to sequence the coding genome identified several genes and pathways that are altered in this disease, including potential therapeutic targets1-5. However, the non-coding genome of DLBCL remains largely unexplored. Here we show that active super-enhancers are highly and specifically hypermutated in 92% of samples from individuals with DLBCL, display signatures of activation-induced cytidine deaminase activity, and are linked to genes that encode B cell developmental regulators and oncogenes. As evidence of oncogenic relevance, we show that the hypermutated super-enhancers linked to the BCL6, BCL2 and CXCR4 proto-oncogenes prevent the binding and transcriptional downregulation of the corresponding target gene by transcriptional repressors, including BLIMP1 (targeting BCL6) and the steroid receptor NR3C1 (targeting BCL2 and CXCR4). Genetic correction of selected mutations restored repressor DNA binding, downregulated target gene expression and led to the counter-selection of cells containing corrected alleles, indicating an oncogenic dependency on the super-enhancer mutations. This pervasive super-enhancer mutational mechanism reveals a major set of genetic lesions deregulating gene expression, which expands the involvement of known oncogenes in DLBCL pathogenesis and identifies new deregulated gene targets of therapeutic relevance.

Iron-Catalysed Carbene Transfer to Isocyanides as a Platform for Heterocycle Synthesis.

An iron-catalysed carbene transfer reaction of diazo compounds to isocyanides has been developed. The resulting ketenimines are trapped in situ with various bisnucleophiles to access a range of densely functionalized heterocycles (pyrimidinones, dihydropyrazolones, 1H-tetrazoles) in a one-pot process. The electron-rich Hieber anion ([Fe(CO)3 NO]- ) facilitates efficient catalytic carbene transfer from acceptor-type α-diazo carbonyl compounds to isocyanides, providing a cost-efficient and benign alternative to similar noble metal-catalysed processes. Based on DFT calculations a plausible reaction mechanism for activation of the α-diazo carbonyl carbene precursor and ketenimine formation is provided.

Catch Recognition in Automated American Football Training Using Machine Learning.

In order to train receivers in American football in a targeted and individual manner, the strengths and weaknesses of the athletes must be evaluated precisely. As human resources are limited, it is beneficial to do it in an automated way. Automated passing machines are already given, therefore the motivation is to design a computer-based system that records and automatically evaluates the athlete's catch attempts. The most fundamental evaluation would be whether the athlete has caught the pass successfully or not. An experiment was carried out to gain data about catch attempts that potentially contain information about the outcome of such. The experiment used a fully automated passing machine which can release passes on command. After a pass was released, an audio and a video sequence of the specific catch attempt was recorded. For this purpose, an audio-visual recording system was developed which was integrated into the passing machine. This system is used to create an audio and video dataset in the amount of 2276 recorded catch attempts. A Convolutional Neural Network (CNN) is used for feature extraction with downstream Long Short-Term Memory (LSTM) to classify the video data. Classification of the audio data is performed using a one-dimensional CNN. With the chosen neural network architecture, an accuracy of 92.19% was achieved in detecting whether a pass had been caught or not. The feasibility for automatic classification of catch attempts during automated catch training is confirmed with this result.

How Solvation Influences the SN2 versus E2 Competition.

We have quantum chemically investigated how solvation influences the competition between the SN2 and E2 pathways of the model F- + C2H5Cl reaction. The system is solvated in a stepwise manner by going from the gas phase, then via microsolvation of one to three explicit solvent molecules, then last to bulk solvation using relativistic density functional theory at (COSMO)-ZORA-OLYP/QZ4P. We explain how and why the mechanistic pathway of the system shifts from E2 in the gas phase to SN2 upon strong solvation of the Lewis base (i.e., nucleophile/protophile). The E2 pathway is preferred under weak solvation of the system by dichloromethane, whereas a switch in reactivity from E2 to SN2 is observed under strong solvation by water. Our activation strain and Kohn-Sham molecular orbital analyses reveal that solvation of the Lewis base has a significant impact on the strength of the Lewis base. We show how strong solvation furnishes a weaker Lewis base that is unable to overcome the high characteristic distortivity associated with the E2 pathway, and thus the SN2 pathway becomes viable.

Cadence Detection in Road Cycling Using Saddle Tube Motion and Machine Learning.

Most commercial cadence-measurement systems in road cycling are strictly limited in their function to the measurement of cadence. Other relevant signals, such as roll angle, inclination or a round kick evaluation, cannot be measured with them. This work proposes an alternative cadence-measurement system with less of the mentioned restrictions, without the need for distinct cadence-measurement apparatus attached to the pedal and shaft of the road bicycle. The proposed design applies an inertial measurement unit (IMU) to the seating pole of the bike. In an experiment, the motion data were gathered. A total of four different road cyclists participated in this study to collect different datasets for neural network training and evaluation. In total, over 10 h of road cycling data were recorded and used to train the neural network. The network's aim was to detect each revolution of the crank within the data. The evaluation of the data has shown that using pure accelerometer data from all three axes led to the best result in combination with the proposed network architecture. A working proof of concept was achieved with an accuracy of approximately 95% on test data. As the proof of concept can also be seen as a new method for measuring cadence, the method was compared with the ground truth. Comparing the ground truth and the predicted cadence, it can be stated that for the relevant range of 50 rpm and above, the prediction over-predicts the cadence with approximately 0.9 rpm with a standard deviation of 2.05 rpm. The results indicate that the proposed design is fully functioning and can be seen as an alternative method to detect the cadence of a road cyclist.

A twofold tale of one mind: revisiting REC's multi-storey story.

The Radical Enactive/Embodied view of Cognition, or REC, claims that all cognition is a matter of skilled performance. Yet REC also makes a distinction between basic and content-involving cognition, arguing that the development of basic to content-involving cognition involves a kink. It might seem that this distinction leads to problematic gaps in REC's story. We address two such alleged gaps in this paper. First, we identify and reply to the concern that REC leads to an "interface problem", according to which REC has to account for the interaction of two minds co-present in the same cognitive activity. We emphasise how REC's view of content-involving cognition in terms of activities that require particular sociocultural practices can resolve these interface concerns. The second potential problematic gap is that REC creates an unjustified difference in kind between animal and human cognition. In response, we clarify and further explicate REC's notion of content, and argue that this notion allows REC to justifiably mark the distinction between basic and content-involving cognition as a difference in kind. We conclude by pointing out in what sense basic and content-involving cognitive activities are the same, yet different. They are the same because they are all forms of skilled performance, yet different as some forms of skilled performance are genuinely different from other forms.

Heterotrimeric Gα12/13 proteins in kidney injury and disease.

Gα12 and Gα13 are ubiquitous members of the heterotrimeric guanine nucleotide-binding protein (G protein) family that play central and integrative roles in the regulation of signal transduction cascades within various cell types in the kidney. Gα12/Gα13 proteins enable the kidney to adapt to an ever-changing environment by transducing stimuli from cell surface receptors and accessory proteins to effector systems. Therefore, perturbations in Gα12/Gα13 levels or their activity can contribute to the pathogenesis of various renal diseases, including renal cancer. This review will highlight and discuss the complex and expanding roles of Gα12/Gα13 proteins on distinct renal pathologies, with emphasis on more recently reported findings. Deciphering how the different Gα12/Gα13 interaction networks participate in the onset and development of renal diseases may lead to the discovery of new therapeutic strategies.

Hepatocyte Nuclear Factor 4-Alpha Is Essential for the Active Epigenetic State at Enhancers in Mouse Liver.

Cell-fate determination is influenced by interactions between master transcription factors (TFs) and cis-regulatory elements. Hepatocyte nuclear factor 4 alpha (HNF4A), a liver-enriched TF, acts as a master controller in specification of hepatic progenitor cells by regulating a network of TFs to control onset of hepatocyte cell fate. Using analysis of genome-wide histone modifications, DNA methylation, and hydroxymethylation in mouse hepatocytes, we show that HNF4A occupies active enhancers in hepatocytes and is essential for active histone and DNA signatures, especially acetylation of lysine 27 of histone 3 (H3K27ac) and 5-hydroxymethylcytosine (5hmC). In mice lacking HNF4A protein in hepatocytes, we observed a decrease in both H3K27ac and hydroxymethylation at regions bound by HNF4A. Mechanistically, HNF4A-associated hydroxymethylation (5hmC) requires its interaction with ten-eleven translocation methylcytosine dioxygenase 3 (TET3), a protein responsible for oxidation from 5mC to 5hmC. Furthermore, HNF4A regulates TET3 expression in liver by directly binding to an enhancer region. Conclusion: In conclusion, we identified that HNF4A is required for the active epigenetic state at enhancers that amplifies transcription of genes in hepatocytes.

Social hierarchy is established and maintained with distinct acts of aggression in male Drosophilamelanogaster.

Social interactions pivot on an animal's experiences, internal states and feedback from others. This complexity drives the need for precise descriptions of behavior to dissect the fine detail of its genetic and neural circuit bases. In laboratory assays, male Drosophila melanogaster reliably exhibit aggression, and its extent is generally measured by scoring lunges, a feature of aggression in which one male quickly thrusts onto his opponent. Here, we introduce an explicit approach to identify both the onset and reversals in hierarchical status between opponents and observe that distinct aggressive acts reproducibly precede, concur or follow the establishment of dominance. We find that lunges are insufficient for establishing dominance. Rather, lunges appear to reflect the dominant state of a male and help in maintaining his social status. Lastly, we characterize the recurring and escalating structure of aggression that emerges through subsequent reversals in dominance. Collectively, this work provides a framework for studying the complexity of agonistic interactions in male flies, enabling its neurogenetic basis to be understood with precision.

mTOR inhibition by metformin impacts monosodium urate crystal-induced inflammation and cell death in gout: a prelude to a new add-on therapy?

OBJECTIVE: Gout is the most common inflammatory arthritis worldwide, and patients experience a heavy burden of cardiovascular and metabolic diseases. The inflammation is caused by the deposition of monosodium urate (MSU) crystals in tissues, especially in the joints, triggering immune cells to mount an inflammatory reaction. Recently, it was shown that MSU crystals can induce mechanistic target of rapamycin (mTOR) signalling in monocytes encountering these crystals in vitro. The mTOR pathway is strongly implicated in cardiovascular and metabolic disease. We hypothesised that inhibiting this pathway in gout might be a novel avenue of treatment in these patients, targeting both inflammation and comorbidities. METHODS: We used a translational approach starting from ex vivo to in vitro and back to in vivo. RESULTS: We show that ex vivo immune cells from patients with gout exhibit higher expression of the mTOR pathway, which we can mimic in vitro by stimulating healthy immune cells (B lymphocytes, monocytes, T lymphocytes) with MSU crystals. Monocytes are the most prominent mTOR expressers. By using live imaging, we demonstrate that monocytes, on encountering MSU crystals, initiate cell death and release a wide array of proinflammatory cytokines. By inhibiting mTOR signalling with metformin or rapamycin, a reduction of cell death and release of inflammatory mediators was observed. Consistent with this, we show that patients with gout who are treated with the mTOR inhibitor metformin have a lower frequency of gout attacks. CONCLUSIONS: We propose mTOR inhibition as a novel therapeutic target of interest in gout treatment.

B-cells and schizophrenia: A promising link or a finding lost in translation?

Recent genetic studies have suggested a potential role for B-cells in the pathogenesis of schizophrenia. Greater insight in the functioning of B-cells in patients with schizophrenia is therefore of importance. In this narrative review we aim to give an overview of the current literature on B-cells and schizophrenia. We found no evidence for altered numbers of these cells in blood. We did find support for increased levels of B-cell related cytokines and certain autoantibodies. Studies on B-cell development and function, or their numbers in cerebrospinal fluid or brain tissue are very limited. Based on the available data we appraise whether various B-cell mediated pathological mechanisms are likely to play a role in schizophrenia and provide directions for future research.

An eco-evolutionary feedback loop between population dynamics and fighter expression affects the evolution of alternative reproductive tactics.

Surprisingly, little is known about how eco-evolutionary feedback loops affect trait dynamics within a single population. Polymorphisms of discrete alternative phenotypes present ideal test beds to investigate this, as the alternative phenotypes typically exhibit contrasting demographic rates mediated through frequency or density dependence, and are thus differentially affected by selection. Alternative reproductive tactics (ARTs), like male fighters and sneakers, are an extreme form of discrete phenotype expression and occur across many taxa. Fighters possess weapons for male-male competition over access to mates, whereas sneakers are defenceless but adopt tactics like female-mimicking. Because fighters in some species mortally injure conspecifics, this raises the question whether fighter expression can feed back to affect population size and structure, thereby altering the selection gradient and evolutionary dynamics of ART expression in an eco-evolutionary feedback loop. Here, we investigated how the eco-evolutionary feedback loop between fighter expression and population size and structure affects the evolution and maintenance of ARTs. We introduced intraspecific killing by fighters in a two-sex, two-ART population model parameterized for the male dimorphic bulb mite (Rhizoglyphus robini) that includes life-history differences between the ARTs and a mating-probability matrix analogous to the classic hawk-dove game. Using adaptive dynamics, we found that the intraspecific killing by fighters can extend the range of life-history parameter values under which ARTs evolve, because fighters that kill other fighters decrease fighter fitness. This effect can be nullified when benefits from killing are incorporated, like increased reproduction through increased energy uptake. The eco-evolutionary feedback effects found here for a dimorphic trait likely also occur in other fitness-related traits, such as behavioural syndromes, parental care and niche construction traits. Current theoretical advances to model eco-evolutionary processes, and empirical steps towards unravelling the underlying drivers, pave the way for understanding how selection affects trait evolution in an eco-evolutionary feedback loop.

Infection Risk Following Common Femoral Artery Endarterectomy Versus a Hybrid Procedure.

BACKGROUND: Hybrid revascularization combines open lower extremity surgery and endovascular procedures to simultaneously treat atherosclerotic lesions on multiple levels in patients with peripheral arterial occlusive disease (PAD). Hybrid surgery appears to be a safe strategy for multilevel stenosis revascularization, though the risk of surgical site infection (SSI) has not been clearly investigated. This study evaluates the development of SSI following common femoral artery endarterectomy (CFE) and hybrid revascularization procedures. METHODS: A retrospective study was performed including all patients undergoing CFE, as standalone or as part of a hybrid procedure, due to PAD between January 2013 and December 2016. Preoperative, intraoperative, clinical, and follow-up information was gathered prospectively and reviewed retrospectively. The presence of SSI was recorded based on criteria of the Centre for Disease Control. RESULTS: A total of 229 CFEs were performed. One hundred thirty-two as a standalone procedure, 65 combined with iliofemoral angioplasty, and 32 combined with peripheral angioplasty. Nineteen patients (8.3%) developed an SSI, of which 4 were deep infections. Ten infections (7.6%) occurred in the CFE-only group, 5 (7.7%) in the iliofemoral hybrid group, and 4 (12.5%) in the peripheral hybrid group (P = 0.65). Five patients (2.1%) required surgery to control the infection. The mean duration of stay was 5 days for patients without SSI versus 20 days for patients who developed an SSI (P < 0.0001). CONCLUSIONS: The hybrid procedure combining open femoral endarterectomy with endovascular revascularization is a safe procedure with no significant differences in infection rates between open surgery, central, or peripheral hybrid revascularization.

The MUC1 mucin protects against Helicobacter pylori pathogenesis in mice by regulation of the NLRP3 inflammasome.

OBJECTIVES: The mucin MUC1, best known for providing an epithelial barrier, is an important protective host factor in both humans and mice during Helicobacter pylori pathogenesis. This study aimed to identify the long-term consequences of MUC1 deficiency on H. pylori pathogenesis and the mechanism by which MUC1 protects against H. pylori gastritis. DESIGN: Wildtype and Muc1(-/-) mice were infected for up to 9 months, and the gastric pathology, immunological response and epigenetic changes assessed. The effects of MUC1 on the inflammasome, a potent inflammatory pathway, were examined in macrophages and H. pylori-infected mice deficient in both MUC1 and inflammasome components. RESULTS: Muc1(-/-) mice began to die 6 months after challenge, indicating Muc1 deficiency made H. pylori a lethal infection. Surprisingly, chimaeric mouse infections revealed MUC1 expression by haematopoietic-derived immune cells limits H. pylori-induced gastritis. Gastritis in infected Muc1(-/-) mice was associated with elevated interleukin (IL)-1ß and epigenetic changes in their gastric mucosa similar to those in transgenic mice overexpressing gastric IL-1ß, implicating MUC1 regulation of an inflammasome. In support of this, infected Muc1(-/-)Casp1(-/-) mice did not develop severe gastritis. Further, MUC1 regulated Nlrp3 expression via an nuclear factor (NF)-κB-dependent pathway and reduced NF-κB pathway activation via inhibition of IRAK4 phosphorylation. The importance of this regulation was proven using Muc1(-/-)Nlrp3(-/-) mice, which did not develop severe gastritis. CONCLUSIONS: MUC1 is an important, previously unidentified negative regulator of the NLRP3 inflammasome. H. pylori activation of the NLRP3 inflammasome is normally tightly regulated by MUC1, and loss of this critical regulation results in the development of severe pathology.

High-resolution mapping of epitopes on the C2 domain of factor VIII by analysis of point mutants using surface plasmon resonance.

Neutralizing anti-factor VIII (FVIII) antibodies that develop in patients with hemophilia A and in murine hemophilia A models, clinically termed "inhibitors," bind to several distinct surfaces on the FVIII-C2 domain. To map these epitopes at high resolution, 60 recombinant FVIII-C2 proteins were generated, each having a single surface-exposed residue mutated to alanine or a conservative substitution. The binding kinetics of these muteins to 11 monoclonal, inhibitory anti-FVIII-C2 antibodies were evaluated by surface plasmon resonance and the results compared with those obtained for wild-type FVIII-C2. Clusters of residues with significantly altered binding kinetics identified "functional" B-cell epitopes, defined as those residues contributing appreciable antigen-antibody avidity. These antibodies were previously shown to neutralize FVIII activity by interfering with proteolytic activation of FVIII by thrombin or factor Xa, or with its binding to phospholipid surfaces, von Willebrand factor, or other components of the intrinsic tenase complex. Fine mapping of epitopes by surface plasmon resonance also indicated surfaces through which FVIII interacts with proteins and phospholipids as it participates in coagulation. Mutations that significantly altered the dissociation times/half-lives identified functionally important interactions within antigen-antibody interfaces and suggested specific sequence modifications to generate novel, less antigenic FVIII proteins with possible therapeutic potential for treatment of inhibitor patients.

Expression of ERAP2 and LST1 is increased before start of therapy in rheumatoid arthritis patients with good clinical response to glucocorticoids.

OBJECTIVES: Glucocorticoids (GC) remain a cornerstone of rheumatoid arthritis (RA) therapy, although a third of patients do not respond adequately. In order to find potential predictors for clinical response, the gene expression profile of CD4+T-cells as important players in the pathogenesis of RA was analysed before pulse therapy with 1000 mg methylprednisolone. METHODS: Patients were treated with 3x1000 mg methylprednisolone in 5 days; hereafter response was determined by the European League Against Rheumatism (EULAR) response criteria. Before start of treatment, CD4+T-cells (and CD14+monocytes) were separated by MACS sorting. Labelled cRNA from CD4+T-cells from 5 responders and 5 non-responders was hybridised to Agilent 4x44K microarray chips and differentially expressed genes were identified via mixed-model analysis of variance based on permutation-based false discovery rates. Selected genes were validated by quantitative real-time PCR (qPCR). RESULTS: Four genes were significantly increased in CD4+T-cells of GC-responders; expression of ERAP2 (endoplasmic reticulum aminopeptidase 2), LST1 (leucocyte-specific transcript 1) and FAM26F (Family With Sequence Similarity 26, Member F) was confirmed by quantitative PCR (qPCR); their expression was inversely correlated with DAS28 at day 5 (LST1 and FAM26F p<0.05; ERAP2: p=0.07). Elevated expression of ERAP2 was also detected by qPCR in CD14+monocytes and after 24 hours in both cell types (all p<0.02). CONCLUSIONS: The increased expression of ERAP2, LST1 and FAM26F in GC-responders before therapy warrants further investigation into their role as potential predictors for the response to GC, and in the inflammatory process of RA.

A systemic sclerosis and systemic lupus erythematosus pan-meta-GWAS reveals new shared susceptibility loci.

Systemic sclerosis (SSc) and systemic lupus erythematosus (SLE) are two archetypal systemic autoimmune diseases which have been shown to share multiple genetic susceptibility loci. In order to gain insight into the genetic basis of these diseases, we performed a pan-meta-analysis of two genome-wide association studies (GWASs) together with a replication stage including additional SSc and SLE cohorts. This increased the sample size to a total of 21,109 (6835 cases and 14,274 controls). We selected for replication 19 SNPs from the GWAS data. We were able to validate KIAA0319L (P = 3.31 × 10(-11), OR = 1.49) as novel susceptibility loci for SSc and SLE. Furthermore, we also determined that the previously described SLE susceptibility loci PXK (P = 3.27 × 10(-11), OR = 1.20) and JAZF1 (P = 1.11 × 10(-8), OR = 1.13) are shared with SSc. Supporting these new discoveries, we observed that KIAA0319L was overexpressed in peripheral blood cells of SSc and SLE patients compared with healthy controls. With these, we add three (KIAA0319L, PXK and JAZF1) and one (KIAA0319L) new susceptibility loci for SSc and SLE, respectively, increasing significantly the knowledge of the genetic basis of autoimmunity.

Highly Selective Relaxation of the OH Stretching Overtones in Isolated HDO Molecules Observed by Infrared Pump-Repump-Probe Spectroscopy.

A quantitative investigation of the relaxation dynamics of higher-lying vibrational states is afforded by a novel method of infrared pump-repump-probe spectroscopy. The technique is used to study the dynamics of OH stretching overtones in NaClO4·HDO monohydrate. We observe a continuous decrease of the energy separation for the first four states, i.e. v01 = 3575 cm(-1), v12 = 3370 cm(-1), and v23 = 3170 cm(-1), respectively. The population lifetime of the first excited state is 7.2 ps, while the one of the second excited state is largely reduced to 1.4 ps. The relaxation of the v = 2 state proceeds nearly quantitatively to the v = 1 state. The new information on the OH stretching overtones demands improved theoretical potentials and modeling of the H bond interactions. This work shows the potential of the new technique for the precise study of complex vibrational relaxation pathways.

Crystal and NMR structures of a Trp-cage mini-protein benchmark for computational fold prediction.

To provide high-resolution X-ray crystallographic structures of a peptide with the Trp-cage fold, we prepared a cyclized version of this motif. Cyclized Trp-cage is remarkably stable and afforded two crystal forms suitable for X-ray diffraction. The resulting higher resolution crystal structures validate the prior NMR models and provide explanations for experimental observations that could not be rationalized by NMR structural data, including the structural basis for the increase in fold stability associated with motif cyclization and the manner in which a polar serine side chain is accommodated in the hydrophobic interior. A hexameric oligomer of the cyclic peptide is found in both crystal forms and indicates that under appropriate conditions, this minimized system may also serve as a model for protein-protein interactions.