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Adenoviral Gene Therapy for Diabetic Keratopathy: Effects on Wound Healing and Stem Cell Marker Expression in Human Organ-cultured Corneas and Limbal Epithelial Cells
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Bioinformatics analysis of signature genes related to cell death in keratoconus

Jinghua Liu1,2, Juan Gao3, Shulei Xing4

  • 1School of Medicine, Nankai University, Tianjin, 300071, China.

Scientific Reports
|June 3, 2024
PubMed

Insights

Researchers identified six key cell death-related genes (TNFAIP3, CDKN1A, HSPA5, MAPK8IP1, PPP1R15A, VEGFA) significantly altered in keratoconus. These genes offer potential insights into the disease

Area of Science:

  • Ophthalmology
  • Genetics
  • Molecular Biology

Background:

  • Keratoconus is a progressive corneal disease causing vision loss.
  • The exact causes of keratoconus remain unclear.
  • Understanding the genetic basis of cell death pathways is crucial for keratoconus research.

Purpose of the Study:

  • To identify genes associated with cell death in keratoconus.
  • To analyze the function of these identified genes.
  • To explore potential therapeutic targets for keratoconus.

Main Methods:

  • Differential gene expression analysis of a keratoconus dataset (GSE151631).
  • Gene Ontology (GO) and KEGG pathway analysis.
  • Intersection of differentially expressed genes with cell death-related gene sets (ferroptosis, autophagy, pyroptosis, disulfidptosis, cuproptosis).
  • Machine learning techniques (LASSO, Random Forest) and ROC curve analysis for gene selection.
  • Gene Set Enrichment Analysis (GSEA).

Main Results:

  • 3558 differentially expressed genes (DEGs) were identified.
  • Six genes (TNFAIP3, CDKN1A, HSPA5, MAPK8IP1, PPP1R15A, VEGFA) related to ferroptosis and autophagy were selected.
  • These six genes showed significantly decreased expression in keratoconus.
  • High diagnostic accuracy (AUC values ranging from 0.726 to 0.944) was observed for these genes.
  • GSEA indicated their involvement in allograft rejection, asthma, and circadian rhythm.

Conclusions:

  • TNFAIP3, CDKN1A, HSPA5, MAPK8IP1, PPP1R15A, and VEGFA are potential key genes in keratoconus pathogenesis.
  • These findings suggest a link between keratoconus, cell death pathways, and autoimmune diseases.
  • Further research focusing on these genes and autoimmune connections may elucidate keratoconus etiology.

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