ENPP2 Promoter Methylation Correlates with Decreased Gene Expression in Breast Cancer: Implementation as a Liquid Biopsy Biomarker

Abstract

Autotaxin (ATX), encoded by the ctonucleotide pyrophosphatase/phosphodiesterase 2 (ENPP2) gene, is a key enzyme in lysophosphatidic acid (LPA) synthesis. We have recently described ENPP2 methylation profiles in health and multiple malignancies and demonstrated correlation to its aberrant expression. Here we focus on breast cancer (BrCa), analyzing in silico publicly available BrCa methylome datasets, to identify differentially methylated CpGs (DMCs) and correlate them with expression. Numerous DMCs were identified between BrCa and healthy breast tissues in the gene body and promoter-associated regions (PA). PA DMCs were upregulated in BrCa tissues in relation to normal, in metastatic BrCa in relation to primary, and in stage I BrCa in relation to normal, and this was correlated to decreased mRNA expression. The first exon DMC was also investigated in circulating cell free DNA (ccfDNA) isolated by BrCa patients; methylation was increased in BrCa in relation to ccfDNA from healthy individuals, confirming in silico results. It also differed between patient groups and was correlated to the presence of multiple metastatic sites. Our data indicate that promoter methylation of ENPP2 arrests its transcription in BrCa and introduce first exon methylation as a putative biomarker for diagnosis and monitoring which can be assessed in liquid biopsy.

Autotaxin in Breast Cancer: Role, Epigenetic Regulation and Clinical Implications

“…Furthermore, in an analysis of circulating cell free DNA (ccfDNA), ENPP2 was also found hypermethylated but failed to find any significant difference between methylation levels of healthy and BC patients [ 63 ]. In contrast to that, in our recent work, methylation of ENPP2 1st exon in ccfDNA was found significant hypermethylated in BC patients as compared to healthy ccfDNA and it was also correlated with the cancer load [ 13 ], suggesting a role of ENPP2 methylation as a BC prognostic biomarker. These controversial results could be methodologically explained due to the different regions of ENPP2 gene that were examined in the patient samples.…”

“…In our recent in silico analysis of ENPP2 methylation in BC tissues, it was found that the promoter CGs were hypermethylated in comparison to normal tissues and mRNA expression was downregulated and inversely correlated with the methylation. Hypermethylation of ENPP2 was also associated with the progression of BC [ 13 ]. Together, these findings suggest that ENPP2 is highly methylated in BC, correlated with aggressiveness and low expression levels.…”

“…In parallel to studies in BC tissues, ENPP2 hypermethylation of promoter associated CGs was also demonstrated in silico. Thus, datasets of ccfDNAs from BC patients showed higher methylation in relation to ccfDNAs from healthy individuals [ 13 ]. We further evaluated ENPP2 methylation in ccfDNA of BC patients in order to examine its clinical value as a biomarker.…”

“…Importantly, ATX and LPA have been recognized as potential diagnostic biomarkers and drug targets for cancer and chronic inflammatory diseases [ 11 ]. Recently, our studies have shown that at the epigenetic level, methylation could play a key role in ATX regulation and pathogenesis [ 12 , 13 ]. Below, we present a review of the literature regarding the role of ATX and ENNP2 expression in the malignancy that it is more studied, i.e., breast cancer (BC), focusing on its potential implementation as a liquid biopsy biomarker.…”

Hypermethylation of tumor suppressor lncRNA MEF2C-AS1 frequently happened in patients at all stages of colorectal carcinogenesis

“…It is noteworthy that promoter methylation plays an important regulatory role in gene expression [ 30 – 32 ]. Although previous studies have reported that MEF2C-AS1 was downregulated in DGC [ 27 ] and CC [ 28 ] lesion tissues, and BC [ 29 ] cells, the current study is the first that systematically described the MEF2C-AS1 methylation status and its influence on expression.…”