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Updated: Oct 5, 2025
Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq
Published on: March 12, 2021
Integrated Analysis of Long Non-Coding RNA -mRNA Profile and Validation in Diabetic Cataract
Xiaoyan Han1,2,3,4, Lei Cai1,2,3,4, Yumeng Shi1,2,3,4
1Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai, China.
Purpose:
To illustrate the expression profile of lncRNAs and mRNAs in diabetic cataract (DC) and explore their potential role in the pathogenesis of DC.
Methods:
LncRNA and mRNA microarray were conducted using the lens epithelium of DC patients (n = 3) and controls from eye bank (n = 3). Further, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were employed to unveil their underlying biological function and signaling pathway. The co-expression network was constructed to explore the relationship between lncRNAs and mRNAs. Then, lens epithelial cells (LECs) were cultured in vitro under high glucose (HG) and normal glucose (NG) groups to further verified the expression profiles of mRNAs. At last, quantitative RT-PCR (qRT-PCR) was performed to confirm the microarray results for the aberrantly expressed lncRNAs, and to unveil the expression prolife of mRNAs in LECs.
Results:
Eight thousand three hundred and twenty-six lncRNAs and 3303 mRNAs were dysregulated in DC. GO analysis unveiled that the upregulated mRNAs, highest enrichment score of the GO term belonged to oxidation-reduction process, while the highest for downregulated mRNAs went to protein lipidation. In the CC category, the most significant terms for upregulated and downregulated mRNAs appeared in intracellular part and intrinsic component of membrane, respectively. As to MF category, the most significant term for upregulated mRNAs was protein binding, and for downregulated mRNAs was catecholamine binding. KEGG pathways analysis demonstrated that the major enrichment score of pathways in upregulated mRNAs included Glycolysis/Gluconeogenesis, lysosome, carbon metabolism and AGE-RAGE signaling pathway. For the downregulated mRNAs, the glycosphingolipid biosynthesis-lacto and neolacto series pathway was included. Three lncRNAs (LINC01508, MAFA-AS1, MIAT) and the Sirtuin 2 are positively related in the co-expression network.
Conclusions:
This study provided an overview of the lncRNAs and mRNAs expression, and suggesting that several aberrantly expressed lncRNAs might participate in the pathogenesis of DC.
