Hypermethylation of TMEM240 predicts poor hormone therapy response and disease progression in breast cancer

Abstract

Background Approximately 25% of patients with early-stage breast cancer experience cancer progression throughout the disease course. Alterations in TMEM240 in breast cancer were identified and investigated to monitor treatment response and disease progression. Methods Circulating methylated TMEM240 in the plasma of breast cancer patients was used to monitor treatment response and disease progression. The Cancer Genome Atlas (TCGA) data in Western countries and Illumina methylation arrays in Taiwanese breast cancer patients were used to identify novel hypermethylated CpG sites and genes related to poor hormone therapy response. Quantitative methylation-specific PCR (QMSP), real-time reverse transcription PCR, and immunohistochemical analyses were performed to measure DNA methylation and mRNA and protein expression levels in 394 samples from Taiwanese and Korean breast cancer patients. TMEM240 gene manipulation, viability, migration assays, RNA-seq, and MetaCore were performed to determine its biological functions and relationship to hormone drug treatment response in breast cancer cells. Results Aberrant methylated TMEM240 was identified in breast cancer patients with poor hormone therapy response using genome-wide methylation analysis in the Taiwan and TCGA breast cancer cohorts. A cell model showed that TMEM240, which is localized to the cell membrane and cytoplasm, represses breast cancer cell proliferation and migration and regulates the expression levels of enzymes involved in estrone and estradiol metabolism. TMEM240 protein expression was observed in normal breast tissues but was not detected in 88.2% (67/76) of breast tumors and in 90.0% (9/10) of metastatic tumors from breast cancer patients. QMSP revealed that in 54.5% (55/101) of Taiwanese breast cancer patients, the methylation level of TMEM240 was at least twofold higher in tumor tissues than in matched normal breast tissues. Patients with hypermethylation of TMEM240 had poor 10-year overall survival (p = 0.003) and poor treatment response, especially hormone therapy response (p < 0.001). Circulating methylated TMEM240 dramatically and gradually decreased and then diminished in patients without disease progression, whereas it returned and its levels in plasma rose again in patients with disease progression. Prediction of disease progression based on circulating methylated TMEM240 was found to have 87.5% sensitivity, 93.1% specificity, and 90.2% accuracy. Conclusions Hypermethylation of TMEM240 is a potential biomarker for treatment response and disease progression monitoring in breast cancer.

Size and Methylation Index of Cell-Free and Cell-Surface-Bound DNA in Blood of Breast Cancer Patients in the Contest of Liquid Biopsy

“…Currently, circulating tumor cells, cfDNA, small RNAs, and exosomes are used for liquid biopsy [ 31 , 32 , 33 ]. The advantages of circulating genetic markers include the opportunity to detect neoplasia-associated point mutations, deletions/inserts, translocations, and amplifications, as well as aberrant cytosine methylation in the CpG-dinucleotides of tumor suppressor genes [ 1 ].…”

Hypermethylation of the Gene Body in SRCIN1 Is Involved in Breast Cancer Cell Proliferation and Is a Potential Blood-Based Biomarker for Early Detection and a Poor Prognosis

“…Genome-wide methylation analysis of 5 paired tumor and normal breast cancer tissues was performed using the Illumina Infinium HumanMethylation450 BeadChip array (Illumina, San Diego, CA, USA) for one sample and the Infinium MethylationEPIC Kit (Illumina) for the remaining 4 samples, as previously reported [26,27]. The two arrays contain more than 450,000 and 850,000 methylation sites, respectively, and provide genomewide coverage of the gene region and CpG island coverage, respectively, including 99% of RefSeq genes.…”

“…SRCIN1 mRNA expression was considered high if the relative expression level (normalized to that of GAPDH) was more than 2 times greater in tumors than in normal breast tissue. However, target genes were considered to have low expression if the relative expression level of the target gene (normalized to that of GAPDH) was less than 0.5 times lower in tumors than in normal breast tissue [27]. The primers and probes used for RT-qPCR are listed in Table S1.…”

Potential Impact of Preoperative Circulating Biomarkers on Individual Escalating/de-Escalating Strategies in Early Breast Cancer

“…The NCT04822792 trial is currently ongoing and enrolling healthy female subjects who are attending gynecological and mammographic control to test a cfDNA methylation-based model for detecting eBC. This non-invasive method has shown its utility in anticipating recurrence, detecting MRD, and evaluating adjuvant treatment efficacy/resistance [145][146][147].…”