Polygenic Risk Score and Rare Variant Burden Identified by Targeted Sequencing in a Group of Patients with Pigment Epithelial Detachment in Age-Related Macular Degeneration

A subset of ophthalmic imaging examination results from 334 patients were subjected to reanalysis to identify a specific group of patients with pigment epithelial detachment (PED) in at least one eye. Overall, we found a subgroup of 47 patients manifesting PED and studied their genotypes in comparison to those of patients with age-related macular degeneration without PED and healthy controls. We established a polygenic risk score that allowed the explanation of 16.3% of the variation within the disease. The highest predictive value was achieved for a model consisting of six non-coding variants: rs760306 (BEST1), rs148662546 (BEST1), rs11569560 (C3), rs74600252 (GUCA1B), rs2240688 (PROM1), and rs185507582 (TCF4). The risk of PED occurrence was found to be the highest in the first tercile, showing a 7.89-fold higher risk compared to the third tercile for AMD without PED (95% CI: 2.87; 21.71, p p < 0.001). In addition, we focused on rare variants in targeted genes. The rare variants’ burden was compared among the groups, but no statistical significance was observed in the number of rare variants, predicted functional effects, or pathogenicity classification

Circular dichroism analysis for multidomain proteins: studies of the irreversible unfolding of Hepatitis C virus helicase

The non-structural protein 3 (NS3) of Hepatitis C virus (HCV) is a bifunctional enzyme with RNA-dependent NTPase/RNA helicase and serine protease activities, and thus represents a promising target for anti-HCV therapy. These functions are performed by two distinct moieties; the N-terminal protease domain and the C-terminal helicase domain that further folds into three structural subdomains. To obtain lower molecular mass proteins suitable for nuclear magnetic resonance studies of helicase-inhibitor complexes, helicase domains 1, 2, and 1+2 devoid of a hydrophobic β-loop were overexpressed and purified. Circular dichroism studies were carried out to confirm the secondary structure content and to determine thermodynamic parameters describing the stability of the proteins. Both thermal and GuHCl-induced unfolding experiments confirmed the multidomain organization of the helicase. The unfolding transition observed for domain 1+2 was in agreement with the model of two well-resolved successive steps corresponding to the independent unfolding of domains 1 and 2, respectively. In the case of the full-length helicase, the presence of domain 3 remarkably changed the transition profile, leading to fast and irreversible transformation of partially unfolded protein

Polygenic Risk Score Impact on Susceptibility to Age-Related Macular Degeneration in Polish Patients

Age-related macular degeneration (AMD) is a common retina degenerative disease with a complex genetic and environmental background. This study aimed to determine the polygenic risk score (PRS) stratification between the AMD case and control patients. The PRS model was established on the targeted sequencing data of a cohort of 471 patients diagnosed with AMD and 167 healthy controls without symptoms of retinal degeneration. The highest predictive value to the target dataset was achieved for a 22-variant model with a p-value lower than threshold PT = 0.0123. The median PRS for cases was higher by 1.1 than for control samples (95% CI: (−1.19; −0.85)). The patients in the highest quantile had a significantly higher relative risk of developing AMD than those in the lowest reference quantile (OR = 35.13, 95% CI: (7.9; 156.1), p < 0.001). The diagnostic ability was investigated using ROC analysis with AUC = 0.76 (95% CI: (0.72; 0.80)). The polygenic susceptibility to AMD may be the starting point to expand AMD diagnostics based on rare highly penetrant variants and investigate associations with disease progression and treatment response in Polish patients in future studies

Virus-Like Particles: Models for Assembly Studies and Foreign Epitope Carriers

Virus-like particles (VLPs), formed by the structural elements of viruses, have received considerable attention over the past two decades. The number of reports on newly obtained VLPs has grown proportionally with the systems developed for the expression of these particles. When expressed in a suitable heterologous system, viral structural proteins involved in capsid or envelope formation often self-assemble into VLPs in the absence of other viral components usually required for virus assembly, such as multiple structural or nonstructural proteins and viral genomes. Protein–protein interactions in VLPs are relatively strong and can result in the formation of stable structures. Several experiments have been reported that may help answer questions regarding the requirements for VLP formation. Knowledge on the assembly process of VLPs is crucial to define the usefulness of such particles for the presentation of their own or foreign epitopes as carriers for transiently expressed proteins as a means of vaccine production. The aim of the present chapter is to outline recent achievements in two important fields of research brought about by the availability of VLPs produced in a foreign host. These are (1) the requirements for VLP assembly and (2) the use of VLPs as carriers for foreign epitopes. To date, reviews in these areas have mainly focused on results obtained with a specific virus genus or family of viruses (1, 2, 3, 4 and 5) and the reader is advised to refer to these reviews for complementary information. Virus-like particles (VLPs), formed by the structural elements of viruses, have received considerable attention over the past two decades. The number of reports on newly obtained VLPs has grown proportionally with the systems developed for the expression of these particles. When expressed in a suitable heterologous system, viral structural proteins involved in capsid or envelope formation often self-assemble into VLPs in the absence of other viral components usually required for virus assembly, such as multiple structural or nonstructural proteins and viral genomes. Protein–protein interactions in VLPs are relatively strong and can result in the formation of stable structures. Several experiments have been reported that may help answer questions regarding the requirements for VLP formation. Knowledge on the assembly process of VLPs is crucial to define the usefulness of such particles for the presentation of their own or foreign epitopes as carriers for transiently expressed proteins as a means of vaccine production. The aim of the present chapter is to outline recent achievements in two important fields of research brought about by the availability of VLPs produced in a foreign host. These are (1) the requirements for VLP assembly and (2) the use of VLPs as carriers for foreign epitopes. To date, reviews in these areas have mainly focused on results obtained with a specific virus genus or family of viruses (1, 2, 3, 4 and 5) and the reader is advised to refer to these reviews for complementary information. Virus-like particles (VLPs), formed by the structural elements of viruses, have received considerable attention over the past two decades. The number of reports on newly obtained VLPs has grown proportionally with the systems developed for the expression of these particles. When expressed in a suitable heterologous system, viral structural proteins involved in capsid or envelope formation often self-assemble into VLPs in the absence of other viral components usually required for virus assembly, such as multiple structural or nonstructural proteins and viral genomes. Protein–protein interactions in VLPs are relatively strong and can result in the formation of stable structures. Several experiments have been reported that may help answer questions regarding the requirements for VLP formation. Knowledge on the assembly process of VLPs is crucial to define the usefulness of such particles for the presentation of their own or foreign epitopes as carriers for transiently expressed proteins as a means of vaccine production. The aim of the present chapter is to outline recent achievements in two important fields of research brought about by the availability of VLPs produced in a foreign host. These are (1) the requirements for VLP assembly and (2) the use of VLPs as carriers for foreign epitopes. To date, reviews in these areas have mainly focused on results obtained with a specific virus genus or family of viruses (1, 2, 3, 4 and 5) and the reader is advised to refer to these reviews for complementary information

Virus-Like Particles: Models for Assembly Studies and Foreign Epitope Carriers

Virus-Like Particles: Models for Assembly Studies and Foreign Epitope Carrier

NS3 Peptide, a Novel Potent Hepatitis C Virus NS3 Helicase Inhibitor: Its Mechanism of Action and Antiviral Activity in the Replicon System▿

Hepatitis C virus (HCV) chronic infections represent one of the major and still unresolved health problems because of low efficiency and high cost of current therapy. Therefore, our studies centered on a viral protein, the NS3 helicase, whose activity is indispensable for replication of the viral RNA, and on its peptide inhibitor that corresponds to a highly conserved arginine-rich sequence of domain 2 of the helicase. The NS3 peptide (p14) was expressed in bacteria. Its 50% inhibitory activity in a fluorometric helicase assay corresponded to 725 nM, while the ATPase activity of NS3 was not affected. Nuclear magnetic resonance (NMR) studies of peptide-protein interactions using the relaxation filtering technique revealed that p14 binds directly to the full-length helicase and its separately expressed domain 1 but not to domain 2. Changes in the NMR chemical shift of backbone amide nuclei (1H and 15N) of domain 1 or p14, measured during complex formation, were used to identify the principal amino acids of both domain 1 and the peptide engaged in their interaction. In the proposed interplay model, p14 contacts the clefts between domains 1 and 2, as well as between domains 1 and 3, preventing substrate binding. This interaction is strongly supported by cross-linking experiments, as well as by kinetic studies performed using a fluorometric assay. The antiviral activity of p14 was tested in a subgenomic HCV replicon assay that showed that the peptide at micromolar concentrations can reduce HCV RNA replication

A Rare Mutation in The APOB Gene Associated with Neurological Manifestations in Familial Hypobetalipoproteinemia

Clinical phenotypes of familial hypobetalipoproteinemia (FHBL) are related to a number of defective apolipoprotein B (APOB) alleles. Fatty liver disease is a typical manifestation, but serious neurological symptoms can appear. In this study, genetic analysis of the APOB gene and ophthalmological diagnostics were performed for family members with FHBL. Five relatives with FHBL, including a proband who developed neurological disorders, were examined. A sequencing analysis of the whole coding region of the APOB gene, including flanking intronic regions, was performed using the next-generation sequencing (NGS) method. Electrophysiological ophthalmological examinations were also done. In the proband and his affected relatives, NGS identified the presence of the pathogenic, rare heterozygous splicing variant c.3696+1G&gt;T. Two known heterozygous missense variants&mdash;c.2188G&gt;A, p.(Val730Ile) and c.8353A&gt;C, p.(Asn2785His)&mdash;in the APOB gene were also detected. In all patients, many ophthalmologic abnormalities in electrophysiological tests were also found. The identified splicing variant c.3696+1G&gt;T can be associated with observed autosomal, dominant FHBL with coexisting neurological symptoms, and both identified missense variants could be excluded as the main cause of observed clinical signs, according to mutation databases and the literature. Electroretinography examination is a sensitive method for the detection of early neuropathy and should therefore be recommended for the care of patients with FHBL

Myoclonus epilepsy and ataxia due to <i>KCNC1</i> mutation:Analysis of 20 cases and K⁺ channel properties

none40siTo comprehensively describe the new syndrome of myoclonus epilepsy and ataxia due to potassium (K(+) ) channel mutation (MEAK), including cellular electrophysiological characterization of observed clinical improvement with fever.mixedOliver, Karen L; Franceschetti, Silvana; Milligan, Carol J; Muona, Mikko; Mandelstam, Simone A; Canafoglia, Laura; Boguszewska-Chachulska, Anna M; Korczyn, Amos; Bisulli, Francesca; Di Bonaventura, Carlo; Ragona, Francesca; Michelucci, Roberto; Ben-Zeev, Bruria; Straussberg, Rachel; Panzica, Ferruccio; Massano, João; Friedman, Daniel; Crespel, Arielle; Engelsen, Bernt A; Andermann, Frederick; Andermann, Eva; Spodar, Krystyna; Lasek-Bal, Anetta; Riguzzi, Patrizia; Pasini, Elena; Tinuper, Paolo; Licchetta, Laura; Gardella, Elena; Lindenau, Matthias; Wulf, Annette; Møller, Rikke S; Benninger, Felix; Afawi, Zaid; Rubboli, Guido; Reid, Christopher A; Maljevic, Snezana; Lerche, Holger; Lehesjoki, Anna-Elina; Petrou, Steven; Berkovic, Samuel FOliver, Karen L; Franceschetti, Silvana; Milligan, Carol J; Muona, Mikko; Mandelstam, Simone A; Canafoglia, Laura; Boguszewska-Chachulska, Anna M; Korczyn, Amos; Bisulli, Francesca; Di Bonaventura, Carlo; Ragona, Francesca; Michelucci, Roberto; Ben-Zeev, Bruria; Straussberg, Rachel; Panzica, Ferruccio; Massano, João; Friedman, Daniel; Crespel, Arielle; Engelsen, Bernt A; Andermann, Frederick; Andermann, Eva; Spodar, Krystyna; Lasek-Bal, Anetta; Riguzzi, Patrizia; Pasini, Elena; Tinuper, Paolo; Licchetta, Laura; Gardella, Elena; Lindenau, Matthias; Wulf, Annette; Møller, Rikke S; Benninger, Felix; Afawi, Zaid; Rubboli, Guido; Reid, Christopher A; Maljevic, Snezana; Lerche, Holger; Lehesjoki, Anna-Elina; Petrou, Steven; Berkovic, Samuel