Methodological differences can affect sequencing depth with a possible impact on the accuracy of genetic diagnosis

For a better interpretation of variants, evidence-based databases, such as ClinVar, compile data on the presumed relationships between variants and phenotypes. In this study, we aimed to analyze the pattern of sequencing depth in variants from whole-exome sequencing data in the 1000 Genomes project phase 3, focusing on the variants present in the ClinVar database that were predicted to affect protein-coding regions. We demonstrate that the distribution of the sequencing depth varies across different sequencing centers (pair-wise comparison, p < 0.001). Most importantly, we found that the distribution pattern of sequencing depth is specific to each facility, making it possible to correctly assign 96.9% of the samples to their sequencing center. Thus, indicating the presence of a systematic bias, related to the methods used in the different facilities, which generates significant variations in breadth and depth in whole-exome sequencing data in clinically relevant regions. Our results show that methodological differences, leading to significant heterogeneity in sequencing depth, may potentially influence the accuracy of genetic diagnosis. Furthermore, our findings highlight how it is still challenging to integrate results from different sequencing centers, which may also have an impact on genomic research.

Effect of the photoinitiator system on the polymerization of secondary methacrylamides of systematically varied structure for dental adhesive applications

OBJECTIVE

The aim of this study was to investigate the influence of the photoinitiator system on the polymerization kinetics of methacrylamide-based monomers as alternatives to methacrylates in adhesives dental-based materials.

METHODS

In total, 16 groups were tested. Monofunctional monomers (2-hydroxyethyl methacrylate) - HEMA; (2-hydroxy-1-ethyl methacrylate) -2EMATE, (2-hydroxyethyl methacrylamide) - HEMAM; and (N-(1-hydroxybutan-2-yl) methacrylamide) -2EM; were combined with bifunctional monomers containing the same polymerizing moieties as the monofunctional counterparts (HEMA-BDI; 2EMATE-BDI; HEMAM-BDI; and 2EM-BDI) at 50/50 M ratios. BHT was used as inhibitor (0.1 wt%) and the photoinitiators used were: CQ + EDMAB (0.2/0.8), BAPO (0.2), IVOCERIN (0.2), and DMPA (0.2), in wt%. The polymerization kinetics were monitored using Near-IR spectroscopy (∼6165 cm-1) in real-time while the specimens were photoactivated with a mercury arc lamp (Acticure 2; 320-500 nm, 300 mW/cm2) for 5 min, and maximum rate of polymerization (Rpmax, in %.s-̄1), degree of conversion at Rpmax (DC@Rpmax, in %), and the final degree of conversion (Final DC, in %) were calculated (n = 3). Initial viscosity was measured with an oscillating rheometer (n = 3). Data were analyzed using Two-way ANOVA for the polymerization kinetics and one-way ANOVA for the viscosity. Multiple comparisons were made using the Tukey's test (∝ = 0.05).

RESULTS

There was statistically significant interaction between monomer and photoinitiator (p < 0.001). For the methacrylates groups, the highest Rpmax was observed for HEMA + DMPA and 2EMATE + BAPO. For methacrylamides groups, the highest Rpmax were observed for HEMAM and 2EM, both with DMPA. Final DC was higher for the methacrylate groups, in comparison with methacrylamide groups, independent of the photoinitiators. However, for the methacrylamide groups, the association with BAPO led to the lowest values of DC. In terms of DC@Rpmax, methacrylate-based systems showed significantly higher values than methacrylamide formulations. DMPA and Ivocerin led to higher values than CQ/EDMAB and BAPO in methacrylamide-based compounds. BAPO systems showed de lowest values for both HEMA and HEMAM formulations. For the viscosity (Pa.s), only 2EM had higher values (1.60 ± 0.15) in comparison with all monomers. In conclusion, polymerization kinetics was affected by the photoinitiators for both monomers. Viscosity was significantly increased with the use of secondary methacrylamide.

SIGNIFICANCE

this work demonstrated the feasibility of using newly-synthesized methacrylamide monomers in conjunction with a series of initiator systems already used in commercial materials.

Effect of the addition of thiourethane oligomers on the sol⿿gel composition of BisGMA/TEGDMA polymer networks

OBJECTIVES

Thiourethane oligomers have been shown to increase the fracture toughness and reduce the polymerization stress of methacrylate-based materials. However, network formation has not been elucidated in these materials yet. The aim of this study was to evaluate how the addition of a thiourethane oligomer (TU) influences the sol/gel composition and network structure of methacrylate-based materials using dynamic mechanical analysis and extraction methods.

MATERIALS AND METHODS

BisGMA/TEGDMA at systematically varied mass ratios (20/80 to 80/20wt%) were mixed with pre-polymerized thiourethane oligomers at 0 (control) or 20wt%, synthesized by combining pentaerythritol tetra-3-mercaptopropionate with dicyclohexylmethane 4,4⿲-Diisocyanate, at 1:2 isocyanate:thiol. 0.1wt% of 2,2-Dimethoxy-2-phenylacetophenone was added as the photoinitiator and 0.3wt% of 2,6-di-tert-butyl-4-methylphenol was added as a free radical inhibitor. Disk specimens (0.8ÿ10mm in diameter, n=3) were photoactivated at 270mW/ (320⿿500nm) for 1min. The degree of conversion (DC) was measured in near-IR (˿6165cm⿿1). Specimens were immersed in two different solvents (water for 7 days or dicholoromethane for 48h). Water sorption (WS) and solubility (SL) were obtained according to ISO 4049. The leachates for both solutions were analyzed with 1H-NMR (400MHz, CDCL3). Bar specimens (1ÿ3ÿ25mm, photocured and then post-processed at 180°C for 8h to DC>95%) were subjected to dynamic mechanical analysis (⿿30 to 230°C) to obtain glass transition temperature (Tg), tan delta curves and crosslinking density (ν). Data was analyzed with two-way ANOVA/Tukey⿿s test (95%).

RESULTS

In general, the presence of TU increased the overall conversion. The WS was similar for all groups, but the SL decreased by 2-fold with the addition of the TU oligomer for all compositions, except BisGMA/TEGDMA 80/20. The BisGMA concentration of the leachates increased with increasing BisGMA in the initial mixture, and with the presence of thiourethane. This compositional drift of the gel with the presence of TU was attributed to the preferential dissolution of TEGDMA into the TU network. Tg and ν decreased with the addition of TU, as expected. The addition of TU produced more homogeneous networks, as evidenced by narrower breadth of the tan delta curve.

CONCLUSION

The addition of TU affected the composition of the sol/gel in crosslinked networks, which were more homogeneous and presented 2-fold less potentially toxic leachates than the methacrylate controls.

CLINICAL SIGNIFICANCE

The addition of TU may produce less cytotoxic materials based on the increased conversion and reduced amount of unreacted extractables from its network after water storage.

Dysregulation of NEUROG2 plays a key role in focal cortical dysplasia

OBJECTIVE

Focal cortical dysplasias (FCDs) are an important cause of drug-resistant epilepsy. In this work, we aimed to investigate whether abnormal gene regulation, mediated by microRNA, could be involved in FCD type II.

METHODS

We used total RNA from the brain tissue of 16 patients with FCD type II and 28 controls. MicroRNA expression was initially assessed by microarray. Quantitative polymerase chain reaction, in situ hybridization, luciferase reporter assays, and deep sequencing for genes in the mTOR pathway were performed to validate and further explore our initial study.

RESULTS

hsa-let-7f (p = 0.039), hsa-miR-31 (p = 0.0078), and hsa-miR34a (p = 0.021) were downregulated in FCD type II, whereas a transcription factor involved in neuronal and glial fate specification, NEUROG2 (p < 0.05), was upregulated. We also found that the RND2 gene, a NEUROG2-target, is upregulated (p < 0.001). In vitro experiments showed that hsa-miR-34a downregulates NEUROG2 by binding to its 5'-untranslated region. Moreover, we observed strong nuclear expression of NEUROG2 in balloon cells and dysmorphic neurons and found that 28.5% of our patients presented brain somatic mutations in genes of the mTOR pathway.

INTERPRETATION

Our findings suggest a new molecular mechanism, in which NEUROG2 has a pivotal and central role in the pathogenesis of FCD type II. In this way, we found that the downregulation of hsa-miR-34a leads to upregulation of NEUROG2, and consequently to overexpression of the RND2 gene. These findings indicate that a faulty coupling in neuronal differentiation and migration mechanisms may explain the presence of aberrant cells and complete dyslamination in FCD type II. Ann Neurol 2018;83:623-635.

[Vasoactive endothelial factors]

Endothelium-derived vasoactive factors are produced by the endothelium activated by effective stimulus, and with paracrine regulatory activity of the tone/proliferation of the vascular smooth muscle and platelet function. They are divided in two groups: endothelium-derived relaxing and contracting factors. Among the endothelium-derived relaxing factors, PG I2, EDRF (NO or other nitrous compound) and EDHF (still unidentified) have been considered Synthetized by the endothelium after stimulation by plasmatic, platelet-derived and endothelium-derived substances and mechanisms, towards the vascular smooth muscle (myorelaxing/cytostatic) and the platelets (antiaggregation). The endothelium-derived contracting factors include the EDCF1 (endothelins, 21 amino acids peptides), EDCF2 (O2-) and TxA2. Its production, induced by stimulus similar to those for relaxing factors, promotes constriction/mitogenesis of the vascular smooth muscle and platelet aggregation. Probably, endothelin-1 has indirect actions over hormonal mechanisms of cardiovascular and renal regulation. The vascular system establishes a tight regulation over the production of these endothelium-derived vasoactive factors. Its loss (usually due to alteration of endothelial responsiveness to stimulation) allows local or generalized modifications of the vascular tone. These can depend on hypertension, atherosclerosis, ischemia-reperfusion lesion, diabetes, inflammation and situations of farmacotoxicity (all developing vasoconstriction/vasospasm) or by septicemia (leading to vasodilation). This disregulation is also involved in the pathogenesis of hypertension, atherosclerosis and ischemia-reperfusion. The vascular tone regulation by endothelium also leads to systemic consequences. Essentially by decreasing cardiac, cerebral and renal blood flow it implies morphologic and functional modifications of these organs.