De novo variation in ARID1B gene causes Coffin-Siris syndrome 1 in a Chinese family with excessive early-onset high myopia.

Coffin-Siris syndrome (CSS) is a rare autosomal dominant inheritance disorder characterized by distinctive facial features, hypoplasia of the distal phalanx or nail of the fifth and additional digits, developmental or cognitive delay of varying degree, hypotonia, hirsutism/hypertrichosis, sparse scalp hair and varying kind of congenital anomalies. CSS can easily be misdiagnosed as other syndromes or disorders with a similar clinical picture because of their genetic and phenotypic heterogeneity. We describde the genotype-phenotype correlation of one patient from a healthy Chinese family with a novel genotype underlying CSS, who was first diagnosed in the ophthalmology department as early-onset high myopia (eoHM). Comprehensive ophthalmic tests as well as other systemic examinations were performed on participants to confirm the phenotype. The genotype was identified using whole exome sequencing, and further verified the results among other family members by Sanger sequencing. Real-time quantitative PCR (RT-qPCR) technology was used to detect the relative mRNA expression levels of candidate genes between proband and normal family members. The pathogenicity of the identified variant was determined by The American College of Medical Genetics and Genomics (ACMG) guidelines. STRING protein-protein interactions (PPIs) network analysis was used to detect the interaction of candidate gene-related proteins with high myopia gene-related proteins. The patient had excessive eoHM, cone-rod dystrophy, coarse face, excessive hair growth on the face, sparse scalp hair, developmental delay, intellectual disability, moderate hearing loss, dental hypoplasia, patent foramen ovale, chronic non-atrophic gastritis, bilateral renal cysts, cisterna magna, and emotional outbursts with aggression. The genetic assessment revealed that the patient carries a de novo heterozygous frameshift insertion variant in the ARID1B c.3981dup (p.Glu1328ArgfsTer5), which are strongly associated with the typical clinical features of CSS patients. The test results of RT-qPCR showed that mRNA expression of the ARID1B gene in the proband was approximately 30% lower than that of the normal control in the family, suggesting that the variant had an impact on the gene function at the level of mRNA expression. The variant was pathogenic as assessed by ACMG guidelines. Analysis of protein interactions in the STRING online database revealed that the ARID1A protein interacts with the high myopia gene-related proteins FGFR3, ASXL1, ERBB3, and SOX4, whereas the ARID1A protein antagonizes the ARID1B protein. Therefore, in this paper, we are the first to report a de novo heterozygous frameshift insertion variant in the ARID1B gene causing CSS with excessive eoHM. Our study extends the genotypic and phenotypic spectrums for ARID1B-CSS and supplies evidence of significant association of eoHM with variant in ARID1B gene. As CSS has high genetic and phenotypic heterogeneity, our findings highlight the importance of molecular genetic testing and an interdisciplinary clinical diagnostic workup to avoid misdiagnosis as some disorders with similar manifestations of CSS.

Characterization and evaluation of cytotoxic and antimicrobial activities of cyclotides from Viola japonica.

Cyclotides are a type of defense peptide most commonly found in the Violaceae family of plants, exhibiting various biological activities. In this study, we focused on the Viola japonica as our research subject and conducted transcriptome sequencing and analysis using high-throughput transcriptomics techniques. During this process, we identified 61 cyclotides, among which 25 were previously documented, while the remaining 36 were designated as vija 1 to vija 36. Mass spectrometry detection showed that 21 putative cyclotides were found in the extract of V. japonica. Through isolation, purification and tandem mass spectrometry, we characterized and investigated the activities of five cyclotides. Our results demonstrated inhibitory effects of these cyclotides on the growth of Acinetobacter baumannii and Bacillus subtilis, with minimum inhibitory concentrations (MICs) of 4.2 µM and 2.1 µM, respectively. Furthermore, time killing kinetic assays revealed that cyclotides at concentration of 4 MICs achieved completely bactericidal effects within 2 h. Additionally, fluorescence staining experiments confirmed that cyclotides disrupt microbial membranes. Moreover, cytotoxicity studies showed that cyclotides possess cytotoxic effects, with IC50 values ranging from 0.1 to 3.5 µM. In summary, the discovery of new cyclotide sequences enhances our understanding of peptide diversity and the exploration of their activity lays the foundation for a deeper investigation into the mechanisms of action of cyclotides.

Enhancing Stability and Albumin Binding Efficiency of α-Conotoxin GI through Fatty Acid Modification.

α-Conotoxin GI is a competitive blocker of muscle-type acetylcholine receptors and holds the potential for being developed as a molecular probe or a lead compound for drug discovery. In this study, four fatty acid-modified α-conotoxin GI analogues of different lengths were synthesized by using a fatty acid modification strategy. Then, we performed a series of in vitro stability assays, albumin binding assays, and pharmacological activity assays to evaluate these modified mutants. The experimental results showed that the presence of fatty acids significantly enhanced the in vitro stability and albumin binding ability of α-conotoxin GI and that this effect was proportional to the length of the fatty acids used. Pharmacological activity tests showed that the modified mutants maintained a good acetylcholine receptor antagonistic activity. The present study shows that fatty acid modification can be an effective strategy to significantly improve conotoxin stability and albumin binding efficiency while maintaining the original targeting ion channel activity.

Use of 6-minute walk test for assessing severity of interstitial lung disease: an observational study.

BACKGROUND: The 6-minute walk test (6MWT) is a potential tool for assessing the severity of interstitial lung disease (ILD). OBJECTIVES: To explore the relationship between 6MWT results and traditional measures including pulmonary function and chest computed tomography(CT) and to determine factors that might influence the 6-minute walk distance (6MWD). METHODS: Seventy-three patients with ILD were enrolled at Peking University First Hospital. All patients underwent 6MWT, pulmonary CT, and pulmonary function tests and their correlations were analyzed. Multivariate regression analysis was used to identify factors that might impact 6MWD.  Results: Thirty (41.4%) of the patients were female and the mean age was 66.1 ± 9.6 years. 6MWD was correlated with forced expiratory volume in 1 second (FEV1), forced vital capacity (FVC), total lung capacity (TLC), diffusing capacity for carbon monoxide (DLCO) and DLCO%pred. The decrease in oxygen saturation (SpO2) after the test was correlated with FEV1%pred, FVC%pred, TLC, TLC%pred, DLCO, DLCO%pred and the percentage of normal lung calculated by quantitative CT. The increase in Borg dyspnea scale was correlated with FEV1, DLCO and the percentage of normal lung. The backward multivariate model (F = 15.257, P < 0.001, adjusted R2 = 0.498) indicated that 6MWD was predicted by age, height, body weight, increase in heart rate, and DLCO. CONCLUSIONS: The 6MWT results were closely correlated with pulmonary function and quantitative CT in patients with ILD. However, in addition to disease severity, 6MWD was also influenced by individual characteristics and the degree of patient effort, which should thus be considered by clinicians when interpreting 6WMT results.

Xp21 DNA microdeletion syndrome in a Chinese family: clinical features show retinitis pigmentosa and chronic granuloma.

Xp21 DNA microdeletion syndrome is a very rare disease characterized by retinitis pigmentosa (RP), chronic granulomatous disease (CGD), and McLeod syndrome (MLS). Due to the complex and diverse clinical manifestations, early diagnosis remains a challenge for many physicians. In this study, for the purpose of determining the pathogenic gene variants and definitive diagnosis in a patient medically backgrounded with RP and CGD from a normal Chinese family, whole-exome sequencing (WES) was performed in this proband and copy number variation (CNV) was further verified in other family members by qPCR. A genetic evaluation revealed that the short arm of the X chromosome in the proband had a deletion CNV Xp21.1p11.4 (37431123-38186681) of approximately 0.755 Mb in size, and contained three contiguous OMIM genes as X-linked Kx blood group antigen (XK), cytochrome b-245 beta chain (CYBB), and RP GTPase regulator (RPGR). The qPCR results confirmed the copy number loss in Xp21.1p11.4 present in the proband and his unaffected mother. According to the American College of Medical Genetics and Genomics (ACMG) guidelines for the CNV interpretation, the deletion of this segment was a pathogenic variant. Our results provided evidence that CNV deletion of Xp21.1p11.4 in the short arm of the X chromosome was a pathogenic variant in such Chinese RP and CGD family, and the McLeod phenotype was not yet available. This study suggests that genetic testing is essential for a definitive diagnosis, which should better assist physicians in prediction, diagnosis, genetic counseling, and guidance for Xp21 DNA microdeletion syndrome.

Estimation of Urban-Rural Land Surface Temperature Difference at Different Elevations in the Qinling-Daba Mountains Using MODIS and the Random Forest Model.

Land surface temperature (LST) variations are very complex in mountainous areas owing to highly heterogeneous terrain and varied environment, which complicates the surface urban heat island (SUHI) in mountain cities. Previous studies on the urban heat island (UHI) effect mostly focus on the flat terrain areas; there are few studies on the UHI effect in mountainous areas, especially on the influence of elevation on the SUHI effect. To determine the SUHI in the Qinling-Daba mountains (China), MODIS LST data were first preprocessed and converted to the same elevations (1500 m, 2000 m, 2500 m, 3000 m, and 3500 m) using a digital elevation model and the random forest method. Then, the average LSTs in urban land, rural land, and cultivated land were calculated separately based on the ranges of the invariable urban, rural, and cultivated areas during 2010-2018, and the urban, rural, and cultivated land LST difference were estimated for the same elevations. Results showed that the accuracy of LST estimated using the random forest method is very high (R2 ≥ 0.9) at elevations of 1500 m, 2000 m, 2500 m, 3000 m and 3500 m. The difference in urban, rural, and cultivated lands' LST has a trend of decrease with increasing elevation, meaning that the SUHI weakens at higher elevations. The average LST of urban areas is 0.52-0.59 °C (0.42-0.57 °C) higher than that of rural and cultivated areas at an elevation of 1500 m (2000 m). The average LST of urban areas is 0.10-1.25 °C lower than that of rural and cultivated areas at elevations of 2500 m, 3000 m, and 3500 m, indicating absence of the SUHI at those elevations.

Diagnostic Performance of Multi-Direction Adjusted Multi-Planar Reconstruction with Helical CT for Evaluating Continuity of the Anterior Cruciate Ligament.

RATIONALE AND OBJECTIVES: To analyze the diagnostic performance of MDA-MPR with CT for evaluating ACL structural continuity. METHODS: A total of 145 patients with highly suspected ACL injury admitted to our hospital between January 2016 and May 2021 were retrospectively enrolled. All patients had undergone examination with MRI, CT, and arthroscopy. Taking arthroscopy results as the gold standard, the diagnostic accuracy for identifying ACL rupture by MRI and MDA-MPR with CT were compared. RESULTS: The receiver operator characteristic curves demonstrated that both MRI and MDA-MPR with CT performed well in the diagnosis of ACL tears. The sensitivities of MRI and MDA-MPR with CT for diagnosing complete ACL tears were 95.16% (59/62) and 90.32% (56/62), respectively. Their specificities in this regard were 77.11% (64/83) and 84.34% (70/83), respectively. MRI had a higher sensitivity but MDA-MPR with CT had a higher specificity for detecting complete ACL tears, and the differences were statistically significant (p <.05). The sensitivities of diagnosing partial ACL tears using MRI and MDA-MPR with CT were 78.79% (26/33) and 75.76% (25/33), respectively, while the specificities were 86.61% (97/112) and 90.18% (101/112), respectively. These differences were non-significant (p >.05). CONCLUSION: MDA-MPR with CT has high diagnostic efficiency for ACL injuries, especially in the diagnosis of complete ACL tears.

Autophagy regulation by microRNAs in chemotherapy resistance (Review).

Chemotherapy, as an adjuvant therapy, utilizes drugs to treat cancer, and resistance to therapeutic drugs limits the efficacy of chemotherapy treatments. Several mechanisms have been proposed to improve the effect of tumor chemotherapy in order to overcome drug resistance. Among these, autophagy mediated by microRNAs (miRNAs) is one of the primary mechanisms. A large number of molecules targeted by miRNAs are involved in each step of the autophagic pathway. Recent advancement in chemotherapy research has revealed that miRNAs involved in the autophagy process target some of these molecules, thereby influencing the therapeutic effect of chemotherapy drugs. Thus, miRNAs appear to be potential tools or targets with which to suppress tumor growth and should be studied in further details for their clinical application against drug resistance.

A new LSTM-based gene expression prediction model: L-GEPM.

Molecular biology combined with in silico machine learning and deep learning has facilitated the broad application of gene expression profiles for gene function prediction, optimal crop breeding, disease-related gene discovery, and drug screening. Although the acquisition cost of genome-wide expression profiles has been steadily declining, the requirement generates a compendium of expression profiles using thousands of samples remains high. The Library of Integrated Network-Based Cellular Signatures (LINCS) program used approximately 1000 landmark genes to predict the expression of the remaining target genes by linear regression; however, this approach ignored the nonlinear features influencing gene expression relationships, limiting the accuracy of the experimental results. We herein propose a gene expression prediction model, L-GEPM, based on long short-term memory (LSTM) neural networks, which captures the nonlinear features affecting gene expression and uses learned features to predict the target genes. By comparing and analyzing experimental errors and fitting the effects of different prediction models, the LSTM neural network-based model, L-GEPM, can achieve low error and a superior fitting effect.

A Novel Approach for Drug-Target Interactions Prediction Based on Multimodal Deep Autoencoder.

Drug targets are biomacromolecules or biomolecular structures that bind to specific drugs and produce therapeutic effects. Therefore, the prediction of drug-target interactions (DTIs) is important for disease therapy. Incorporating multiple similarity measures for drugs and targets is of essence for improving the accuracy of prediction of DTIs. However, existing studies with multiple similarity measures ignored the global structure information of similarity measures, and required manual extraction features of drug-target pairs, ignoring the non-linear relationship among features. In this paper, we proposed a novel approach MDADTI for DTIs prediction based on MDA. MDADTI applied random walk with restart method and positive pointwise mutual information to calculate the topological similarity matrices of drugs and targets, capturing the global structure information of similarity measures. Then, MDADTI applied multimodal deep autoencoder to fuse multiple topological similarity matrices of drugs and targets, automatically learned the low-dimensional features of drugs and targets, and applied deep neural network to predict DTIs. The results of 5-repeats of 10-fold cross-validation under three different cross-validation settings indicated that MDADTI is superior to the other four baseline methods. In addition, we validated the predictions of the MDADTI in six drug-target interactions reference databases, and the results showed that MDADTI can effectively identify unknown DTIs.

SIN-KNO: A method of gene regulatory network inference using single-cell transcription and gene knockout data.

As a tool of interpreting and analyzing genetic data, gene regulatory network (GRN) could reveal regulatory relationships between genes, proteins, and small molecules, as well as understand physiological activities and functions within biological cells, interact in pathways, and how to make changes in the organism. Traditional GRN research focuses on the analysis of the regulatory relationships through the average of cellular gene expressions. These methods are difficult to identify the cell heterogeneity of gene expression. Existing methods for inferring GRN using single-cell transcriptional data lack expression information when genes reach steady state, and the high dimensionality of single-cell data leads to high temporal and spatial complexity of the algorithm. In order to solve the problem in traditional GRN inference methods, including the lack of cellular heterogeneity information, single-cell data complexity and lack of steady-state information, we propose a method for GRN inference using single-cell transcription and gene knockout data, called SINgle-cell transcription data-KNOckout data (SIN-KNO), which focuses on combining dynamic and steady-state information of regulatory relationship contained in gene expression. Capturing cell heterogeneity information could help understand the gene expression difference in different cells. So, we could observe gene expression changes more accurately. Gene knockout data could observe the gene expression levels at steady-state of all other genes when one gene is knockout. Classifying the genes before analyzing the single-cell data could determine a large number of non-existent regulation, greatly reducing the number of regulation required for inference. In order to show the efficiency, the proposed method has been compared with several typical methods in this area including GENIE3, JUMP3, and SINCERITIES. The results of the evaluation indicate that the proposed method can analyze the diversified information contained in the two types of data, establish a more accurate gene regulation network, and improve the computational efficiency. The method provides a new thinking for dealing with large datasets and high computational complexity of single-cell data in the GRN inference.

RGS17 inhibits tumorigenesis and improves 5-fluorouracil sensitivity in nasopharyngeal carcinoma.

BACKGROUND: Nasopharyngeal carcinoma (NPC) is a poorly differentiated malignant tumor, and 5-fluorouracil (5-FU) is one of the most effective chemotherapeutic drugs used for the treatment of NPC. Abnormal expression of RGS17 had been shown to improve the sensitivity of many cancers to chemotherapy; however, the effects of RGS17 on NPC remain unclear. METHODS: We cultured NPC cell lines and altered the RGS17 expression with vector. Subsequently colony formation assays and CCK8 cell viability assay was used to test the proliferation of NPC cells, flow cytometry was used to determine the percentage of apoptotic cells, MMP kit and flow cytometry was used to measure the mitochondrial membrane potential, and a xenograft tumour model was attached to investigate the effects of RGS17 on the growth of NPC cells in vivo. Additionally, RT-PCR and western blot was induced to examine the expression of RGS17 and the mechanism. RESULTS: Here, we report for the first time that RGS17 is downregulated in NPC cell lines and that RGS17 overexpression significantly reduces cell proliferation, decreases the mitochondrial membrane potential, and induces cell apoptosis in NPC cells. In vivo, RGS17 also inhibits the tumorigenicity of NPC. In addition, RGS17 could significantly improve the sensitivity of NPC cells to 5-FU. Furthermore, investigation into the underlying mechanisms showed that RGS17 upregulated the levels of IRE1α, p53, and active caspase-3 and cleaved PARP. CONCLUSION: These results indicate that RGS17 could play important roles in the proliferation, apoptosis, and chemotherapeutic sensitivity of NPC cells.

Intranasal endoscopic prelacrimal recess approach for maxillary sinus inverted papilloma.

PURPOSE: This study aims to determine the indications and effectiveness of transnasal endoscopic prelacrimal recess approach (PLRA) in patients with maxillary sinus inverted papilloma (IP). METHODS: We retrospectively analyzed 71 patients treated in our institution for maxillary sinus IP between August 2008 and April 2015. 20 patients underwent endoscopic surgery via PLRA. All the patients who had postoperative follow-up for 3 years were enrolled. Demographic data, surgical technique, location of IP attachment, intra- and postoperative complications, follow-up duration and recurrence were recorded. RESULTS: The outpatient follow-up period was 3-10 years after surgery. Recurrence of IP was seen in 6 (8.5%) of 71 patients, including 1 patient in the PLRA group. The recurrence rate was 5% in the PLRA group. Six of 71 patients experienced postoperative complications, but none was observed in the PLRA group. CONCLUSION: Transnasal endoscopic PLRA is a minimally invasive, safe and effective method for maxillary sinus IP. The indication for PLRA is tumor pedicle located on the antero-inferior or infero-lateral wall or at multiple attachment sites of the maxillary sinus.

Characterization of a cadmium resistance Lactococcus lactis subsp. lactis strain by antioxidant assays and proteome profiles methods.

Heavy metal contamination poses a major threat to the environment and human health for their potential toxicity and non-biodegradable properties. At present, some probiotics bacteria are reported to have great potential to eliminate heavy metals from food and water. In this study, resistance properties of a newly isolated Lactococcus lactis subsp. lactis for cadmium were studied by antioxidant assays and proteomics analysis. Antioxidant capacity of this strain was significantly activated under cadmium stress indicated by Fenton reaction, DPPH assay, SOD assay and GSH assay. Intracellular antioxidant enzyme systems, such as superoxide dismutase, glutathione reductase and catalase were suggested to play vital roles in the activated antioxidant capacity. The up-regulated cadA was associated with the activated P-type ATPases that plays an important role in cadmium resistance. Proteomics analysis identified 12 over-expressed proteins under 50mg/L cadmium stress and these proteins are abundant in oxidative stress response and energy metabolism regulation, which were considered as consequences as cadmium resistance of the strain. Thus, the probiotics Lactococcus lactis subsp. lactis may resist cadmium stress through antioxidant approach and enhanced energy metabolism. The food grade lactis strain may be applied in metal decontamination in environment and food/feed.

[Different intranasal corticosteroids effects on nasal airway remodeling of allergic rhinitis murine and matrix metalloproteinase-9].

OBJECTIVE: To discuss the effect of different doses intranasal corticosteroids on remodeling of allergic rhinitis (AR) mice nasal mucosa and expression level of matrix metalloproteinase-9 (MMP-9). METHOD: Thirty BALB/c female mice were divided into five groups randomly and received OVA or normal saline (NS) with intraperitoneal injection or nasal challenge, respectively. The treatment groups received additional different doses of budesonide (0.6 µg/20 g, 3.0 µg/20 g and 15.0 µg/20 g) daily for 16 weeks. We assessed the nasal symptoms at 4 and 16 weeks. Collected the mice nasal tissue, and then stained with hematoxylin-eosin, Masson's Trichrome, and periodic acid-schiff respectively to evaluate airway remodeling at 16 weeks. MMP-9 was measured with enzyme-linked immunosorbent assay (ELISA). Result: Times of rubbing, sneezes and infiltrate of eosinophil increased more in B group than in A group, and subepithelial fibrosis, collagen deposition, goblet cell hyperplasia, and submucosal gland hypertrophy were only observed in B group at 16 weeks. The nasal symptoms and eosinophil infiltration were inhibited by treatment with budesonide from a dose of 0.6 µg onwards, while the prevention of structure changes was only observed with 3.0 µg onwards. In addition, intranasal budesonide reduced MMP-9 in the nasal of AR mice. CONCLUSION: The study suggests that higher dose intranasal corticosteroids might inhibit the airway remodeling of nasal mucosa by reducing MMP-9.

Relationship between single nucleotide polymorphism of interleukin-18 and susceptibility to pulmonary tuberculosis in the Chinese Han population.

Interleukin-18 (IL-18) is a multi-functional cytokine capable of inducing either Th1 or Th2 polarization depending on the immunologic milieu. IL-18 may influence the host response to Mycobacterium tuberculosis (M.tb) infection. To investigate the relationship between single nucleotide polymorphisms of the IL-18 and susceptibility to pulmonary tuberculosis in the Chinese Han population, the IL-18 gene was sequenced to detect polymorphisms and to examine the genotype frequencies in 300 patients and 702 healthy controls. DNA sequencing revealed three IL-18 variants: rs1946518, rs5744247, and rs549908. It also revealed that allele A of rs1946518 confers a 1.47-fold increased risk of developing tuberculosis (TB) (P = 0.0001, OR [95%CI] = 1.47 [1.21-1.78]), and that the C allele of rs5744247 confers a 0.77-fold decreased risk of disease (P = 0.01, R [95%CI] = 0.77 [0.632-0.937]). The genotypes rs1946518, rs5744247 and rs549908 were found to be significantly associated with TB. Estimation of the frequencies of haplotypes revealed a potential risk haplotype AGA (P = 0.01, OR [95%CI] = 1.41 [1.15-1.72]) and a protective haplotype CCA (P = 0.01, OR [95%CI] = 0.70 [0.57-0.85]) for TB. The present findings suggest that polymorphisms in the IL-18 gene may affect susceptibility to TB and increase the risk of developing the disease in the Chinese Han population.

Analysis of the association between BTNL2 polymorphism and tuberculosis in Chinese Han population.

BTNL2 gene, a MHC class II gene-linked butyrophilin family member, has been recently associated with the inflammatory autoimmune diseases, such as tuberculosis, sarcoidosis and leprosy. This diseases show phenotypic features of granulomatous disease. Multiple single nucleotide polymorphisms in BTNL2 have been investigated as a candidate gene for tuberculosis in a case-control association study in the South African Coloured population. But, no significant association was detected between any of the polymorphisms investigated and TB, including rs2076530 SNP that was previously found to be associated with sarcoidosis. In this study, we genotyped 6 SNPs using SNaPshot in 286 tuberculosis cases and 608 controls in Chinese. Our genetic study revealed a significant association between the rs3763313, rs9268494, rs9268492 SNPs in the BTNL2 gene and tuberculosis. And haplotypes 1-5, and 8 (C-A-G-T-G-A, C-A-G-T-G-G, C-A-T-G-C-A, C-A-T-G-C-G, and C-G-T-G-C-G, T-A-T-G-C-A) presented a significant association with susceptibility to tuberculosis. We found that BTNL2 gene was linked to tuberculosis in Chinese Han population.