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International Ophthalmology
Erschienen in: International Ophthalmology 1/2024

01.12.2024 | Original Paper

Analysis and validation of potential ICD-related biomarkers in development of myopia using machine learning

verfasst von: Yun Zhang, Yanli Liu, Meixia An

Erschienen in: International Ophthalmology | Ausgabe 1/2024

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Abstract

Purpose

We aimed to identify and verify potential biomarkers in the development of myopia associated with immunogenic cell death (ICD).

Methods

We download high myopia (HM) dataset GSE136701 from Gene Expression Omnibus. Differentially expressed genes in HM were identified to overlapped with ICD-related genes. Least absolute shrinkage and selection operator were used to select the Hub genes. Furthermore, the correlation between the hub genes and immune infiltration, immune response activities, and hub genes Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis was investigated using Spearman's rank correlation. Prediction of the miRNAs upstream of the Hub genes was based on the TargetScan database. We used guinea pig lens-induced myopia model’s scleral tissues performed quantitative real-time polymerase chain reaction.

Results

We identified overlapped with ICD-related genes (LY96, IL1A, IL33, and AGER) and two genes (LY96 and AGER) as hub genes. Single sample gene set enrichment analysis and Spearman’s rank correlation revealed that hub gene expression levels in HM were significantly correlated with the infiltration percentages of CD56dim natural killer cells, macrophages, immature B cells, and the immune response activities of APC co-stimulation and Kyoto Encyclopedia of Genes and Genomes pathways, such as terpenoid backbone biosynthesis, aminoacyl-trna biosynthesis, Huntington’s disease, oxidative phosphorylation; there were a few additional signaling pathways compared to normal samples. Additionally, several miRNA were predicted as upstream regulators of LY96 and AGER. LY96 was identified as a significantly differentially expressed biomarker in myopia guinea pig’s scleral tissues, as verified by qPCR.

Conclusion

LY96 was identified and verified as a ICD-related potential myopia biomarker. Molecular mechanisms or pathways involved in myopia development by LY96 requires further research.
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Metadaten
Titel
Analysis and validation of potential ICD-related biomarkers in development of myopia using machine learning
verfasst von
Yun Zhang
Yanli Liu
Meixia An
Publikationsdatum
01.12.2024
Verlag
Springer Netherlands
Erschienen in
International Ophthalmology / Ausgabe 1/2024
Print ISSN: 0165-5701
Elektronische ISSN: 1573-2630
DOI
https://doi.org/10.1007/s10792-024-02986-1

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