β-Lactamases are enzymes that can break down β-lactam substrates, such as antibiotics, preventing the use of these antibiotics for the treatment of various infectious diseases. However, some... Show moreβ-Lactamases are enzymes that can break down β-lactam substrates, such as antibiotics, preventing the use of these antibiotics for the treatment of various infectious diseases. However, some compounds, β-lactamase inhibitors, can block these enzymes allowing for possible treatments using a combination of antibiotic and inhibitor. BlaC is the β-lactamase of Mycobacterium tuberculosis, the bacteria that cause tuberculosis, and is used as a model for protein evolution. To understand if and how BlaC can develop resistance against certain inhibitors we studied the evolutionary adaptability of this enzyme. We used laboratory evolution and various biochemical techniques to characterize several mutations in BlaC and subsequently tested the effect of combining mutations. One of the findings is that BlaC can easily become less sensitive to the inhibitor sulbactam by partially blocking the entrance to the active site. Interestingly, this was accompanied by increased sensitivity to another inhibitor, avibactam, that could not be compensated for by other mutations.Generally, Escherichia coli bacteria are used to test the effects of BlaC variants in cells, as they are easy and safe to use in the lab. We show that results obtained for E. coli can be extrapolated to conditions that resemble tuberculosis disease in humans: the M. marinum infection model of zebrafish. All these findings are of interest for the future development of combination therapies to treat tuberculosis. Show less
Hollander, L.S. den; Béquignon, O.J.M.; Wang, X.; Wezel, K. van; Broekhuis, J.; Gorostiola González, M.; ... ; Heitman, L.H. 2022
CC chemokine receptor 2 (CCR2), a G protein-coupled receptor, plays a role in many cancer-related processes such as metastasis formation and immunosuppression. Since ∼ 20 % of human cancers contain... Show moreCC chemokine receptor 2 (CCR2), a G protein-coupled receptor, plays a role in many cancer-related processes such as metastasis formation and immunosuppression. Since ∼ 20 % of human cancers contain mutations in G protein-coupled receptors, ten cancer-associated CCR2 mutants obtained from the Genome Data Commons were investigated for their effect on receptor functionality and antagonist binding. Mutations were selected based on either their vicinity to CCR2's orthosteric or allosteric binding sites or their presence in conserved amino acid motifs. One of the mutant receptors, namely S101P2.63 with a mutation near the orthosteric binding site, did not express on the cell surface. All other studied mutants showed a decrease in or a lack of G protein activation in response to the main endogenous CCR2 ligand CCL2, but no change in potency was observed. Furthermore, INCB3344 and LUF7482 were chosen as representative orthosteric and allosteric antagonists, respectively. No change in potency was observed in a functional assay, but mutations located at F1163.28 impacted orthosteric antagonist binding significantly, while allosteric antagonist binding was abolished for L134Q3.46 and D137N3.49 mutants. As CC chemokine receptor 2 is an attractive drug target in cancer, the negative effect of these mutations on receptor functionality and drugability should be considered in the drug discovery process. Show less
G protein-coupled receptors (GPCRs), one of the largest families of membrane proteins, are responsive to a diverse set of physiological endogenous ligands including hormones and neurotransmitters.... Show moreG protein-coupled receptors (GPCRs), one of the largest families of membrane proteins, are responsive to a diverse set of physiological endogenous ligands including hormones and neurotransmitters. Due to the various GPCR ligand binding domains present on GPCRs and their sensitivities to a diverse array of ligands, these proteins have shown to be very ‘druggable’ as they are the main target for an estimated 30% of approved drugs. A growing body of evidence shows a prominent role of GPCRs in all phases of cancer with a mutation frequency of approximately 20% in all cancers. Mutations occurring in GPCRs can severely alter their normal function and may ultimately convert their physiological and pathological roles. One particular class of rhodopsin-like GPCRs included in this thesis are the adenosine receptors (ARs). Due to the accumulation of adenosine in the tumor microenvironment, all four subtypes of ARs might be targets for the development of novel approaches for the treatment of cancer. For each of the four subtypes, a number of somatic mutations have been identified in patient isolates. In this thesis, we examined them on receptor activation and ligand binding using reference adenosine receptor ligands, and determined the impact mutations have on these pharmacological readouts. Show less
Noortman, W.A.; Vriens, D.; Geus-Oei, L.F. de; Slump, C.H.; Aarntzen, E.H.; Berkel, A. van; ... ; Velden, F.H.P. van 2022
Objectives: Based on germline and somatic mutation profiles, pheochromocytomas and paragangliomas (PPGLs) can be classified into different clusters. We investigated the use of [F-18]FDG-PET/CT... Show moreObjectives: Based on germline and somatic mutation profiles, pheochromocytomas and paragangliomas (PPGLs) can be classified into different clusters. We investigated the use of [F-18]FDG-PET/CT radiomics, SUVmax and biochemical profile for the identification of the genetic clusters of PPGLs. Methods: In this single-centre cohort, 40 PPGLs (13 cluster 1, 18 cluster 2, 9 sporadic) were delineated using a 41% adaptive threshold of SUVpeak ([F-18]FDG-PET) and manually (low-dose CT; ldCT). Using PyRadiomics, 211 radiomic features were extracted. Stratified 5-fold cross-validation for the identification of the genetic cluster was performed using multinomial logistic regression with dimensionality reduction incorporated per fold. Classification performances of biochemistry, SUVmax and PET(/CT) radiomic models were compared and presented as mean (multiclass) test AUCs over the five folds. Results were validated using a sham experiment, randomly shuffling the outcome labels. Results: The model with biochemistry only could identify the genetic cluster (multiclass AUC 0.60). The three-factor PET model had the best classification performance (multiclass AUC 0.88). A simplified model with only SUVmax performed almost similarly. Addition of ldCT features and biochemistry decreased the classification performances. All sham AUCs were approximately 0.50. Conclusion: PET radiomics achieves a better identification of PPGLs compared to biochemistry, SUVmax, ldCT radiomics and combined approaches, especially for the differentiation of sporadic PPGLs. Nevertheless, a model with SUVmax alone might be preferred clinically, weighing model performances against laborious radiomic analysis. The limited added value of radiomics to the overall classification performance for PPGL should be validated in a larger external cohort. Show less
Overexpression of the adenosine A1 receptor (A1AR) has been detected in various cancer cell lines. However, the role of A1AR in tumor development is still unclear. Thirteen A1AR mutations were... Show moreOverexpression of the adenosine A1 receptor (A1AR) has been detected in various cancer cell lines. However, the role of A1AR in tumor development is still unclear. Thirteen A1AR mutations were identified in the Cancer Genome Atlas from cancer patient samples. We have investigated the pharmacology of the mutations located at the 7-transmembrane domain using a yeast system. Concentration-growth curves were obtained with the full agonist CPA and compared to the wild type hA1AR. H78L3.23 and S246T6.47 showed increased constitutive activity, while only the constitutive activity of S246T6.47 could be reduced to wild type levels by the inverse agonist DPCPX. Decreased constitutive activity was observed on five mutant receptors, among which A52V2.47 and W188C5.46 showed a diminished potency for CPA. Lastly, a complete loss of activation was observed in five mutant receptors. A selection of mutations was also investigated in a mammalian system, showing comparable effects on receptor activation as in the yeast system, except for residues pointing toward the membrane. Taken together, this study will enrich the view of the receptor structure and function of A1AR, enlightening the consequences of these mutations in cancer. Ultimately, this may provide an opportunity for precision medicine for cancer patients with pathological phenotypes involving these mutations. Show less
Boer, I. de; Terwindt, G.M.; Maagdenberg, A.M.J.M. van den 2020
Migraine is a common brain disorder with a large genetic component. Of the two main migraine types, migraine with aura and migraine without aura, the genetic underpinning in the former is least... Show moreMigraine is a common brain disorder with a large genetic component. Of the two main migraine types, migraine with aura and migraine without aura, the genetic underpinning in the former is least understood. Given the evidence from epidemiological studies in cohorts and families that the genetic contribution is highest in migraine with aura, this seems paradoxical. Various genetic approaches have been applied to identify genetic factors that confer risk for migraine. Initially, so-called candidate gene associations studies (CGAS) have been performed that test DNA variants in genes prioritized based on presumed a priori knowledge of migraine pathophysiology. More recently, genome-wide association studies (GWAS) tested variants in any gene in an hypothesis-free manner. Whereas GWAS in migraine without aura, or the more general diagnosis migraine have already identified dozens of gene variants, the specific hunt for gene variants in migraine with aura has been disappointing. The only GWAS specifically investigating migraine with aura yielded only one single associated single nucleotide polymorphism (SNP), near MTDH and PGCP, with genome-wide significance. However, interrogation of all genotyped SNPs, so beyond this one significant hit, was more successful and led to the notion that migraine with aura and migraine without aura are genetically more alike than different. Until now, most relevant genetic discoveries related to migraine with aura came from investigating monogenetic syndromes with migraine aura as a prominent phenotype (i.e. FHM, CADASIL and FASPS). This review will highlight the genetic findings relevant to migraine with aura. Show less
Background The effect of risk-reducing salpingo-oophorectomy (RRSO) on breast cancer risk for BRCA1 and BRCA2 mutation carriers is uncertain. Retrospective analyses have suggested a protective... Show moreBackground The effect of risk-reducing salpingo-oophorectomy (RRSO) on breast cancer risk for BRCA1 and BRCA2 mutation carriers is uncertain. Retrospective analyses have suggested a protective effect but may be substantially biased. Prospective studies have had limited power, particularly for BRCA2 mutation carriers. Further, previous studies have not considered the effect of RRSO in the context of natural menopause. Methods A multi-centre prospective cohort of 2272 BRCA1 and 1605 BRCA2 mutation carriers was followed for a mean of 5.4 and 4.9 years, respectively; 426 women developed incident breast cancer. RRSO was modelled as a time-dependent covariate in Cox regression, and its effect assessed in premenopausal and postmenopausal women. Results There was no association between RRSO and breast cancer for BRCA1 (HR = 1.23; 95% CI 0.94-1.61) or BRCA2 (HR = 0.88; 95% CI 0.62-1.24) mutation carriers. For BRCA2 mutation carriers, HRs were 0.68 (95% CI 0.40-1.15) and 1.07 (95% CI 0.69-1.64) for RRSO carried out before or after age 45 years, respectively. The HR for BRCA2 mutation carriers decreased with increasing time since RRSO (HR = 0.51; 95% CI 0.26-0.99 for 5 years or longer after RRSO). Estimates for premenopausal women were similar. Conclusion We found no evidence that RRSO reduces breast cancer risk for BRCA1 mutation carriers. A potentially beneficial effect for BRCA2 mutation carriers was observed, particularly after 5 years following RRSO. These results may inform counselling and management of carriers with respect to RRSO. Show less
Current prenatal diagnostics is mainly based on obtaining fetal DNA through invasive procedures such as chorionic villi sampling (CVS) or amniocentesis. These procedures are associated with a small... Show moreCurrent prenatal diagnostics is mainly based on obtaining fetal DNA through invasive procedures such as chorionic villi sampling (CVS) or amniocentesis. These procedures are associated with a small, but significant risk of fetal loss. The discovery of the presence of cell-free fetal DNA (cffDNA) in maternal plasma opened possibilities for less of noninvasive alternative procedures. CffDNA is comprised of small fragments of fetal extracellular DNA derived from placental cells that go into apoptosis and can be detected already early in gestation. However, the majority of total cell-free DNA in maternal plasma is of maternal origin and the fetal contribution in the first trimester is relatively small. In this thesis, we describe novel applications and approaches for the use of cffDNA in noninvasive prenatal testing and diagnostics for a wide variaty of genetics defects such as fetal trisomy 21 (Down syndrome), hereditary breast cancer mutation detection and noninvasive detection of the expanded CAG repeat in Huntington disease. Show less
Harland, M.; Petljak, M.; Robles-Espinoza, C.D.; Ding, Z.H.; Gruis, N.A.; Doorn, R. van; ... ; Bishop, D.T. 2016
The studies presented in this thesis explored several pathogenic mechanisms underlying von Willebrand disease that is characterized by a quantitative or functional deficiency of von Willebrand... Show moreThe studies presented in this thesis explored several pathogenic mechanisms underlying von Willebrand disease that is characterized by a quantitative or functional deficiency of von Willebrand factor, in particular with respect to intracellular storage in Weibel-Palade body and regulated secretion of von Willebrand factor. By using molecular biology, confocal and electron microscopic techniques, storage and secretion of von Willebrand factor were analyzed for von Willebrand disease variants identified in the patients. These studies advanced our understanding of von Willebrand disease at the molecular and cellular levels. HEK293 cells and endothelial cells derived from patients__ peripheral blood were established as two useful model-systems for examining von Willebrand factor structure-function relationships in the context of von Willebrand disease. Using these model-systems we have demonstrated that von Willebrand factor mutations may impair its storage and secretion and thus lead to a quantitative deficiency of this factor in the patients. Furthermore, we demonstrated that alteration in the structure of von Willebrand factor, by natural mutations that occur in von Willebrand disease patients, modulates von Willebrand factor string formation and function. We propose that alteration in von Willebrand factor string formation and function may be another new mechanism that contributes to the bleeding tendency in von Willebrand disease. Show less
