ArrayExpress Uploader0humanplacebopre1.5PLumAplacebopost0NLumBsoypre46.9PLumBsoypre5.9PLumAsoypost169PLumAsoypre155Nbasalsoypre38.3PLumAsoypre4.8PLumAplacebopost2.1PLumAplacebopre3.6PLumAsoypost9.7PLumAsoypre3.76PLumAplacebopre0.33PLumAplacebopost0.36PLumBsoypre0.61PLumBplacebopre0.36Nbasalplacebopost0.34PLumAsoypre0.35PLumAsoypre0.34PLumAplacebopre0.35PLumAplacebopost0.53PLumAsoypost0.34PLumBsoypre1.4PLumAsoypre27PLumBsoypre84.5Nbasalplacebopre0.33Nbasalsoypost0.34Nbasalsoypost110PLumBsoypre0.34NHer2soypre0.33Nbasalsoypre9.62PLumBplacebopost1.64PLumBplacebopost4.5PLumAplacebopost1.45PLumAsoypost1.12Nbasalplacebopost1.86PLumAsoypost37.01NHer2placebopre1.25PLumAsoypost93.3PLumBsoypost1.93PLumAsoypost201.02PLumBplacebopost2.47PLumAplacebopre6.89PLumAsoypost387.86Nbasalplacebopost6.45PLumAplacebopost3.31PLumBplacebopost1.32PLumBsoypost1.15Nbasalplacebopre1.29PLumAsoypost51.61PLumBsoypre6.26PLumB1995arrayexpress_sid4Background There are conflicting reports on the impact of soy on breast carcinogenesis. This study examines the effects of soy...E-GEOD-58792/profile/8773/arrayexpressuploader551breastbreast cancercancercellgenomeproteinDec.12, 2014Falseeffects-of-soy-supplementation-on-gene-expressionE-GEOD-58792_A-AFFY-44Effects of soy supplementation on gene expression in breast cancerJul.10, 2014Background There are conflicting reports on the impact of soy on breast carcinogenesis. This study examines the effects of soy supplementation on breast cancer-related genes and pathways. Methods Women (n = 140) with early-stage breast cancer were randomized to soy protein supplementation (n = 70) or placebo (n = 70) for 7 to 30 days, from diagnosis until surgery. Adherence was determined by plasma isoflavones: genistein and daidzein. Gene expression changes were evaluated by NanoString inin pre- and post-treatment tumor tissue. Genome-wide expression analysis was performed on post-treatment tissue. Proliferation (Ki67) and apoptosis (Cas3) were assessed by immunohistochemistry. Results Plasma isoflavones rose in the soy group (two-sided Wilcoxon rank-sum test, P < .001) and did not change in the placebo group. In paired analysis of pre- and post-treatment samples, 21 genes (out of 202) showed altered expression (two-sided Student’s t-test, P < .05). Several genes including FANCC and UGT2A1 revealed different magnitude and direction of expression changes between the two groups (two-sided Student’s t-test, P < .05). A high-genistein signature consisting of 126 differentially expressed genes was identified from microarray analysis of tumors. This signature was characterized by overexpression (>2 fold) of cell cycle transcripts, including those which promote cell proliferation, such as FGFR2, E2F5, BUB1, CCNB2, MYBL2, CDK1, and CDC20 (P < .01). Soy intake did not result in statistically significant changes in Ki67 or Cas3. Conclusions Gene expression associated with soy intake and high plasma genistein define a signature characterized by overexpression of FGFR2 and genes that drive cell cycle and proliferation pathways. These findings raise the concerns that in a subset of women soy could adversely affect gene expression in breast cancer. Genome-wide expression analysis was performed on breast cancer tissue from women following treatment with soy (n=28) or placebo (n=23).http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-58792http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-58792/samples/