Cigarette smoke modulates methylation levels of LEF1-AS1 and impedes its expression: An experimental study

Cigarette smoke (CS) contains carcinogenic substances and influences genetic regulation and epigenetic modifications, such as DNA methylation. It plays a role in the development of various cancers, including colon, bladder, lung cancer, and leukemia. Long non-coding RNAs play a significant role in controlling several pathways in the cell, including lymphoid enhancer-binding factor 1 antisense RNA 1 (LEF1-AS1), which is found overexpressed in lung, oral, glioblastoma, and colon cancers and downregulated in leukemias. We investigated the impact of CS on DNA methylation of the promoter region of LEF1-AS1 as well as its expression in endothelial cells.

This experimental study was designed to investigate the effects of cigarette smoke on the methylation status of the promoter region of LEF1-AS1 in smoker and non-smoker samples and its expression in relevant cell models. To measure the alternations of DNA methylation, extracted DNA samples from 64 male subjects (32 smokers and 32 non-smokers) were bisulfite-treated and amplified using polymerase chain reaction (PCR) with methylation-specific PCR primers. Furthermore, to define the impact of CS on LEF1-AS1 expression, human umbilical vein endothelial cells (HUVECs) were fed with media containing CS for 3 and 6 hours. The expression analysis of LEF1-AS1 was performed using the GTEx (Genotype-Tissue Expression) database, including an assessment of its expression in various cancers such as lung and brain cancers. The functional analysis of the LEF1-AS1 gene was conducted across multiple tissues using data from the GENT2 databases, along with meta-survival and functional enrichment analysis.

The results indicated an average increase of 19.8% in DNA methylation of the promoter region of LEF1-AS1 in the samples from the smokers compared with those from the non-smokers, as well as a significant reduction of LEF1-AS1 expression level in the HUVECs (45% and 83%) after treatment with CS (3 and 6 Hours), respectively. LEF1-AS1 expression varied significantly across tumor types when compared to their normal counterparts. Some cancers, such as lung and brain, showed increased expression, suggesting cancer-specific overexpression of LEF1-AS1. Variability in expression across cancers and normal tissues implies potential heterogeneity in gene regulation. A meta-survival analysis of the LEF1-AS1 gene (e.g. GSE31546, GSE31548, GSE19188), revealed hazard ratios (HR) ranging widely, with some studies (e.g. GSE31546, HR=12.02) suggesting increased risk, though confidence intervals often included 1, indicating uncertainty. Low heterogeneity (I²=16%, p=0.26) suggests consistency among studies, but the overall findings lack strong statistical significance.

Our findings indicate that CS alters LEF1-AS1 DNA methylation and causes an inhibition of LEF1-AS1 expression.