Table 4 Summary of methylation research using breast tissue

Erin W. Hofstatter

SQ, N

Illumina 450K

・DNA methylation Age of normal breast tissue was strongly correlated with chronological age

・Compared to unaffected women, breast cancer patients exhibited significant age acceleration in their normal breast tissue

・Smoking was positively correlated with epigenetic aging in normal breast tissue

James R. Castle

T, SQ, N

Illumina 27K and 450K

・DNA methylation age in Tumor was on average 7 years older than chronological

・HER2(+) and HR(+) breast cancer demonstrated significant acceleration in DNA methylation ages, while there was no significant difference in triple-negative breast cancer

Kevin C. Johnson

T, SQ, N

Illumina 450K

・DNA methylation was not strongly associated with the other evaluated breast cancer risk factors instead of age

Chrstine B. Ambrosone

T, N

Illumina 450K

・Average methylation levels at loci within CGIs and CGI-shores were consistently higher in tumor than normal. On the other hand, these of loci outside of CGIs (ex: CGI-shelves and open sea) were lower in tumors.

・Average methylation levels at loci within CGIs were higher in ER(+) tumors compared to ER(-) tumors

Min-Ae Song

N

Illumina 450K

・Methylation was correlated with expression of the corresponding gene and with DNA methyltransferase protein DNMT3A

・Sites with increased methylation were predominantly in CpG islands and non-enhancers, and with decreased methylation were generally located in intergenic regions, non-CpG Islands, and enhancers

・Expression of DNMT3A and KRR1 and DHRS12 were positively associated with age.

Andrew E. T

T, SQ, N

Illumina 450K

・Epigenetic field defects in breast cancer are widespread

・Genomic distribution is highly non-random affecting binding sites of transcription factors specifying chromatin architecture and stem-cell differentiation pathways.

Bin Xiao

T, N

Illumina 450K and HiSeq 2000 RNA seq

・The correlation analysis of 122 methylation site–mRNA expression pairs revealed that 59 pairs were significantly correlated (42 were negatively and 17 were positively correlated)

・ VIM, EPHX3, ACVR1, ANGPT1, TPM3, ALOX15, DIO1, KCNJ2, RSPH9, SOSTDC1, SYCP2, MACF1, TDRD5 and CELSR3 were significantly related to breast cancer prognosis

Xinhua Liu

T,SQ,N

Illumina 450K

・Lots of CpGs were hyper-methylated in breast cancer compared with adjacent normal tissues, which tend to be negatively correlated with gene expressions.

・Eight CpGs located at RIIAD1, ENPP2, ESPN, and ETS1, were hyper-methylated in tumor