Trio RNA sequencing in a cohort of medically complex children.

Genome sequencing (GS) is a powerful test for the diagnosis of rare genetic disorders. Although GS can enumerate most non-coding variation, determining which non-coding variants are disease-causing is challenging. RNA sequencing (RNA-seq) has emerged as an important tool to help address this issue, but its diagnostic utility remains understudied, and the added value of a trio design is unknown. We performed GS plus RNA-seq from blood using an automated clinical-grade high-throughput platform on 97 individuals from 39 families where the proband was a child with unexplained medical complexity. RNA-seq was an effective adjunct test when paired with GS. It enabled clarification of putative splice variants in three families, but it did not reveal variants not already identified by GS analysis. Trio RNA-seq decreased the number of candidates requiring manual review when filtering for de novo dominant disease-causing variants, allowing for the exclusion of 16% of gene-expression outliers and 27% of allele-specific-expression outliers. However, clear diagnostic benefit from the trio design was not observed. Blood-based RNA-seq can facilitate genome analysis in children with suspected undiagnosed genetic disease. In contrast to DNA sequencing, the clinical advantages of a trio RNA-seq design may be more limited.

Integrated omics analyses clarifies ATRX copy number variant of uncertain significance.

Partial duplications of genes can be challenging to detect and interpret and, therefore, likely represent an underreported cause of human disease. X-linked dominant variants in ATRX are associated with Alpha-thalassemia/impaired intellectual development syndrome, X-linked (ATR-X syndrome), a clinically heterogeneous disease generally presenting with intellectual disability, hypotonia, characteristic facies, genital anomalies, and alpha-thalassemia. We describe an affected male with a de novo hemizygous intragenic duplication of ~43.6 kb in ATRX, detected by research genome sequencing following non-diagnostic clinical testing. RNA sequencing and DNA methylation episignature analyses were central in variant interpretation, and this duplication was subsequently interpreted as disease-causing. This represents the smallest reported tandem duplication within ATRX associated with disease. This case demonstrates the diagnostic utility of integrating multiple omics technologies, which can ultimately lead to a definitive diagnosis for rare disease patients.

Long-read genome sequencing reveals a novel intronic retroelement insertion in NR5A1 associated with 46,XY differences of sexual development.

Despite significant advancements in rare genetic disease diagnostics, many patients with rare genetic disease remain without a molecular diagnosis. Novel tools and methods are needed to improve the detection of disease-associated variants and understand the genetic basis of many rare diseases. Long-read genome sequencing provides improved sequencing in highly repetitive, homologous, and low-complexity regions, and improved assessment of structural variation and complex genomic rearrangements compared to short-read genome sequencing. As such, it is a promising method to explore overlooked genetic variants in rare diseases with a high suspicion of a genetic basis. We therefore applied PacBio HiFi sequencing in a large multi-generational family presenting with autosomal dominant 46,XY differences of sexual development (DSD), for whom extensive molecular testing over multiple decades had failed to identify a molecular diagnosis. This revealed a rare SINE-VNTR-Alu retroelement insertion in intron 4 of NR5A1, a gene in which loss-of-function variants are an established cause of 46,XY DSD. The insertion segregated among affected family members and was associated with loss-of-expression of alleles in cis, demonstrating a functional impact on NR5A1. This case highlights the power of long-read genome sequencing to detect genomic variants that have previously been intractable to detection by standard short-read genomic testing.

Embedding Single Pd Atoms on NiGa Intermetallic Surfaces for Efficient and Selective Alkyne Hydrogenation.

Catalytic removal of alkynes is essential in industry for producing polymer-grade alkenes from steam cracking processes. Non-noble Ni-based catalysts hold promise as effective alternatives to industrial Pd-based catalysts but suffer from low activity. Here we report embedding of single-atom Pd onto the NiGa intermetallic surface with replacing Ga atoms via a well-defined synthesis strategy to design Pd1-NiGa catalyst for alkyne semi-hydrogenation. The fabricated Pd1Ni2Ga1 ensemble sites deliver remarkably higher specific mass activity under superb alkene selectivity of >96 % than the state-of-the-art catalysts under industry-relevant conditions. Integrated experimental and computational studies reveal that the single-atom Pd synergizes with the neighbouring Ni sites to facilitate the σ-adsorption of alkyne and dissociation of hydrogen while suppress the alkene adsorption. Such synergistic effects confer the single-atom Pd on the NiGa intermetallic with a Midas touch for alkyne semi-hydrogenation, providing an effective strategy for stimulating low active Ni-based catalysts for other selective hydrogenations in industry.

Coupled Palladium-Tungsten Bimetallic Nanosheets/TiO2 Hybrids with Enhanced Catalytic Activity and Stability for the Oxidative Removal of Benzene.

Since the conventional Pd-based catalysts often suffer severe deactivation by water, development of a catalyst with good activity and moisture-resistance ability is of importance in effectively controlling emissions of volatile organic compounds (VOCs). Herein, we report the efficient synthesis of ultrathin palladium-tungsten bimetallic nanosheets with exceptionally high dispersion of tungsten species. The supported catalyst (TiO2/PdW) shows good performance for benzene oxidation, and 90% conversion is achieved at a temperature of 200 °C and a space velocity of 40 000 mL g-1 h-1. The TiO2/PdW catalyst also exhibits better water-tolerant ability than the traditional Pd/TiO2 catalyst. The high catalytic efficiency can be explained by the facile redox cycle of the active Pd2+/Pd0 couple in the close-contact PdO x-WO x-TiO2 arrangement. We propose that the reason for good tolerance to water is that the lattice oxygen of the TiO2/PdW catalyst can effectively replenish the oxygen in active PdO x sites consumed by benzene oxidation. A four-step benzene transformation mechanism promoted by the catalyst is proposed. The present work provides a useful idea for the rational design of efficient bimetallic catalysts for the removal of VOCs under the high humidity conditions.

A validated heart-specific model for splice-disrupting variants in childhood heart disease.

BACKGROUND: Congenital heart disease (CHD) is the most common congenital anomaly. Almost 90% of isolated cases have an unexplained genetic etiology after clinical testing. Non-canonical splice variants that disrupt mRNA splicing through the loss or creation of exon boundaries are not routinely captured and/or evaluated by standard clinical genetic tests. Recent computational algorithms such as SpliceAI have shown an ability to predict such variants, but are not specific to cardiac-expressed genes and transcriptional isoforms. METHODS: We used genome sequencing (GS) (n = 1101 CHD probands) and myocardial RNA-Sequencing (RNA-Seq) (n = 154 CHD and n = 43 cardiomyopathy probands) to identify and validate splice disrupting variants, and to develop a heart-specific model for canonical and non-canonical splice variants that can be applied to patients with CHD and cardiomyopathy. Two thousand five hundred seventy GS samples from the Medical Genome Reference Bank were analyzed as healthy controls. RESULTS: Of 8583 rare DNA splice-disrupting variants initially identified using SpliceAI, 100 were associated with altered splice junctions in the corresponding patient myocardium affecting 95 genes. Using strength of myocardial gene expression and genome-wide DNA variant features that were confirmed to affect splicing in myocardial RNA, we trained a machine learning model for predicting cardiac-specific splice-disrupting variants (AUC 0.86 on internal validation). In a validation set of 48 CHD probands, the cardiac-specific model outperformed a SpliceAI model alone (AUC 0.94 vs 0.67 respectively). Application of this model to an additional 947 CHD probands with only GS data identified 1% patients with canonical and 11% patients with non-canonical splice-disrupting variants in CHD genes. Forty-nine percent of predicted splice-disrupting variants were intronic and > 10 bp from existing splice junctions. The burden of high-confidence splice-disrupting variants in CHD genes was 1.28-fold higher in CHD cases compared with healthy controls. CONCLUSIONS: A new cardiac-specific in silico model was developed using complementary GS and RNA-Seq data that improved genetic yield by identifying a significant burden of non-canonical splice variants associated with CHD that would not be detectable through panel or exome sequencing.

RNA sequencing resolves novel DYNC2H1 variants causing short-rib thoracic dysplasia type 3: Case report.

BACKGROUND: Intronic variants outside the canonical splice site are challenging to interpret and therefore likely represent an underreported cause of human disease. Autosomal recessive variants in DYNC2H1 are associated with short-rib thoracic dysplasia 3 with or without polydactyly (SRTD3), a clinically heterogeneous disease generally presenting with short ribs, shortened tubular bones, narrow thorax and acetabular roof anomalies. We describe a case of SRTD3 with compound heterozygous frameshift and intronic variants and highlight the essential role of RNA sequencing (RNA-Seq) in variant interpretation. METHODS: Following inconclusive clinical genetic testing identifying a likely pathogenic frameshift variant and an intronic variant of uncertain significance (VUS) in DYNC2H1 in trans, the family enrolled in the Care4Rare Canada research program, where RNA-Seq studies were performed. RESULTS: The proband presented with post-axial polydactyly of all four limbs, a significantly small chest with a pectus excavatum and anterior flaring of the ribs. RNA-Seq investigations revealed a novel splice junction as a result of the intronic VUS and significantly decreased DYNC2H1 gene expression in the proband. CONCLUSION: This case demonstrates the diagnostic utility of RNA-Seq for variant interpretation following inconclusive clinical testing, which can ultimately lead to diagnosis for patients with rare disease.

Repurposing non-antifungal drugs auranofin and pentamidine in combination as fungistatic antifungal agents against C. albicans.

Fungal infection is a serious global health issue, causing approximately 1.5 million mortalities annually. However, clinically available anti-fungal drugs are limited, especially for multidrug-resistant fungal infections. Therefore, new antifungal drugs are urgently needed to address this clinical challenge. In this study, we proposed two non-antifungal drugs, auranofin and pentamidine, in combination to fight against multidrug-resistant C. albicans. The insufficient antifungal activity of anti-rheumatic drug auranofin is partially due to fungal membrane barrier preventing the drug uptake, and anti-protozoal drug pentamidine was used here to improve the permeability of membrane. The auranofin/pentamidine combination displayed synergistic inhibitory effect against both drug-susceptible and drug-resistant C. albicans, as well as biofilm, and significantly reduced the minimum inhibitory concentration of each drug. At non-antifungal concentration, pentamidine can disrupt the membrane integrity and increase membrane permeability, leading to enhanced cellular uptake of auranofin in C. albicans. This repurposing strategy using the combination of non-antifungal drugs with complementary antifungal mechanism may provide a novel approach for discovery of antifungal drugs to fight against multidrug-resistant fungal infections.

Supramolecular Polymer Gel Lubricant with Excellent Mechanical Stability and Tribological Performances.

Lubricants performing better in machinery systems would lead to the remarkable reduction of environmental pollution problems and the significant improvement of fuel economy. A new family of supramolecular polymer gel lubricants with urea groups has been successfully prepared via self-assembling noncovalent bonds. These newly designed supramolecular polymer gels were well characterized with field-emission scanning electron microscopy, proton nuclear magnetic resonance, attenuated total reflection-Fourier transform infrared spectroscopy, a rheometer, oscillating reciprocating friction, and a wear tester. Compared to low molecular weight supramolecular gels, the covalent and noncovalent bonds cooperated in the supramolecular polymer gel based on macromolecules. Hence, the mechanical properties and viscoelasticity of gel lubricants are greater than those of the low molecular weight supramolecular gels. Furthermore, owing to the longer chain length of polymer gelators, the thickness of the adsorbed film formed on the surface lubricated by macromolecules is thicker than that on the surface lubricated by low molecular weight supramolecular gels, which positively correlates with the lubricating property, making supramolecular polymer gels based on macromolecules better than low molecular weight supramolecular gels. Excitingly, the supramolecular polymer gels based on macromolecules exhibit more excellent thermal reversibility, creep recovery, and thixotropic properties, which not only achieve the lubricating property but also lead to the remarkable reduction of environmental pollution problems due to oil creeping.

The implications of an integrated management model of prenatal diagnosis/postnatal treatment for premature infants with critical congenital heart disease-a case-control study.

Background: The high death rate and medical costs of critical congenital heart disease (CCHD) in preterm infants has resulted in significant burdens on both countries and individuals. It is unclear how this affects the mortality of the integrated management model of prenatal diagnosis/postnatal treatment. This study explored the effects of the delivery classification scale for fetal heart and postnatal infants' CCHD on prenatal and postnatal integrated treatment strategies to improve the effectiveness of disease management in CCHD. Methods: This study was a case-control study, which retrospectively analyzed the clinical data of 79 preterm infants (<37 weeks) who underwent prenatal diagnosis and postpartum treatment in Guangdong Provincial People' s Hospital (China) from June 2017 to June 2019. According to the diagnostic and exclusion criteria, the subjects were divided into prenatal and postpartum diagnostic groups. The clinical characteristics and survival outcomes of patients were collected and compared. The delivery classification scale was used for risk stratification and patient management. Results: Among the 79 patients included in this study, 48 (60.76%) were diagnosed prenatally, and 31 (39.24%) were diagnosed postpartum. The prenatal diagnosis group was born slightly earlier during the gestation period [35.00 (33.29-35.86) vs. 35.57 (34.14-36.71) weeks, P<0.05], and their mothers were older (33.23±5.22 vs. 30.43±6.37 years, P<0.05). The difference in the admission age between the groups was statistically significant [0 (0-5.5) vs. 7 (5-16) days, P<0.001]. The median survival time of the prenatal diagnosis group was higher than the postnatal diagnosis group [48 months (95% CI: 40.78-57.29) vs. 39 months (95% CI: 34.41-44.32), P<0.05]. The 3-year survival rates of the classes I, II, and III were 92.31% (12/13), 59.09% (13/22), and 38.46% (5/13), respectively. The survival of class I as denoted in the delivery classification scale was better than classes II or III (class I vs. II, P<0.05; class I vs. III, P<0.05). Unexpectedly, the hospitalisation costs were lower and total in-hospital days were shorter in the postnatal diagnosis group. Conclusions: The results indicated that the integrated management of a prenatal diagnosis/postnatal treatment approach in premature infants may be effective. Furthermore, the delivery classification scale has a particular prognostic value for CCHD. The authors anticipate that their management model will be able to contribute to the shift from a reactive monodisciplinary system to a proactive, multidisciplinary and dynamic management paradigm in premature infants with CCHD in the near future.

Effects of TiO2 doping on the performance of thermochemical energy storage based on Mn2O3/Mn3O4 redox materials.

A thermochemical energy storage (TCES) system can adjust problems of unstable energy supply for solar concentrating power plants. Mn2O3/Mn3O4 system is a promising TCES system, but it has the problem of a difficult reoxidation process. In this paper, TiO2 was doped into the manganese oxide TCES system to solve this problem and the factors which influence the performance of this method were analyzed. The different performances between commercial Mn2O3 (Mn) and Mn2O3 synthesized by the Pechini method (PCMn), and different scales of doping agents (25Ti, 100Ti) were compared. Because of the formation of the Mn2TiO4, adding TiO2 into the manganese oxide TCES system could improve its reoxidation process obviously. During single complete redox process, PCMn had better performance than Mn whether doped with TiO2 or not, but Mn had a higher optimum oxidation temperature and a narrow temperature range of the redox reactions after adding TiO2. Adding 25Ti could bring higher energy storage density than adding 100Ti, and the optimal doping ratio was 0.05. As the doping ratio of 25Ti was increased, the activation energy (E a) was increased and then decreased. The E a of the samples doped with 25Ti was higher than that doped with 100Ti. Moreover, the E a of the 25Mn0.05 was decreased firstly and then was increased in the later stage of the reaction. The doped Mn samples exhibited better performance and lower attenuation than the doped PCMn samples after 30 cycles. During cyclic tests, the Mn2TiO4 was initially formed at the boundary between Mn2O3 and TiO2, and it was generated continuously with the extension of operating time. Therefore, the operating temperature, morphology of the Mn2O3, the doping agents, the doping ratio, and the phase change with the operating time should be all considered when doping TiO2 into the Mn2O3/Mn3O4 TCES system to improve its performance. Moreover, the results obtained from Mn-Ti systems would make a lot sense when other similar systems are considered, such as Mn-Fe, Mn-Si, Mn-Cr, etc.

The significance of an integrated management mode of prenatal diagnosis-postnatal treatment for critical congenital heart disease in newborns.

BACKGROUND: Congenital heart disease (CHD) is the most common congenital defect in human beings. The purpose of this article is to investigate impact of an integrated management mode of 'prenatal diagnosis-postnatal treatment' on birth, surgery, prognosis and complications associated with critical CHD (CCHD) in newborns. METHODS: A retrospective analysis of the medical records of newborns diagnosed with CCHD were divided into two groups: prenatal diagnosis and postnatal diagnosis. The demographics, clinical characteristics, surgical status, prognosis and complications of the two groups were compared and the differences identified. RESULTS: Among the 290 newborns with CCHD, 97 (33.4%) were prenatally diagnosed and 193 (66.6%) were postnatally diagnosed. Newborns in the prenatal diagnostic group were hospitalized immediately after birth, whereas the median age of admission was 6.00 (3.00-12.00) days in postnatal diagnostic group, P=0.000. In terms of postnatal symptoms and signs, the incidence of anhelation, cyanosis and cardiac murmur was higher in the postnatal diagnostic group. The rates of preoperative intubation, postoperative open chest exploration and treatment abandonment were higher in the postnatal diagnostic group. The postnatal diagnostic group was more prone to postoperative complications, such as pneumonia and hypoxic-ischemic brain damage. The preoperative mortality [0 (0.0%) vs. 12 (6.2%), P=0.028] in the prenatal diagnostic group was lower than that in the postnatal diagnostic group. And the one-year survival rate of the prenatal diagnostic group was higher (log-rank test P=0.034). CONCLUSIONS: The integrated management mode of prenatal diagnosis-postnatal treatment can improve postnatal symptoms, reduces complications, reduces preoperative mortality and increases one-year survival rates in newborns with CCHD.

The Application of a Bone Marrow Mesenchymal Stem Cell Membrane in the Vascularization of a Decellularized Tracheal Scaffold.

Airway stenosis is a common problem in the neonatal intensive care unit (NICU) and pediatric intensive care unit (PICU). A tissue-engineered trachea is a new therapeutic method and a research hotspot. Successful vascularization is the key to the application of a tissue-engineered trachea. However, successful vascularization studies lack a complete description. In this study, it was assumed that rabbit bone marrow mesenchymal stem cells were obtained and induced by ascorbic acid to detect the tissue structure, ultrastructure, and gene expression of the extracellular matrix. A vascular endothelial cell culture medium was added in vitro to induce the vascularization of the stem cell sheet (SCS), and the immunohistochemistry and gene expression of vascular endothelial cell markers were detected. At the same time, vascular growth-related factors were added and detected during SCS construction. After the SCS and decellularized tracheal (DT) were constructed, a tetrandrine allograft was performed to observe its vascularization potential. We established the architecture and identified rabbit bone marrow mesenchymal stem cell membranes by 14 days of ascorbic acid, studied the role of a vascularized membrane in inducing bone marrow mesenchymal stem cells by in vitro ascorbic acid, and assessed the role of combining the stem cell membranes and noncellular tracheal scaffolds in vivo. Fourteen experiments confirmed that cell membranes promote angiogenesis at gene level. The results of 21-day in vitro experiments showed that the composite tissue-engineered trachea had strong angiogenesis. In vivo experiments show that a composite tissue-engineered trachea has strong potential for angiogenesis. It promotes the understanding of diseases of airway stenosis and tissue-engineered tracheal regeneration in newborns and small infants.