Dataset: Effects of soy supplementation on gene expression in breast cancer

Background There are conflicting reports on the impact of soy on breast carcinogenesis. This study examines the effects of soy...

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Background 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).

Species:: human
Samples:: 51
Source:: E-GEOD-58792
Updated:: Dec.12, 2014
Registered:: Jul.10, 2014

Factors: (via ArrayExpress)

Sample	PREDICTED MOLECULAR SUBTYPE	MENOPAUSAL STATUS	TREATMENT	ER.STATUS	PLASMA GENISTEIN NG/ML
GSM1419673	LumA	pre	placebo	P	1.5
GSM1419672	LumB	post	placebo	N	0
GSM141967	LumB	pre	soy	P	46.9
GSM1419670	LumA	pre	soy	P	5.9
GSM1419669	LumA	post	soy	P	169
GSM1419668	basal	pre	soy	N	155
GSM1419667	LumA	pre	soy	P	38.3
GSM1419666	LumA	pre	soy	P	4.8
GSM1419665	LumA	post	placebo	P	2.1
GSM1419664	LumA	pre	placebo	P	3.6
GSM1419663	LumA	post	soy	P	9.7
GSM1419662	LumA	pre	soy	P	3.76
GSM141966	LumA	pre	placebo	P	0.33
GSM1419660	LumB	post	placebo	P	0.36
GSM1419659	LumB	pre	soy	P	0.61
GSM1419658	basal	pre	placebo	N	0.36
GSM1419657	LumA	post	placebo	P	0.34
GSM1419656	LumA	pre	soy	P	0.35
GSM1419655	LumA	pre	soy	P	0.34
GSM1419654	LumA	pre	placebo	P	0.35
GSM1419653	LumA	post	placebo	P	0.53
GSM1419652	LumB	post	soy	P	0.34
GSM141965	LumA	pre	soy	P	1.4
GSM1419650	LumB	pre	soy	P	27
GSM1419649	basal	pre	soy	N	84.5
GSM1419648	basal	pre	placebo	N	0.33
GSM1419647	basal	post	soy	N	0.34
GSM1419646	LumB	post	soy	P	110
GSM1419645	Her2	pre	soy	N	0.34
GSM1419644	basal	pre	soy	N	0.33
GSM1419643	LumB	pre	soy	P	9.62
GSM1419642	LumB	post	placebo	P	1.64
GSM141964	LumA	post	placebo	P	4.5
GSM1419640	LumA	post	placebo	P	1.45
GSM1419639	basal	post	soy	N	1.12
GSM1419638	LumA	post	placebo	P	1.86
GSM1419637	Her2	post	soy	N	37.01
GSM1419636	LumA	pre	placebo	P	1.25
GSM1419635	LumB	post	soy	P	93.3
GSM1419634	LumA	post	soy	P	1.93
GSM1419633	LumB	post	soy	P	201.02
GSM1419632	LumA	post	placebo	P	2.47
GSM141963	LumA	pre	placebo	P	6.89
GSM1419630	basal	post	soy	N	387.86
GSM1419629	LumA	post	placebo	P	6.45
GSM1419628	LumB	post	placebo	P	3.31
GSM1419627	LumB	post	placebo	P	1.32
GSM1419626	basal	post	soy	N	1.15
GSM1419625	LumA	pre	placebo	P	1.29
GSM1419624	LumB	post	soy	P	51.61
GSM1419623	LumB	pre	soy	P	6.26