Circulating Cell-Free DNA in Breast Cancer: Searching for Hidden Information towards Precision Medicine

Drosouni

Fanidis

et al. 2022

IJMS

Self Cite

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.

Section: Introductionmentioning

confidence: 99%

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

Drosouni

Fanidis

et al. 2022

IJMS

Self Cite

“…DNA methylation is the most studied epigenetic mechanism that is highly involved in the regulation of gene expression in BrCa cells [3]. Aberrant methylation in BrCa tissues or in liquid biopsies has been characterized and correlated to diagnosis [4][5][6], prognosis [7][8][9] and the prediction of treatment response [10,11], leading to emerging biomarkers in the BrCa management cascade. Recently, the introduction of genome-wide methylation analyses enables the simultaneous study of up to hundreds of thousands of CpG sites, and produces highdimensional datasets which can allow in-depth understanding of the events of methylation in BrCa pathogenesis, as well as its translation to clinical solutions.…”

Section: Introductionmentioning

confidence: 99%

Deciphering the Methylation Landscape in Breast Cancer: Diagnostic and Prognostic Biosignatures through Automated Machine Learning

Karaglani

Manolopoulos

et al. 2021

Cancers

Self Cite

DNA methylation plays an important role in breast cancer (BrCa) pathogenesis and could contribute to driving its personalized management. We performed a complete bioinformatic analysis in BrCa whole methylome datasets, analyzed using the Illumina methylation 450 bead-chip array. Differential methylation analysis vs. clinical end-points resulted in 11,176 to 27,786 differentially methylated genes (DMGs). Innovative automated machine learning (AutoML) was employed to construct signatures with translational value. Three highly performing and low-feature-number signatures were built: (1) A 5-gene signature discriminating BrCa patients from healthy individuals (area under the curve (AUC): 0.994 (0.982–1.000)). (2) A 3-gene signature identifying BrCa metastatic disease (AUC: 0.986 (0.921–1.000)). (3) Six equivalent 5-gene signatures diagnosing early disease (AUC: 0.973 (0.920–1.000)). Validation in independent patient groups verified performance. Bioinformatic tools for functional analysis and protein interaction prediction were also employed. All protein encoding features included in the signatures were associated with BrCa-related pathways. Functional analysis of DMGs highlighted the regulation of transcription as the main biological process, the nucleus as the main cellular component and transcription factor activity and sequence-specific DNA binding as the main molecular functions. Overall, three high-performance diagnostic/prognostic signatures were built and are readily available for improving BrCa precision management upon prospective clinical validation. Revisiting archived methylomes through novel bioinformatic approaches revealed significant clarifying knowledge for the contribution of gene methylation events in breast carcinogenesis.

“…Epigenetic regulation of ENPP2 has been previously reported [ 13 ]. DNA methylation, a well-studied epigenetic mechanism, can regulate gene expression [ 14 ], and aberrant gene-specific methylation has been correlated with many pathologies, such as cancer [ 15 , 16 , 17 , 18 , 19 , 20 ]. However, data on the methylation profile of ENPP2 in health and pathology are fragmented.…”

Section: Introductionmentioning

confidence: 99%

ENPP2 Methylation in Health and Cancer

Fanidis

Aidinis

et al. 2021

IJMS

Self Cite

Autotaxin (ATX) encoded by Ectonucleotide Pyrophosphatase/Phosphodiesterase 2 (ENPP2) is a key enzyme in Lysophosphatidic Acid (LPA) synthesis implicated in cancer. Although its aberrant expression has been reported, ENPP2 methylation profiles in health and malignancy are not described. We examined in silico the methylation of ENPP2 analyzing publicly available methylome datasets, to identify Differentially Methylated CpGs (DMCs) which were then correlated with expression at gene and isoform levels. Significance indication was set to be FDR corrected p-value < 0.05. Healthy tissues presented methylation in all gene body CGs and lower levels in Promoter Associated (PA) regions, whereas in the majority of the tumors examined (HCC, melanoma, CRC, LC and PC) the methylation pattern was reversed. DMCs identified in the promoter were located in sites recognized by multiple transcription factors, suggesting involvement in gene expression. Alterations in methylation were correlated to an aggressive phenotype in cancer cell lines. In prostate and lung adenocarcinomas, increased methylation of PA CGs was correlated to decreased ENPP2 mRNA expression and to poor prognosis parameters. Collectively, our results corroborate that methylation is an active level of ATX expression regulation in cancer. Our study provides an extended description of the methylation status of ENPP2 in health and cancer and points out specific DMCs of value as prognostic biomarkers.