title: Differential DNA methylation analysis of breast cancer reveals the impact of immune signaling in radiation therapy.
abstract: Radiotherapy (RT) is a central treatment modality for breast cancer patients. The purpose of our study was to investigate the DNA methylation changes in tumors following RT, and to identify epigenetic markers predicting treatment outcome. Paired biopsies from patients with inoperable breast cancer were collected both before irradiation (n = 20) and after receiving 10-24 Gray (Gy) (n = 19). DNA methylation analysis was performed by using Illumina Infinium 27K arrays. Fourteen genes were selected for technical validation by pyrosequencing. Eighty-two differentially methylated genes were identified in irradiated (n = 11) versus nonirradiated (n = 19) samples (false discovery rate, FDR = 1.1%). Methylation levels in pathways belonging to the immune system were most altered after RT. Based on methylation levels before irradiation, a panel of five genes (H2AFY, CTSA, LTC4S, IL5RA and RB1) were significantly associated with clinical response (p = 0.041). Furthermore, the degree of methylation changes for 2,516 probes correlated with the given radiation dose. Within the 2,516 probes, an enrichment for pathways involved in cellular immune response, proliferation and apoptosis was identified (FDR < 5%). Here, we observed clear differences in methylation levels induced by radiation, some associated with response to treatment. Our study adds knowledge on the molecular mechanisms behind radiation response.
authors.affiliation: Department of Genetics, Institute for Cancer Research, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway.
authors.forename: Ann Rita
authors.initials: AR
authors.lastname: Halvorsen
authors.forename: Aslaug
authors.initials: A
authors.lastname: Helland
authors.forename: Thomas
authors.initials: T
authors.lastname: Fleischer
authors.forename: Karen Marie
authors.initials: KM
authors.lastname: Haug
authors.forename: Grethe Irene
authors.initials: GI
authors.lastname: Grenaker Alnaes
authors.forename: Daniel
authors.initials: D
authors.lastname: Nebdal
authors.forename: Randi G
authors.initials: RG
authors.lastname: Syljuåsen
authors.forename: Nizar
authors.initials: N
authors.lastname: Touleimat
authors.forename: Florence
authors.initials: F
authors.lastname: Busato
authors.forename: Jörg
authors.initials: J
authors.lastname: Tost
authors.forename: Anna B
authors.initials: AB
authors.lastname: Saetersdal
authors.forename: Anne-Lise
authors.initials: AL
authors.lastname: Børresen-Dale
authors.forename: Vessela
authors.initials: V
authors.lastname: Kristensen
authors.forename: Hege
authors.initials: H
authors.lastname: Edvardsen
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics*; D001940:Breast / Q000378:metabolism*; D001943:Breast Neoplasms / Q000235:genetics* / Q000276:immunology / Q000532:radiotherapy*; D019175:DNA Methylation; D057890:Epigenomics; D005260:Female; D020869:Gene Expression Profiling; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D060888:Real-Time Polymerase Chain Reaction; D015398:Signal Transduction; D014407:Tumor Cells, Cultured
chemical_list: D014408:Biomarkers, Tumor
keywords: breast cancer; dose dependent; immune response; irradiation; methylation