Association of KIF26B and COL4A4 gene polymorphisms with the risk of keratoconus in a sample of Iranian population

Transcriptome and proteome revealed the differences in 3 colors of earlobe in Jiangshan Black-bone chicken

The earlobe is a featherless, exposed thickening located beneath the ear canal of chickens, which plays a visual signaling role in age, performance, mental vitality, reproduction, and other aspects. However, despite its importance, there have been few studies on the color differences and formation mechanisms of chicken earlobes, particularly the structurally blue earlobes characteristic of the Jiangshan black-bone chicken. In this study, we explored the physiological mechanisms that may influence the formation of differently colored earlobes using 3 types of earlobes from Jiangshan black-bone chickens: light peacock green (Green group), dark peacock green (Blue group), and dark reddish purple (Black group). All 3 earlobe colors exhibited positive melanin Masson-Fontana staining, and the thickness of collagen fibers in the dermis decreased in the order of Green, Blue, and Black groups. A total of 1,953 differentially expressed genes (DEGs) were detected in the 3 earlobes through mRNA sequencing, among which the GO term "collagen trimer" was significantly enriched in DEGs between groups. Additionally, 716 differentially expressed proteins (DEPs) were identified in the 3 earlobes using 4D-DIA proteomics, with the term "collagen fibril organization" being significantly enriched in DEPs between the Green and Black groups. Integrated analysis of transcriptome and proteome data revealed that 12 DEGs and DEPs were commonly differentially expressed between the Green and Black groups, including the gene LUM (corneal keratan sulfate proteoglycan), which was significantly enriched in the "collagen fibril organization" GO term. In conclusion, our study suggests that LUM plays a crucial role in the formation of peacock green earlobes in Jiangshan black-bone chickens. The high level of LUM in peacock green (Green and Blue groups) may affect collagen nanostructures, leading to a stronger effect of melanin-supported dermal collagen on the production of non-iridescent structural colors through coherent scattering, resulting in a bright structural blue color in Jiangshan black-bone chickens. In contrast, the low expression of LUM in dark reddish purple (Black group) reduces the reflection of non-iridescent structural colors, making the earlobe color appear almost black, similar to melanin.

Heritability of Corneal Parameters in Nuclear Families With Keratoconus

Purpose

This study aimed to investigate the heritability of corneal parameters obtained by Pentacam in nuclear families with keratoconus (KC).

Methods

A total of 82 patients with KC and their biological parents (n = 164) were recruited in the current study. All subjects underwent corneal tomography with Pentacam. Family units were analyzed to calculate the heritability of corneal parameters by linear mixed effects model using the R statistical software.

Results

The pachymetry at apex, pupil, and thinnest point were all significantly heritable at 43.26%, 42.63%, and 43.09%, respectively. The heritability of flat meridian keratometry, steep meridian keratometry, and mean keratometry in the anterior surface were 10.36%, 9.05%, and 10.21%, respectively, and that of flat meridian keratometry, steep meridian keratometry, and mean keratometry in the posterior surface were 8.44%, 9.67%, and 9.06%, respectively. The posterior radius of curvature had higher heritability in comparison with anterior radius of curvature (19.16% vs. 14.37%). Moreover, among combined topometric indices, the heritability of index of vertical asymmetry was the highest (19.49%), and that of central keratoconus index was the lowest (6.64%).

Conclusions

The present study demonstrated a substantial heritability of corneal parameters in nuclear families with KC. The pachymetric indices are heritable and may be suitable as KC endophenotypes, suggesting a necessity to discover the genes associated with corneal thickness in KC.

Translational Relevance

The pachymetric indices are heritable and may be suitable as KC endophenotypes, indicating that the pachymetric indices might be a corneal characteristic to predict the occurrence of KC.

Systematically Displaying the Pathogenesis of Keratoconus via Multi-Level Related Gene Enrichment-Based Review

Keratoconus (KC) is an etiologically heterogeneous corneal ectatic disorder. To systematically display the pathogenesis of keratoconus (KC), this study reviewed all the reported genes involved in KC, and performed an enrichment analysis of genes identified at the genome, transcription, and protein levels respectively. Combined analysis of multi-level results revealed their shared genes, gene ontology (GO), and pathway terms, to explore the possible pathogenesis of KC. After an initial search, 80 candidate genes, 2,933 transcriptional differential genes, and 947 differential proteins were collected. The candidate genes were significantly enriched in extracellular matrix (ECM) related terms, Wnt signaling pathway and cytokine activities. The enriched GO/pathway terms of transcription and protein levels highlight the importance of ECM, cell adhesion, and inflammatory once again. Combined analysis of multi-levels identified 13 genes, 43 GOs, and 12 pathways. The pathogenic relationships among these overlapping factors maybe as follows. The gene mutations/variants caused insufficient protein dosage or abnormal function, together with environmental stimulation, leading to the related functions and pathways changes in the corneal cells. These included response to the glucocorticoid and reactive oxygen species; regulation of various signaling (P13K-AKT, MAPK and NF-kappaB), apoptosis and aging; upregulation of cytokines and collagen-related enzymes; and downregulation of collagen and other ECM-related proteins. These undoubtedly lead to a reduction of extracellular components and induction of cell apoptosis, resulting in the loosening and thinning of corneal tissue structure. This study, in addition to providing information about the genes involved, also provides an integrated insight into the gene-based etiology and pathogenesis of KC.

Screening of Biological Target Molecules Related to Glucocorticoid-Induced Cataract (GIC) on the Basis of Constructing ceRNA Network

Glucocorticoid-induced cataract (GIC)-associated biomarkers were screened by ceRNA network construction. The GIC samples' GSE3040 were obtained from the NCBI-GEO database. R's Limma package was used to identify differentially expressed RNAs (DERs) between the normal and GIC samples group (4- and 16-h). The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enrichment analysis for the mRNAs in the constructed GIC lncRNA-miRNA-mRNA ceRNA regulation network was implemented. A total of 1665 and 1443 DERs were obtained in the 4- and 16-h group, respectively. At two time points, 256 overlapping DERs were identified, of which 210 (17 lncRNAs and 203 mRNAs) had significant differential expression (4 down- and 206 up-regulated). A total of 534 co-expressed ligation pairs (all up-regulated) were obtained. A ceRNA regulation network was constructed. RPS6KA5, GAB1, CCR7, CCL2, COL4A4, and PPARG were obtained and significantly enriched in the 4 KEGG signaling pathways and were featured as GIC target molecules.

IL1A and IL1B gene polymorphisms and keratoconus susceptibility: evidence from an updated meta-analysis

Background: Several single-nucleotide polymorphisms (SNPs) in IL1B genes have been associated with KTCN. However, the results of these studies were not conclusive. This meta-analysis association study is aimed to quantitatively estimate the association of IL1B rs16944 (g.4490T>C) and rs1143627 (g.4970C>T), and IL1A rs2071376 (c.615 + 169C>A) polymorphisms with KTCN susceptibility.Materials and Methods: Systematic literature search was performed in Web of Science, MEDLINE, PubMed, Scopus, and Google Scholar databases. The odds ratios (ORs) and 95% confidence intervals (CI) were calculated assuming different contrasted genetic models.Results: The reference T allele of IL1B (g.4490T>C) polymorphism was significantly associated with decreased KTCN risk under all assessed genetic models. Regarding the reference C allele of IL1B (g.4970C>T) polymorphism, decreased risk of KTCN was found. The reference C allele of IL1A (c.615 + 169C>A) polymorphism conferred a decreased risk of KTCN under heterozygous codominant (AC vs. AA), homozygous codominant (CC vs. AA), and dominant (AC+CC vs. AA) genetic models. The pooling estimates showed that the T C haplotype was associated with a significant increase in KTCN risk. In contrast, the T T haplotype was correlated with a decreased risk of KTCN. With the assumption of a prior probability of 0.25, the false-positive report probability (FPRP) values were less than 0.2, indicating the observed significant associations were notable.Conclusion: These findings propose that the studied IL1B polymorphisms and the IL1A variation have opposite effects on KTCN susceptibility. More large-scale replication studies are warranted to illuminate the precise role of these SNPs on the etiology of eye disorders.