Therapeutics development against the Apicomplexa Parasites Plasmodium falciparum and Toxoplasma gondii

Apicomplexa parasites are the cause of two of the world’s most widespread diseases; malaria and toxoplasmosis. Malaria affects two billion people worldwide in some of the poorest regions of the world. Over a million people a year die from malaria, the majority of which are pregnant women or children under the age of 5. Plasmodium falciparum is by far the most lethal cause of malaria and is endemic to many regions of sub-Saharan Africa. Toxoplasma gondii is the most common parasitic infection of human brain and eyes and is suspected to affect one third of the world’s population. Rising drug resistance and the inadequacies of current treatments have spurred a global effort for the development of new therapies targeting these parasites Cytochrome bc1 (cyt. bc1) is a proven drug target for both treatment and prophylaxis of P. falciparum and T. gondii. Atovaquone, a potent broad- spectrum anti-parasitic drug, targets the Qo site, one of two active sites within cytochrome, b collapsing the mitochondrial membrane potential and killing the parasites. Single mutations within the Qo site render atovaquone ineffective and incidences of resistance are rising. Previous work has focussed on overcoming resistance through the design/redesign of compounds targeting the well understood Qo site. Here we show the binding modes of GSK’s next-generation antimalarial 4(1H)-pyridones and a novel 4(1H)-quinolone to the Qi site of cyt. bc1. These structures reveal the mechanism by which the compounds are able to overcome resistance and point in a new direction for antimalarial drug development. This work reaffirms the importance of structural observation in drug development. Merozoite surface protein 1–19 (MSP119) is an important target in vaccine development against malaria. Recent work has shown that cupredoxins bind MSP119 of P. falciparum and result in death for the parasite. Rusticyanin, the most potent of these, has been extensively studied and various mutants have been produced a range of redox potentials and acid stability properties. Here, initial studies of the complex between P. falciparum MSP119 and rusticyanin are carried out and analysed

Regularization Dependence of Running Couplings in Softly Broken Supersymmetry

We discuss the dependence of running couplings on the choice of regularization method in a general softly-broken N=1 supersymmetric theory. Regularization by dimensional reduction respects supersymmetry, but standard dimensional regularization does not. We find expressions for the differences between running couplings in the modified minimal subtraction schemes of these two regularization methods, to one loop order. We also find the two-loop renormalization group equations for gaugino masses in both schemes, and discuss the application of these results to the Minimal Supersymmetric Standard Model.Comment: 11 pages. v2: Signs of equations (1.2) and (4.2) are fixe

Machine learning models predict the primary sites of head and neck squamous cell carcinoma metastases based on DNA methylation

In head and neck squamous cell cancers (HNSCs) that present as metastases with an unknown primary (HNSC-CUPs), the identification of a primary tumor improves therapy options and increases patient survival. However, the currently available diagnostic methods are laborious and do not offer a sufficient detection rate. Predictive machine learning models based on DNA methylation profiles have recently emerged as a promising technique for tumor classification. We applied this technique to HNSC to develop a tool that can improve the diagnostic work-up for HNSC-CUPs. On a reference cohort of 405 primary HNSC samples, we developed four classifiers based on different machine learning models [random forest (RF), neural network (NN), elastic net penalized logistic regression (LOGREG), and support vector machine (SVM)] that predict the primary site of HNSC tumors from their DNA methylation profile. The classifiers achieved high classification accuracies (RF = 83%, NN = 88%, LOGREG = SVM = 89%) on an independent cohort of 64 HNSC metastases. Further, the NN, LOGREG, and SVM models significantly outperformed p16 status as a marker for an origin in the oropharynx. In conclusion, the DNA methylation profiles of HNSC metastases are characteristic for their primary sites, and the classifiers developed in this study, which are made available to the scientific community, can provide valuable information to guide the diagnostic work-up of HNSC-CUP. (c) 2021 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland

Inositol 1,4,5-trisphosphate supports the arrhythmogenic action of endothelin-1 on ventricular cardiac myocytes

Although ventricular cardiomyocytes express inositol 1,4,5-trisphosphate [Ins(1,4,5)Ρ3] receptors, it is unclear how these Ca2+ channels contribute to the effects of Gq-coupled agonists. Endothelin-1 augmented the amplitude of pacing-evoked Ca2+ signals (positive inotropy), and caused an increasing frequency of spontaneous diastolic Ca2+-release transients. Both effects of endothelin-1 were blocked by an antagonist of phospholipase C, suggesting that Ins(1,4,5)Ρ3 and/or diacylglycerol production was necessary. The endothelin-1-mediated spontaneous Ca2+ transients were abolished by application of 2-aminoethoxydiphenyl borate (2-APB), an antagonist of Ins(1,4,5)Ρ3 receptors. Incubation of electrically-paced ventricular myocytes with a membrane-permeant Ins(1,4,5)Ρ3 ester provoked the occurrence of spontaneous diastolic Ca2+ transients with the same characteristics and sensitivity to 2-APB as the events stimulated by endothelin-1. In addition to evoking spontaneous Ca2+ transients, stimulation of ventricular myocytes with the Ins(1,4,5)Ρ3 ester caused a positive inotropic effect. The effects of endothelin-1 were compared with two other stimuli, isoproterenol and digoxin, which are known to induce inotropy and spontaneous Ca2+ transients by overloading intracellular Ca2+ stores. The events evoked by isoproterenol and digoxin were dissimilar from those triggered by endothelin-1 in several ways. We propose that Ins(1,4,5)Ρ3 receptors support the development of both inotropy and spontaneous pro-arrhythmic Ca2+ signals in ventricular myocytes stimulated with a Gq-coupled agonist

On the Yang-Mills two-loop effective action with wordline methods

We derive the two-loop effective action for covariantly constant field strength of pure Yang-Mills theory in the presence of an infrared scale. The computation is done in the framework of the worldline formalism, based on a generalization procedure of constructing multiloop effective actions in terms of the bosonic worldline path integral. The two-loop beta-function is correctly reproduced. This is the first derivation in the worldline formulation, and serves as a nontrivial check on the consistency of the multiloop generalization procedure in the worldline formalism.Comment: 8 pages, 4 figure

Decoupling of the ϵ\epsilon-scalar mass in softly broken supersymmetry

It has been shown recently that the introduction of an unphysical $\epsilon$-scalar mass $\tilde{m}$ is necessary for the proper renormalization of softly broken supersymmetric theories by dimensional reduction (\drbar). In these theories, both the two-loop $\beta$-functions of the scalar masses and their one-loop finite corrections depend on $\tilde{m}^2$. We find, however, that the dependence on $\tilde{m}^2$ can be completely removed by slightly modifying the \drbar renormalization scheme. We also show that previous \drbar calculations of one-loop corrections in supersymmetry which ignored the $\tilde{m}^2$ contribution correspond to using this modified scheme.Comment: 7 pages, LTH-336, NUB-3094-94TH, KEK-TH-40

Phase 1b/2a study of galunisertib, a small molecule inhibitor of transforming growth factor-beta receptor I, in combination with standard temozolomide-based radiochemotherapy in patients with newly diagnosed malignant glioma

Altres ajuts: This trial was funded by Eli Lilly and Company.The online version of this article contains supplementary material, which is available to authorized users

Trapping of a polyketide synthase module after C−C bond formation reveals transient acyl carrier domain interactions

Modular polyketide synthases (PKSs) are giant assembly lines that produce an impressive range of biologically active compounds. However, our understanding of the structural dynamics of these megasynthases, specifically the delivery of acyl carrier protein (ACP)‐bound building blocks to the catalytic site of the ketosynthase (KS) domain, remains severely limited. Using a multipronged structural approach, we report details of the inter‐domain interactions after C−C bond formation in a chain‐branching module of the rhizoxin PKS. Mechanism‐based crosslinking of an engineered module was achieved using a synthetic substrate surrogate that serves as a Michael acceptor. The crosslinked protein allowed us to identify an asymmetric state of the dimeric protein complex upon C−C bond formation by cryo‐electron microscopy (cryo‐EM). The possible existence of two ACP binding sites, one of them a potential “parking position” for substrate loading, was also indicated by AlphaFold2 predictions. NMR spectroscopy showed that a transient complex is formed in solution, independent of the linker domains, and photochemical crosslinking/mass spectrometry of the standalone domains allowed us to pinpoint the interdomain interaction sites. The structural insights into a branching PKS module arrested after C−C bond formation allows a better understanding of domain dynamics and provides valuable information for the rational design of modular assembly lines

Mucosal melanomas of different anatomic sites share a common global DNA methylation profile with cutaneous melanoma but show location-dependent patterns of genetic and epigenetic alterations

Cutaneous, ocular, and mucosal melanomas are histologically indistinguishable tumors that are driven by a different spectrum of genetic alterations. With current methods, identification of the site of origin of a melanoma metastasis is challenging. DNA methylation profiling has shown promise for the identification of the site of tumor origin in various settings. Here we explore the DNA methylation landscape of melanomas from different sites and analyze if different melanoma origins can be distinguished by their epigenetic profile. We performed DNA methylation analysis, next generation DNA panel sequencing, and copy number analysis of 82 non-cutaneous and 25 cutaneous melanoma samples. We further analyzed eight normal melanocyte cell culture preparations. DNA methylation analysis separated uveal melanomas from melanomas of other primary sites. Mucosal, conjunctival, and cutaneous melanomas shared a common global DNA methylation profile. Still, we observed location-dependent DNA methylation differences in cancer-related genes, such as low frequencies of RARB (7/63) and CDKN2A promoter methylation (6/63) in mucosal melanomas, or a high frequency of APC promoter methylation in conjunctival melanomas (6/9). Furthermore, all investigated melanomas of the paranasal sinus showed loss of PTEN expression (9/9), mainly caused by promoter methylation. This was less frequently seen in melanomas of other sites (24/98). Copy number analysis revealed recurrent amplifications in mucosal melanomas, including chromosomes 4q, 5p, 11q and 12q. Most melanomas of the oral cavity showed gains of chromosome 5p with TERT amplification (8/10), while 11q amplifications were enriched in melanomas of the nasal cavity (7/16). In summary, mucosal, conjunctival, and cutaneous melanomas show a surprisingly similar global DNA methylation profile and identification of the site of origin by DNA methylation testing is likely not feasible. Still, our study demonstrates tumor location-dependent differences of promoter methylation frequencies in specific cancer-related genes together with tumor site-specific enrichment for specific chromosomal changes and genetic mutations. (c) 2021 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland

DNA methylation signature is prognostic of choroid plexus tumor aggressiveness

Abstract: Background: Histological grading of choroid plexus tumors (CPTs) remains the best prognostic tool to distinguish between aggressive choroid plexus carcinoma (CPC) and the more benign choroid plexus papilloma (CPP) or atypical choroid plexus papilloma (aCPP); however, these distinctions can be challenging. Standard treatment of CPC is very aggressive and often leads to severe damage to the young child’s brain. Therefore, it is crucial to distinguish between CPC and less aggressive entities (CPP or aCPP) to avoid unnecessary exposure of the young patient to neurotoxic therapy. To better stratify CPTs, we utilized DNA methylation (DNAm) to identify prognostic epigenetic biomarkers for CPCs. Methods: We obtained DNA methylation profiles of 34 CPTs using the HumanMethylation450 BeadChip from Illumina, and the data was analyzed using the Illumina Genome Studio analysis software. Validation of differentially methylated CpG sites chosen as biomarkers was performed using pyrosequencing analysis on additional 22 CPTs. Sensitivity testing of the CPC DNAm signature was performed on a replication cohort of 61 CPT tumors obtained from Neuropathology, University Hospital Münster, Germany. Results: Generated genome-wide DNAm profiles of CPTs showed significant differences in DNAm between CPCs and the CPPs or aCPPs. The prediction of clinical outcome could be improved by combining the DNAm profile with the mutational status of TP53. CPCs with homozygous TP53 mutations clustered as a group separate from those carrying a heterozygous TP53 mutation or CPCs with wild type TP53 (TP53-wt) and showed the worst survival outcome. Specific DNAm signatures for CPCs revealed AK1, PER2, and PLSCR4 as potential biomarkers for CPC that can be used to improve molecular stratification for diagnosis and treatment. Conclusions: We demonstrate that combining specific DNAm signature for CPCs with histological approaches better differentiate aggressive tumors from those that are not life threatening. These findings have important implications for future prognostic risk prediction in clinical disease management