Genome-wide DNA methylation profiling identifies epigenetic signatures of gastric cardiac intestinal metaplasia

Abstract

Background: Measuring the DNA methylome may offer the opportunity to identify novel disease biomarkers and insights into disease mechanisms. Although aberrant DNA methylation has been investigated in many human cancers and precancerous lesions, the DNA methylation landscape of gastric cardiac intestinal metaplasia (IM) remains unknown. Therefore, we aimed to investigate the genome-wide DNA methylation landscape and to search for potential epigenetic biomarkers of gastric cardiac IM. Methods: Histopathologic profiling was performed on a total of 118 gastric cardiac biopsies from cancer-free individuals. Genome-wide DNA methylation analysis was performed on 11 gastric cardiac mucosal biopsies (IM = 7; normal = 4) using Illumina 850K microarrays. Transcriptional relevance of any candidate epigenetic biomarker was validated by qRT-PCR. Results: The detection rate of gastric cardiac IM was 23% (27/118) in cancer-free individuals. Genome-wide DNA methylation profiling showed a global decrease in methylation in IM compared with normal tissues (median methylation = 0.64 and 0.70 for gastric cardiac IM and normal tissues, respectively). Differential methylation analysis between gastric cardiac IM and normal tissues identified 38,237 differentially methylated probes (DMPs) with a majority of sites showing hypermethylation in IM compared with normal tissues (56.3% vs. 43.7%). Subsequent analysis revealed a significant enrichment of hypermethylated DMPs in promoter and CpG islands (p < 0.001 for both, Pearson χ 2 test). For DMPs located in promoter CpG islands showing extreme hypermethylation, the candidate gene with the largest number of DMPs (n = 7) was mapped to HOXA5. Accordingly, mRNA expression of HOXA5 was significantly reduced in IM compared to normal tissue. Conclusions: Our results suggest the implication of alterations in DNA methylation in gastric cardiac IM and highlight that HOXA5 hypermethylation may be a promising epigenetic biomarker, emphasizing the role of aberrant HOXA5 expression in the pathogenesis of gastric cardiac IM.

Molecular Alterations in Gastric Intestinal Metaplasia

“…Another study performed the analysis of DNA methylation in gastric cardiac mucosa. It revealed that apart from promoter hypermethylation, a reduced mRNA expression of the homeobox A5 (HOXA5) gene (which functions as a tumor suppressor in the development of GC) was also observed in gastric cardiac IM, suggesting a possible role of this gene in the development of gastric IM [62]. A Brazilian study investigated the expression of telomerase reverse transcriptase (TERT) gene mRNA in normal gastric mucosa, precancerous gastric lesions, and gastric cancer.…”

Epigenome-Wide Association Study Reveals Differential Methylation Sites and Association of Gene Expression Regulation with Ischemic Moyamoya Disease in Adults

“…All cells were cultured in endothelial cell culture medium for 10-15 generations to eliminate the effects of cell growth factors produced by naive protocells as much as possible. All media were composed of 500 mL basal nutrients, 25 mL fetal bovine serum, 5 mL endothelial cell growth factors, and 5 mL penicillin solution ( 41 ). When the cells were more than 90% confluent, the medium was replaced, and the cells were washed several times with 2 mL phosphate buffered saline (PBS) to eliminate the residual cell growth factors.…”

“…Reagents A and B were mixed and incubated for 20 min. The mixed reagent (400 μ L per well) was added to the corresponding 24-well plate, which was replaced with serum containing colorectal cell culture medium after 6 h ( 41 ).…”

Molecular Landscapes of Gastric Pre-Neoplastic and Pre-Invasive Lesions

“…Differences in commitment between complete and incomplete IM are also highlighted by the different expression of gastric (SOX2) and intestinal (CDX2) transcription factors: while CDX2 is expressed in all types of IM, SOX2 is negative in 93% of complete IM and positive in 85% of incomplete types [ 60 ]. Despite the fact that some authors [ 61 , 62 , 63 , 64 , 65 , 66 , 67 , 68 , 69 , 70 , 71 , 72 , 73 , 74 ] suggest that incomplete IM is associated with increased risk of GC, there is no conclusive evidence of differences in cancer progression among IM types, and IM characterization is not currently recommended in clinical practice [ 59 ].…”

“…In contrast, global intragenic hypomethylation has not been detected in IM, representing a later event in Correa’s cascade. Finally, Lin and colleagues [ 69 ] suggest that hypermethylation of HOXA5 has a role in the development of gastric cardiac IM.…”