Multi-dataset identification of innovative feature genes and molecular mechanisms in keratoconus.

This study aimed to identify feature genes and explore the molecular mechanisms of keratoconus (KC). We downloaded data files from NCBI GEO public database. The Limma package was used for differential expression analysis of gene profiles. Lasso regression was used to identify the feature genes. The CIBERSORT algorithm was used to infer the proportion of immune-infiltrating cells and analyse the correlation between gene expression levels and immune cells. Related transcription factors and miRNAs of key genes were predicted using the Cistrome DB and Mircode databases. Analysis of expression differences in disease genes was based on the GeneCards database. The CMap was used to analyse targeted therapeutic drugs. IHC was performed to verify the expression levels of ATOH7 and MYRF in corneas. Exactly 593 upregulated and 473 downregulated genes were identified. Lasso regression analysis identified ATOH7, DBNDD1, RNF217-AS1, ARL11, MYRF and SNORA74B as feature genes for KC. All key genes were correlated with immune infiltration and the levels of activated memory CD4+ T cells and plasma cells were significantly increased. miRNA, IRF and STAT families were correlated to feature genes. The expression levels of key genes were significantly correlated to KC-related genes. Entinostat, ochratoxin-a, diphencyprone and GSK-3-inhibitor-II were predicted as potential KC medications. The expression of MYRF was significantly higher in the KC samples, contrary to the expression of ATOH7. KC is related to both immune infiltration and genetic factors. MYRF and ATOH7 were newly identified and verified feature genes of KC.

Identification of feature genes and molecular mechanisms involved in cell communication in uveal melanoma through analysis of single­cell sequencing data.

Uveal melanoma (UM) is a highly metastatic cancer with resistance to immunotherapy. The present study aimed to identify novel feature genes and molecular mechanisms in UM through analysis of single-cell sequencing data. For this purpose, data were downloaded from The Cancer Genome Atlas and National Center for Biotechnology Information Gene Expression Omnibus public databases. The statistical analysis function of the CellPhoneDB software package was used to analyze the ligand-receptor relationships of the feature genes. The Metascape database was used to perform the functional annotation of notable gene sets. The randomForestSRC package and random survival forest algorithm were applied to screen feature genes. The CIBERSORT algorithm was used to analyze the RNA-sequencing data and infer the relative proportions of the 22 immune-infiltrating cell types. In vitro, small interfering RNAs were used to knockdown the expression of target genes in C918 cells. The migration capability and viability of these cells were then assessed by gap closure and Cell Counting Kit-8 assays. In total, 13 single-cell sample subtypes were clustered by t-distributed Stochastic Neighbor Embedding and annotated by the R package, SingleR, into 7 cell categories: Tissue stem cells, epithelial cells, fibroblasts, macrophages, natural killer cells, neurons and endothelial cells. The interactions in NK cells|Endothelial cells, Neurons|Endothelial cells, CD74_APP, and SPP1_PTGER4 were more significant than those in the other subsets. T-Box transcription factor 2, tropomyosin 4, plexin D1 (PLXND1), G protein subunit α I2 (GNAI2) and SEC14-like lipid binding 1 were identified as the feature genes in UM. These marker genes were found to be significantly enriched in pathways such as vasculature development, focal adhesion and cell adhesion molecule binding. Significant correlations were observed between key genes and immune cells as well as immune factors. Relationships were also observed between the expression levels of the key genes and multiple disease-related genes. Knockdown of PLXND1 and GNAI2 expression led to significantly lower viability and gap closure rates of C918 cells. Therefore, the results of the present study uncovered cell communication between endothelial cells and other cell types, identified innovative key genes and provided potential targets of gene therapy in UM.

Molecular Diodes Induced by a Schottky Barrier with a Gold-Silicon Doped Electrode.

To create complementary metal oxide semiconductor compatible molecular devices, more insights into the electrode property regarding its metal/semiconductor doping level and creating a functional molecular device are required. In this work, we constructed an EGaIn/alkanethiol/Au-Si molecular diode (with a rectification ratio R of 50.70) induced by Schottky barriers within a gold-silicon doped electrode instead of the functional property of molecules. The relationship between the rectification ratio and the number of methylene units in alkanethiol was analyzed, revealing a gradual increase in the ratio from 3.33 for C6H14S to 50.70 for C16H34S. The rectification ratio of the junction is well modulated by the temperature due to the change in the Schottky barrier. Such a mechanism is explained by the energy band diagrams of the surface space charge region and a combination of density functional theory and Keldysh-Green formalism calculations.

Changes in phenolic compounds of Phyllanthus emblica juice during different storage temperature and pH conditions.

The aim of this experiment was to investigate the effect of storage temperature and pH on phenolic compounds of Phyllanthus emblica juice. Juice was stored at different temperatures and pH for 15 days and sampled on 2-day intervals. The browning index (BI, ABS420 nm), pH, centrifugal precipitation rate (CPR), and phenolic compounds were evaluated. The results showed 4°C and pH 2.5 could effectively inhibit browning and slow down pH drop of P. emblica juice. The result of orthogonal partial least square-discriminant analysis showed P. emblica juice stored at 4°C and pH 2.5 still had a similar phenolic composition, but at 20°C, 37°C, and pH 3.5, the score plots were concentrated only in the first 3 days. Additionally, gallic acid (GA) and ellagic acid (EA) were screened out to be the differential compounds for browning of P. emblica juice. The contents of GA, epigallocatechin (EGC), corilagin (CL), gallocatechin gallate (GCG), chebulagic acid (CA), 1,2,3,4,6-O-galloyl-d-glucose (PGG), and EA were more stable at 4°C and pH 2.5. Overall, during storage at 4°C and pH 2.5, it could inhibit the increase of GA and EA and decrease of CL, GCG, CA, and PGG, whereas EGC did not show significant difference between storage conditions. The CPR was higher at 4°C, while pH 2.5 could reduce the CPR. In conclusion, in order to maintain stability of phenolic compounds and extended storage period, the P. emblica juice could be stored at low temperature and adjust the pH to increase the stability of juice system.

Prevalence and clinical outcomes of sarcopenia in patients with esophageal, gastric or colorectal cancers receiving preoperative neoadjuvant therapy: A meta-analysis.

Objective: To investigate the prevalence of sarcopenia and its impact on clinical outcomes in patients with esophageal, gastric, or colorectal cancer (EC, GC, and CRC) receiving neoadjuvant therapy through Meta-analysis. Methods: We searched the PubMed, Embase databases, and Cochrane Library for the prevalence of sarcopenia and its impact on clinical outcomes in EC, GC, or CRC patients treated with neoadjuvant therapy (NAT) from inception to November 2022. The primary endpoints were the prevalence of sarcopenia and overall survival in patients with EC, GC, or CRC treated with NAT. Secondary outcomes included recurrence-free survival, total postoperative complications, grade 3-4 chemotherapy toxicity, and 30-day mortality after surgery. Results: Thirty-one retrospective studies with 3651 subjects were included. In a fixed-effects model, the prevalence of muscle loss was higher in patients with EC, GC, or CRC at 50% (95% CI â€‹= â€‹42% to 58%). The results of the multivariate analysis showed that preoperative patients with sarcopenia had a 1.91 times shorter overall survival (95% CI â€‹= â€‹1.61-2.27) and a 1.77 times shorter recurrence-free survival time (95% CI â€‹= â€‹1.33-2.35) than patients without sarcopenia, and that patients with sarcopenia had a higher risk of total postoperative complications than patients without sarcopenia OR â€‹= â€‹1.27 (95% CI â€‹= â€‹1.03-1.57). However, the two groups had no statistical difference in grade 3-4 chemotherapy toxicity (P â€‹= â€‹0.84) or 30-d postoperative mortality (P â€‹= â€‹0.88). Conclusions: The prevalence of sarcopenia in patients with EC, GC, or CRC during NAT is high, and it is associated with poorer clinical outcomes. Clinicians should closely monitor the changes in patients' body composition and guide patients to carry out a reasonable diet and appropriate exercise to improve their poor prognosis and quality of life. Systematic review registration: CRD42023387817.

Psychometric Properties of the Chinese Version of the Functional Assessment of Chronic Illness Therapy - Palliative Care (FACIT-Pal) in Patients With Advanced Cancer.

CONTEXT: The Functional Assessment of Chronic Illness Therapy-Palliative Care (FACIT-Pal) has been widely used in assessing the quality of life (QOL) of patients with life-limiting illness. However, the Chinese version of the FACIT-Pal has not been psychometrically validated yet. OBJECTIVES: The purpose of this study was to psychometrically validate the FACIT-Pal in Chinese patients with advanced cancer. METHODS: 160 patients with advanced cancer in mainland China participated in this cross-sectional study. The scalability of the instrument was determined by the item-total correlations and the reliability was tested by examining the Cronbach's alpha coefficients. The construct and concurrent validity of the FACIT-Pal were also examined. RESULTS: The item-total correlation coefficients ranged from 0.25 to 0.72 (P < .01). Cronbach's alpha coefficient of the Chinese version of the FACIT-Pal was 0.94, ranging from 0.78 to 0.89 for subscales. Confirmatory factor analysis (CFA) results provided support for the measurement structure of the 26-item Functional Assessment of Cancer Therapy-General (FACT-G). Exploratory factor analysis (EFA) of the 19-item palliative care subscale identified five factors accounting for 62.21% of the total variance. Total/subscale scores of the FACIT-Pal were positively correlated with that of the Functional Assessment of Chronic Illness Therapy-Spiritual Well-Being 12 Item Scale (FACIT-Sp-12) (r = 0.338-0.811, P < .01), as well as with the Karnofsky Performance Scale (KPS) scores (r = 0.163-0.273, P < .05), except for the correlation between social/family well-being subscale score and KPS score. CONCLUSION: The Chinese version of the FACIT-Pal demonstrates desirable psychometric properties for evaluating QOL in Chinese patients with advanced cancer.

Causal effect of vitamin D on myasthenia gravis: a two-sample Mendelian randomization study.

Introduction: Observational studies suggest that vitamin D supplementation may be effective in preventing myasthenia gravis (MG). However, the causal relationship between circulating vitamin D levels and MG remains unclear. This study aimed to examine the genetic causality of circulating vitamin D and MG using data from large population-based genome-wide association studies (GWAS). Methods: SNPs (single nucleotide polymorphisms) strongly associated with exposure were selected. Two-sample Mendelian Randomization (MR) was performed with inverse variance weighting (IVW), MR-Egger (Mendelian randomization-Egger), weight median and MR-PRESSO (Mendelian randomization pleiotropy residual sum and outlier) methods. Heterogeneity was tested via IVW and MR-Egger. Pleiotropy was tested using MR-Egger intercept test and MR-PRESSO method. MR-PRESSO was also used to detect outliers. Leave-one-out analysis was used to identify SNPs with potential effect. Reverse MR analysis was also performed. Result: In IVW, circulating vitamin D levels had no causal effect on MG [OR = 0.91 (0.67-1.22), p = 0.532] and MG had no causal effect on circulating vitamin D [OR = 1.01 (099-1.02), p = 0.663]. No heterogeneity or pleiotropy was observed (p > 0.05). Other MR methods also agreed with IVW results. Conclusion: This study provides the causal relationship between genetically predicted circulating vitamin D levels and MG and provides new insights into the genetics of MG.

Novel Mutations in COL6A3 That Associated With Peters' Anomaly Caused Abnormal Intracellular Protein Retention and Decreased Cellular Resistance to Oxidative Stress.

Peters' anomaly (PA) is a rare form of anterior segment dysgenesis characterized by central corneal opacity accompanied by iridocorneal or lenticulo-corneal adhesions. Although genetic mutations, particularly those affecting transcription factors that function in eye development, are known to cause PA, the etiology of this disease remains poorly understood. In this study, 23 patients with PA were recruited for panel sequencing. Four out of 23 patients were found to carry variants in known PA causal genes, PITX2 and PITX3. More importantly, two homozygous mutations (NM_057164: p.Val86Ala and p.Arg689Cys) in the COL6A3 gene (collagen type VI alpha-3 chain) that correlated with the phenotype of type I PA were identified, and then validated by following whole-exome sequencing. The expression profile of the COL6A3 gene in the cornea and the impact of the mutations on protein physiological processing and cellular function were further explored. It was shown that COL6A3 presented relatively high expression in the cornea. The mutant COL6A3 protein was relatively retained intracellularly, and its expression reduced cellular resistance to oxidative stress through an enhanced endoplasmic reticulum stress response. Taken together, our findings expanded the known genetic spectrum of PA, and provided evidence for the involvement of COL6A3 or collagen VI in ocular anterior segment development, thereby offering new insight for future investigations targeting PA.

Novel Mutations Associated With Various Types of Corneal Dystrophies in a Han Chinese Population.

Aims: To study the genetic spectra of corneal dystrophies (CDs) in Han Chinese patients using next-generation sequencing (NGS). Methods: NGS-based targeted region sequencing was performed to evaluate 71 CD patients of Han Chinese ethnicity. A custom-made capture panel was designed to capture all coding exons and untranslated regions plus 25 bp of intronic flanking sequences of 801 candidate genes for eye diseases. The Genome Analysis Tool Kit Best Practices pipeline and an intensive computational prediction pipeline were applied for the analysis of pathogenic variants. Results: We achieved a mutation detection rate of 59.2% by NGS. Eighteen known mutations in CD-related genes were found in 42 out of 71 patients, and these cases showed a genotype-phenotype correlation consistent with previous reports. Nine novel variants that were likely pathogenic were found in various genes, including CHST6, TGFBI, SLC4A11, AGBL1, and COL17A1. These variants were all predicted to be protein-damaging by an intensive computational analysis. Conclusions: This study expands the spectra of genetic mutations associated with various types of CDs in the Chinese population and highlights the clinical utility of targeted NGS for genetically heterogeneous CD.

Compound heterozygous mutations in SMO associated with anterior segment dysgenesis and morning glory syndrome.

Eye development in vertebrates is a highly coordinated multistep process while defects in key factors might lead to severe congenital ocular disorders. SMO encodes a G protein-coupled receptor that functions in Hedgehog signal transduction, an essential step during eye development. Here we reported the first identification of compound heterozygous mutations (c.G338A; p.R113Q and c.C1619T; p.A540V) in the SMO gene in a patient with both anterior segment dysgenesis (congenital corneal opacity, cataract) and morning glory syndrome, using trio-based whole exome sequencing. The clinical manifestations of this patient were quite consistent with the phenotypes observed in murine SMO null mutants. In silico bioinformatics analyses showed that the newly identified mutations revealed extremely low allele frequencies in the general populations, and were predicted to affect SMO protein stability and residues physiochemical properties. Further investigations revealed a significant decrease of SMO expression in the patient compared with healthy controls (0.71 ±â€¯0.04 vs. 1.49 ±â€¯0.29, P = 0.0265). Therefore, this study pinpoints, for the first time, the potential key sites in SMO that contribute to the maintenance of healthy ocular development, highlighting potential targets for upcoming gene therapy.

A comprehensive evaluation of 181 reported CHST6 variants in patients with macular corneal dystrophy.

Macular corneal dystrophy (MCD) is an autosomal recessive disease featured by bilateral progressive stromal clouding and loss of vision, consequently necessitating corneal transplantation. Variants in CHST6 gene have been recognized as the most critical genetic components in MCD. Although many CHST6 variants have been described until now, the detailed mechanisms underlying MCD are still far from understood. In this study, we integrated all the reported CHST6 variants described in 408 MCD cases, and performed a comprehensive evaluation to better illustrate the causality of these variants. The results showed that majority of these variants (165 out of 181) could be classified as pathogenic or likely pathogenic. Interestingly, we also identified several disease causal variants with ethnic specificity. In addition, the results underscored the strong correlation between mutant frequency and residue conservation in the general population (Spearman's correlation coefficient = -0.311, P = 1.20E-05), thus providing potential candidate targets for further genetic manipulation. The current study highlighted the demand of further functional investigations to evaluate the causality of CHST6 variants, so as to promote earlier accurate diagnosis of MCD and future development of potential targets for genetic therapy.

Evaluating the association between calpastatin (CAST) gene and keratoconus in the Han Chinese population.

PURPOSE: To investigate whether calpastatin (CAST) gene polymorphisms are in association with keratoconus (KC) in Han Chinese population. METHODS: Four SNPs (rs4434401, rs7704167, rs26504, and rs10053056) in CAST gene were genotyped in 120 unrelated Han Chinese KC patients and 305 age and gender matched healthy controls, using TaqMan SNP genotyping method. PLINK and LDmatrix software was used for data analysis. RESULTS: SNP rs4434401, whose contribution to KC susceptibility has been established in Caucasians, still kept its effect in our population. The C allele frequency of rs4434401 was markedly higher in cases (27.7%) than in the controls (20.7%, P = 0.03654, OR = 1.47, 95%CI = 1.02-2.11). The genotype distribution of rs4434401 showed marginal difference between KC cases and controls. The allelic and genotype frequencies of other three tested SNPs showed no significant difference between cases and controls. CONCLUSION: We confirmed previous report that SNP(s) in CAST gene conferred risk for KC susceptibility in Han Chinese population, suggesting the potential contribution of CAST gene to KC development.