Carol J. Fabian

Supplementary Figure S5. α and β diversity indexes in patients by age in the 6-month fecal samples. A. Shannon index B. Bray-Curtis β-diversity principal coordinate analysis (PCoA).

Supplementary Figure S2. Red blood cell (RBC) n-6:n-3 PUFA ratios. A. Women randomized to placebo did not display differences in erythrocyte phospholipid ratio of n-6:n-3 PUFA. B. Women randomized to omega-3 displayed a significantly reduced erythrocyte phospholipid ratio of n-6:n-3 PUFA. C. Percent (%) change in erythrocyte phospholipid ratio of n-6:n-3 PUFA.

Supplementary Figure S1. Workflow Chart Describing Fecal Metagenomic Sequencing Processing for Microbial GUS Gene Analysis by Loop Structure Classifications.

Supplementary Table S1. Baseline characteristics for women in the weight loss intervention who had 6- month fecal samples available for analysis. Mean ± SD; (range).

Obesity is associated with gut dysbiosis, chronic inflammation, and insulin resistance. We assessed the proportional change in fecal microbial populations in a pilot study (n = 34) of peri/postmenopausal women with a body mass index ≥28 kg/m2 who were randomized to receive either 3.25 g/day of omega-3 fatty acids or a placebo during a weight loss intervention. Body composition was assessed using dual X-ray absorptiometry, and fecal and blood samples were collected. The median weight change was −10%. Among participants who lost ≥10% of their weight, those assigned to omega-3 fatty acids showed the greatest decrease in the Firmicutes:Bacteroidetes ratio and displayed favorable changes in systemic biomarkers. Notable increases in the proportional abundance of short-chain fatty acid (SCFA)–producing microbes including Phocaeicola vulgatus and Alistipes putredinis were observed in women receiving omega-3, which correlated with improvements in breast cancer biomarkers such as bioavailable estradiol, adiponectin:leptin ratio, and C-reactive protein levels. Women administered omega-3 fatty acids displayed increased % change in plasma SCFA propionate and decreased butyrate, suggesting that intervention differentially modulated circulating bacteria-derived SCFA metabolites. High-dose omega-3 fatty acids, when added to a behavioral weight loss intervention, promoted beneficial shifts in the gut microbiome and associated with improved breast cancer risk factor biomarkers. Prevention Relevance:Obesity is a modifiable risk factor for breast cancer, characterized by chronic inflammation and altered adipokines. This trial addresses the need to enhance weight loss by targeting underlying metabolic and inflammatory drivers. We show that omega-3 polyunsaturated fatty acids (eicosapentaenoic acid/docosahexaenoic acid) shift SCFA-producing microbiota, increase propionate, and correlate with improved breast cancer risk factor biomarkers.

Supplementary Table S2. Representativeness of Study Participants

Supplementary Figure S4. α and β diversity indexes in patients by menopause and hormone replacement therapy use in the 6-month fecal samples. A. Shannon index B. Bray-Curtis β-diversity principal coordinate analysis (PCoA).

Supplementary Figure S3. α and β diversity indexes in patients with matched baseline and 6-month fecal samples. A. Shannon index B. Bray-Curtis β-diversity principal coordinate analysis (PCoA).

Obesity is associated with gut dysbiosis, chronic inflammation, and insulin resistance. We assessed the proportional change in fecal microbial populations in a pilot study (n = 34) of peri/postmenopausal women with a body mass index ≥28 kg/m2 who were randomized to receive either 3.25 g/day of omega-3 fatty acids or a placebo during a weight loss intervention. Body composition was assessed using dual X-ray absorptiometry, and fecal and blood samples were collected. The median weight change was −10%. Among participants who lost ≥10% of their weight, those assigned to omega-3 fatty acids showed the greatest decrease in the Firmicutes:Bacteroidetes ratio and displayed favorable changes in systemic biomarkers. Notable increases in the proportional abundance of short-chain fatty acid (SCFA)–producing microbes including Phocaeicola vulgatus and Alistipes putredinis were observed in women receiving omega-3, which correlated with improvements in breast cancer biomarkers such as bioavailable estradiol, adiponectin:leptin ratio, and C-reactive protein levels. Women administered omega-3 fatty acids displayed increased % change in plasma SCFA propionate and decreased butyrate, suggesting that intervention differentially modulated circulating bacteria-derived SCFA metabolites. High-dose omega-3 fatty acids, when added to a behavioral weight loss intervention, promoted beneficial shifts in the gut microbiome and associated with improved breast cancer risk factor biomarkers. Prevention Relevance: Obesity is a modifiable risk factor for breast cancer, characterized by chronic inflammation and altered adipokines. This trial addresses the need to enhance weight loss by targeting underlying metabolic and inflammatory drivers. We show that omega-3 polyunsaturated fatty acids (eicosapentaenoic acid/docosahexaenoic acid) shift SCFA-producing microbiota, increase propionate, and correlate with improved breast cancer risk factor biomarkers.

Overtreatment of patients with ductal carcinoma in situ (DCIS) is driven by a lack of a reliable prognostic biomarker. Widespread mammographic screening has resulted in a substantial increase in women diagnosed with DCIS. To improve patient risk stratification, we investigate circulating tumor cells (CTCs) as a biomarker for DCIS patients’ biological aggressiveness and as an indicator of early dissemination. We apply microfluidics to enrich CTCs from 34 patients with DCIS and find a significantly higher concentration of CTCs compared to in healthy controls. We profile CTCs and matched DCIS tissues using single-cell RNA sequencing. We find that CTCs express higher clonal aberrations when compared to white blood cells from the same samples, and clonal comparisons between matched tissue and CTC samples provide evidence for an evolutionary bottleneck model. mRNA expression in CTC reveals EMT/MET and immunoregulatory pathway regulation with a suggestion of racial differences. Last, we provide support for early dissemination in DCIS using a Mouse IntraDuctal model.