Prognostic biomarker identification and tumor classification in breast cancer patients by methylation and transcriptome analysis

Abstract

Breast cancer (BC) is one of the most common and heterogeneous malignancies. Although prognosis of breast cancer has improved with the development of early screening, the mechanisms underlying tumorigenesis and progression remain incompletely understood. DNA methylation has been implicated in tumorigenesis and tumor development, and so here we screened methylation-driven genes and explored their prognostic values in breast cancer. RNA-Seq transcriptome data and DNA methylation data of the TCGA-BRCA dataset were obtained from The Cancer Genome Atlas. Differentially-expressed genes and differentially-methylated genes were identified separately. The intersected 783 samples with both RNA-Seq data and DNA methylation data were selected for further analysis. Fifty-six methylation-driven genes were identified using the MethylMix R package and ten prognosis methylation-driven genes (CDO1, CELF2, ITPAIPL1, KCNH8, PTK6, RAB25, RIC3, USP44, ZSCAN1, and ZSCAN23) were further screened by combined methylation and gene expression analysis. Based on the methylation data of the screened ten methylation-driven genes, six subgroups were identified with the ConsensusClusterPlus R package. The protein levels of the ten prognostic methylation-driven genes were detected by immunohistochemical experiments. Moreover, based on the RNA-Seq data, a signature calculating the risk score of each patient was developed with stepwise regression. The risk score and other clinical features (age and stage) were confirmed to be independent prognostic factors by univariate and multivariate Cox regression analyses. Finally, a prognostic nomogram incorporating all the significant factors was integrated to predict the 3-, 5-, and 7-year overall survival. Taken together, the methylation-driven genes identified here may be potential biomarkers of breast cancer.

High-Titer Anti-ZSCAN1 Antibodies in a Toddler Clinically Diagnosed with Apparent Rapid-Onset Obesity with Hypothalamic Dysfunction, Hypoventilation, and Autonomic Dysregulation Syndrome

“…It is a transcription factor that belongs to the C2H2 domain-containing zinc finger protein family. In recent years, a number of reports link the high methylation and/or low expression levels of the ZSCAN1 gene to proliferation in cervical and breast cancers [ 43 , 44 ]. In breast cancer, ZSCAN1 acts as a tumor suppressor by inhibiting TAZ, which is a component of the Hippo (YAP/TAZ) pathway, an intracellular signaling network, the deregulation of which is known to promote tumor growth [ 45 ].…”

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

“…A relevant work showed that ENNP2 was highly methylated in BC tissues, also presenting low mRNA expression levels compared to adjacent tissues [ 60 ]. Furthermore, in silico studies based on TCGA datasets reported high methylation of ENPP2 in BC and characterized it as a methylation-driven gene in cancer [ 61 , 62 ]. 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.…”

USP44 Promoter Methylation in Plasma Cell-Free DNA in Prostate Cancer

“…USP44 methylation is reported so far in a small number of studies in breast cancer, colorectal neoplasia, and non-small cell lung cancer [12][13][14]. RNA-sequencing (RNA-Seq) transcriptome data and DNA methylation data of the TCGA-BRCA revealed that USP44 methylation could be potential biomarker of breast cancer [15]. Experiments in breast cancer cell lines revealed that USP44 hypermethylation promotes cell proliferation and metastasis [12].…”