RNA-Seq Study of Human Lens Epithelial Cells: Differentially Expressed Genes and Pathways in Steroid, Uveitic, Post-Vitrectomy, and Senile Cataracts

Secondary causes of cataract contribute to significant morbidity, but their pathogeneses are not well understood. This RNA sequencing study aimed to be the first to quantify and compare the transcriptome of the uveitic, steroid-induced, and post-vitrectomy cataract, using age-related cataracts (ARCs) as the study control. Between March and July 2023 in Melbourne (VIC, Australia), human anterior lens capsules were prospectively collected during surgery from ARCs (n = 36), as well as steroid-induced (n = 23), uveitic (n = 25), and post-vitrectomy (n = 13) cataracts, and they were stabilized in RNAlater reagent. The Australian Genome Research Facility performed RNA isolation with RNeasy Mini and library preparation and sequencing using the Illumina workflow. Quality control was performed with the Agilent 2200 TapeStation. Bioinformatic analysis of RNA sequencing data identified differentially expressed genes (DEGs), defined as those with a log fold change ≥ 1 and false discovery rate (FDR) < 0.05. Differential gene expression analysis demonstrated significant differences between the transcriptome of age-related versus uveitic cataract (345 DEGs), steroid-induced versus uveitic cataract (117 DEGs), and age-related versus post-vitrectomy cataract (30 DEGs in the subgroup without removal of silicone oil [ROSO] and 1347 DEGs in the subgroup with ROSO). No DEGs were identified between age-related and steroid-induced cataracts. To our knowledge, this is the first large-scale gene expression study focusing on these secondary cataracts. This dataset will assist in forming a broader knowledge base of secondary cataract pathogenesis and inform future research in this area, particularly in the selection of specific genes and investigating their impact on cataract development through animal model studies.