Transcriptome RNA-Seq Analysis of Normal and Keratoconus Corneal Epithelium
1 Department of Clinical Laboratory Sciences, Faculty of Applied Medical Science, Libyan International Medical University, Benghazi, Libya.
2 Department of Biological Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
3 Department of Molecular Diagnostic, Faculty of Biomedical Sciences, University of Benghazi, Libya.
4 Department of Medicine, School of Medicine, University of Leeds, Leeds, UK.
5 Department of Medicine, Faculty of Medicine, Libyan International Medical University, Benghazi, Libya.
6 Department of Histology, Faculty of Medicine, University of Benghazi, Benghazi, Libya.
Research Article
International Journal of Frontiers in Life Science Research, 2024, 06(02), 027–043.
Article DOI: 10.53294/ijflsr.2024.6.2.0032
Publication history:
Received on 25 March 2024; revised on 08 May 2024; accepted on 11 May 2024
Abstract:
Background: Keratoconus (KTCN) is a progressive eye condition characterised by thin, misshapen corneas arising in the teens or early twenties, and can cause visual disability. While this can be corrected with glasses or contact lenses, collagen cross-linking of the cornea slows disease progression. In advanced disease, patients undergo transplantation of the corneal epithelial layer with normal donor tissue. The cause of KTCN is unknown, but there is evidence for both environmental and genetic bases.
Material and Methods: RNA-Seq data from published work by Kabza et al., 2017, was used to investigate the pathology of cornea tissue, analysing twenty-five KTCN and twenty-five non-KTCN samples from RNA-seq experiments. Principal component analysis plots were used to identify how characteristics impact development of keratoconus.
Results: The findings show that KTCN is more common in teenagers and young adults, and all 25 KTCN samples were for individuals under 30 years old. Principal component analysis also showed that approximately 35% of samples were from individuals who rubbed their eyes. It also showed that KTCN is more common in males, representing over 65% of samples. Differential expression analysis of RNA-sequencing data was used to identify differentially expressed genes, downregulated genes were found to be enriched in many pathways, including cytokinecytokine receptor interaction pathways, and played a role in keratoconus development.
Conclusion: Upregulated genes were enhanced in six pathways, including the peroxisome pathway. A potential relation was found between defects in peroxisome and keratoconus development. Overexpression of peroxisome genes increases phytanic acid levels, and causes Zellweger spectrum, affecting the cornea and potentially leading to keratoconus.
Keywords:
Keratoconus; Differential expression analysis; Pathway overrepresentation analysis; Upregulated and downregulated genes; Peroxisome genes
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