Correlation between small-scale methylation changes and gene expression during the development of myopia

DNA methylation biomarkers and myopia: a multi-omics study integrating GWAS, mQTL and eQTL data

BACKGROUND

This study aimed to identify DNA methylation biomarkers associated with myopia using summary-data-based Mendelian randomization (SMR).

METHODS

A systematic search of the PubMed, Web of Science, Cochrane Library, and Embase databases was conducted up to March 27, 2024. SMR analyses were performed to integrate genome-wide association study (GWAS) with methylation quantitative trait loci (mQTL) and expression quantitative trait loci (eQTL) studies. The heterogeneity in the dependent instrument (HEIDI) test was utilized to distinguish pleiotropic associations from linkage disequilibrium.

RESULTS

The systematic review identified 26 DNA methylation biomarkers in five studies, with no overlap observed among those identified by different studies. After integrating GWAS with multi-omics data of mQTL and eQTL, six genes were significantly associated with myopia: PRMT6 (cg00944433 and cg15468180), SH3YL1 (cg03299269, cg11361895, and cg13354988), ZKSCAN4 (cg01192291), GATS (cg17830204), NPAT (cg04826772), and UBE2I (cg03545757 and cg08025960).

CONCLUSIONS

We identified six methylation biomarkers associated with the risk of myopia that may be helpful to elucidate the etiology mechanisms of myopia. Further experimental validation studies are required to corroborate these findings.

PAX6 gene promoter methylation is correlated with myopia in Chinese adolescents: a pilot sutdy

PURPOSE

A large number of epidemiological studies have shown that myopia is a complex disease involving genetic, environmental, and behavioral factors. The purpose of this study was to explore the role of PAX6 gene methylation in myopia in Chinese adolescents.

METHODS

Eighty junior high school students were divided into four groups based on their vision test results: mild myopia, moderate myopia, severe myopia, and non-myopia control. The methylation level of PAX6 gene promoter was detected by bisulfate pyrosequencing.

RESULTS

The methylation level of PAX6 gene in myopia group (8.06% ± 1.43%) was slightly but significantly higher than that in non-myopia controls (7.26% ± 1.17%). In addition, PAX6 gene methylation levels presented a decreasing pattern along with the aggravation of myopia. Post-hoc analysis indicated significant inter-group differences for the mild myopia group and other groups (All p < .05). In the subgroup analysis by gender, the methylation level of PAX6 gene promoter in girls was higher than that in boys (p = .023). The ROC curves showed a high accuracy of PAX6 gene methylation to predict mild myopia (AUC (95% CI) = 0.828 (0.709-0.947), p < .001).

CONCLUSIONS

The methylation of PAX6 gene might play a role in the onset and progression of myopia in Chinese adolescents. And this could potentially explore the potential molecular mechanisms of juvenile myopia in the future.

Crosstalk between heredity and environment in myopia: An overview

In recent years, the prevalence of myopia has gradually increased, and it has become a significant global public health problem in the 21st century, posing a serious challenge to human eye health. Currently, it is confirmed that the development of myopia is attributed to the combined action of genes and environmental factors. Thus, elucidating the risk factors and pathogenesis of myopia is of great significance for the prevention and control of myopia. To elucidate the impact of gene-environment interaction on myopia, we used the Pubmed database to search for literature related to myopia. Search terms are as follows: myopia, genes, environmental factors, gene-environment interaction, and treatment. This paper reviews the effects of gene and environmental interaction on myopia.

DNA methylation analysis to differentiate reference, breed, and parent-of-origin effects in the bovine pangenome era

BACKGROUND

Most DNA methylation studies have used a single reference genome with little attention paid to the bias introduced due to the reference chosen. Reference genome artifacts and genetic variation, including single nucleotide polymorphisms (SNPs) and structural variants (SVs), can lead to differences in methylation sites (CpGs) between individuals of the same species. We analyzed whole-genome bisulfite sequencing data from the fetal liver of Angus (Bos taurus taurus), Brahman (Bos taurus indicus), and reciprocally crossed samples. Using reference genomes for each breed from the Bovine Pangenome Consortium, we investigated the influence of reference genome choice on the breed and parent-of-origin effects in methylome analyses.

RESULTS

Our findings revealed that ∼75% of CpG sites were shared between Angus and Brahman, ∼5% were breed specific, and ∼20% were unresolved. We demonstrated up to ∼2% quantification bias in global methylation when an incorrect reference genome was used. Furthermore, we found that SNPs impacted CpGs 13 times more than other autosomal sites (P < $5 \times {10}^{ - 324}$) and SVs contained 1.18 times (P < $5 \times {10}^{ - 324}$) more CpGs than non-SVs. We found a poor overlap between differentially methylated regions (DMRs) and differentially expressed genes (DEGs) and suggest that DMRs may be impacting enhancers that target these DEGs. DMRs overlapped with imprinted genes, of which 1, DGAT1, which is important for fat metabolism and weight gain, was found in the breed-specific and sire-of-origin comparisons.

CONCLUSIONS

This work demonstrates the need to consider reference genome effects to explore genetic and epigenetic differences accurately and identify DMRs involved in controlling certain genes.

Hypoxia Affects HIF-1/LDH-A Signaling Pathway by Methylation Modification and Transcriptional Regulation in Japanese Flounder (Paralichthys olivaceus)

Simple Summary

With global climate change and increased aquaculture production, fishes in natural waters or aquaculture systems are easily subjected to hypoxic stress. However, our understanding about their responsive mechanisms to hypoxia is still limited. Japanese flounder (Paralichthys olivaceus) is a widely cultivated marine economical flatfish, whose hypoxic responsive mechanisms are not fully researched. In this study, responses to hypoxia were investigated at blood physiological, biochemical, hormonal, and molecular levels. Responsive mechanisms of the HIF-1/LDH-A signaling pathway in epigenetic modification and transcriptional regulation were also researched. These results are important for enriching the theory of environmental responsive mechanisms and guiding aquaculture.

Abstract

Japanese flounder (Paralichthys olivaceus) responsive mechanisms to hypoxia are still not fully understood. Therefore, we performed an acute hypoxic treatment (dissolved oxygen at 2.07 ± 0.08 mg/L) on Japanese flounder. It was confirmed that the hypoxic stress affected the physiological phenotype through changes in blood physiology (RBC, HGB, WBC), biochemistry (LDH, ALP, ALT, GLU, TC, TG, ALB), and hormone (cortisol) indicators. Hypoxia inducible factor-1 (HIF-1), an essential oxygen homeostasis mediator in organisms consisting of an inducible HIF-1α and a constitutive HIF-1β, and its target gene LDH-A were deeply studied. Results showed that HIF-1α and LDH-A genes were co-expressed and significantly affected by hypoxic stress. The dual-luciferase reporter assay confirmed that transcription factor HIF-1 transcriptionally regulated the LDH-A gene, and its transcription binding sequence was GGACGTGA located at −2343~−2336. The DNA methylation status of HIF-1α and LDH-A genes were detected to understand the mechanism of environmental stress on genes. It was found that hypoxia affected the HIF-1α gene and LDH-A gene methylation levels. The study uncovered HIF-1/LDH-A signaling pathway responsive mechanisms of Japanese flounder to hypoxia in epigenetic modification and transcriptional regulation. Our study is significant to further the understanding of environmental responsive mechanisms as well as providing a reference for aquaculture.

Decreased Levels of DNA Methylation in the PCDHA Gene Cluster as a Risk Factor for Early-Onset High Myopia in Young Children

Purpose

High myopia (HM), an eye disorder with at least –6.0 diopters refractive error, has a complex etiology with environmental, genetic, and likely epigenetic factors involved. To complement the DNA methylation assessment in children with HM, we analyzed genes that had significantly lower DNA methylation levels.

Methods

The DNA methylation pattern was studied based on the genome-wide methylation data of 18 Polish children with HM paired with 18 controls. Genes overlapping CG dinucleotides with decreased methylation level in HM cases were assessed by enrichment analyses. From those, genes with CG dinucleotides in promoter regions were further evaluated based on exome sequencing (ES) data of 16 patients with HM from unrelated Polish families, Sanger sequencing data of the studied children, and the RNA sequencing data of human retinal ARPE-19 cells.

Results

The CG dinucleotide with the most decreased methylation level in cases was identified in a promoter region of PCDHA10 that overlaps intronic regions of PCDHA1–9 of the PCDHA gene cluster in myopia 5q31 locus. Also, two single nucleotide variants, rs200661444, detected in our ES, and rs246073, previously found as associated with a refractive error in a genome-wide association study, were revealed within this gene cluster. Additionally, genes previously linked to ocular phenotypes, myopia-related traits, or loci, including ADAM20, ZFAND6, ETS1, ABHD13, SBSPON, SORBS2, LMOD3, ATXN1, and FARP2, were found to have decreased methylation.

Conclusions

Alterations in the methylation pattern of specific CG dinucleotides may be associated with early-onset HM, so this could be used to develop noninvasive biomarkers of HM in children and adolescents.