title: DNA methylation array analysis identifies breast cancer associated RPTOR, MGRN1 and RAPSN hypomethylation in peripheral blood DNA.
abstract: DNA methylation changes in peripheral blood DNA have been shown to be associated with solid tumors. We sought to identify methylation alterations in whole blood DNA that are associated with breast cancer (BC). Epigenome-wide DNA methylation profiling on blood DNA from BC cases and healthy controls was performed by applying Infinium HumanMethylation450K BeadChips. Promising CpG sites were selected and validated in three independent larger sample cohorts via MassARRAY EpiTyper assays. CpG sites located in three genes (cg06418238 in RPTOR, cg00736299 in MGRN1 and cg27466532 in RAPSN), which showed significant hypomethylation in BC patients compared to healthy controls in the discovery cohort (p < 1.00 x 10-6) were selected and successfully validated in three independent cohorts (validation I, n =211; validation II, n=378; validation III, n=520). The observed methylation differences are likely not cell-type specific, as the differences were only seen in whole blood, but not in specific sub cell-types of leucocytes. Moreover, we observed in quartile analysis that women in the lower methylation quartiles of these three loci had higher ORs than women in the higher quartiles. The combined AUC of three loci was 0.79 (95%CI 0.73-0.85) in validation cohort I, and was 0.60 (95%CI 0.54-0.66) and 0.62 (95%CI 0.57-0.67) in validation cohort II and III, respectively. Our study suggests that hypomethylation of CpG sites in RPTOR, MGRN1 and RAPSN in blood is associated with BC and might serve as blood-based marker supplements for BC if these could be verified in prospective studies.
authors: Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg, Germany.|Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg, Germany.
authors: Qiuqiong
authors: Q
authors: Tang
authors: Division of Biostatistics (C060), German Cancer Research Center (DKFZ), Heidelberg, Germany.
authors: Tim
authors: T
authors: Holland-Letz
authors: Division of Biostatistics (C060), German Cancer Research Center (DKFZ), Heidelberg, Germany.
authors: Alla
authors: A
authors: Slynko
authors: Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg, Germany.|Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg, Germany.
authors: Katarina
authors: K
authors: Cuk
authors: Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg, Germany.
authors: Frederik
authors: F
authors: Marme
authors: Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg, Germany.
authors: Sarah
authors: S
authors: Schott
authors: Department of Gynecology and Obstetrics, University Women's Clinic, Heidelberg, Germany.
authors: Jörg
authors: J
authors: Heil
authors: Department of Biophysics, Center for Integrated Physiology and Molecular Medicine (CIPMM), Saarland University, Homburg (Saar), Germany.
authors: Bin
authors: B
authors: Qu
authors: Department of Gynecology and Obstetrics, University Women's Clinic, Heidelberg, Germany.
authors: Michael
authors: M
authors: Golatta
authors: Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany.
authors: Melanie
authors: M
authors: Bewerunge-Hudler
authors: Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany.
authors: Christian
authors: C
authors: Sutter
authors: Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg, Germany.|Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg, Germany.
authors: Harald
authors: H
authors: Surowy
authors: Centre of Familial Breast and Ovarian Cancer, Department of Gynaecology and Obstetrics and Centre for Integrated Oncology (CIO), Center for Molecular Medicine Cologne (CMMC), University Hospital of Cologne, Cologne, Germany.
authors: Barbara
authors: B
authors: Wappenschmidt
authors: Centre of Familial Breast and Ovarian Cancer, Department of Gynaecology and Obstetrics and Centre for Integrated Oncology (CIO), Center for Molecular Medicine Cologne (CMMC), University Hospital of Cologne, Cologne, Germany.
authors: Rita
authors: R
authors: Schmutzler
authors: Department of Biophysics, Center for Integrated Physiology and Molecular Medicine (CIPMM), Saarland University, Homburg (Saar), Germany.
authors: Markus
authors: M
authors: Hoth
authors: Institute of Transfusion Medicine and Immunology, Medical Faculty Mannheim, University of Heidelberg, German Red Cross Blood Service Baden, Württemberg, Hessen, Mannheim, Germany.
authors: Peter
authors: P
authors: Bugert
authors: Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany.
authors: Claus R
authors: CR
authors: Bartram
authors: Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg, Germany.
authors: Christof
authors: C
authors: Sohn
authors: Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg, Germany.|National Centre for Tumor Diseases, Heidelberg, Germany.
authors: Andreas
authors: A
authors: Schneeweiss
authors: Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg, Germany.|Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg, Germany.
authors: Rongxi
authors: R
authors: Yang
authors: Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg, Germany.|Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg, Germany.
authors: Barbara
authors: B
authors: Burwinkel
mesh_terms: D000328:Adult; D000368:Aged; D019540:Area Under Curve; D014408:Biomarkers, Tumor / Q000097:blood / Q000235:genetics*; D001943:Breast Neoplasms / Q000097:blood / Q000235:genetics* / Q000473:pathology; D000074141:Circulating Tumor DNA / Q000097:blood / Q000235:genetics*; D018899:CpG Islands; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D020022:Genetic Predisposition to Disease; D006801:Humans; D016015:Logistic Models; D008875:Middle Aged; D009124:Muscle Proteins / Q000097:blood / Q000235:genetics*; D016017:Odds Ratio; D020411:Oligonucleotide Array Sequence Analysis; D011237:Predictive Value of Tests; D012372:ROC Curve; D000076223:Regulatory-Associated Protein of mTOR / Q000097:blood / Q000235:genetics*; D015203:Reproducibility of Results; D012189:Retrospective Studies; D012307:Risk Factors; D044767:Ubiquitin-Protein Ligases / Q000097:blood / Q000235:genetics*
chemical_list: D014408:Biomarkers, Tumor; D000074141:Circulating Tumor DNA; D009124:Muscle Proteins; C463659:RPTOR protein, human; D000076223:Regulatory-Associated Protein of mTOR; C051609:peripheral membrane protein 43K; C470690:MGRN1 protein, human; D044767:Ubiquitin-Protein Ligases
keywords: DNA methylation; MGRN1; RAPSN; RPTOR; breast cancer