Survival curves of six chromosomal regions associated with significant differences in survival between patients with and without AI.

<p>Red circles = tumors demonstrating AI, blue squares = tumors without detectable AI. For chromosome 16q22–q24, those patients with AI at chromosome 16q22–q24 have significantly better survival than those with retention of chromosome 16q22–q24.</p

Scatter plot of levels of AI by chromosomal region.

<p>Chromosomal regions are on the x-axis, average level of AI on the y-axis. Chromosomes with significantly different frequencies between DOD and DFS groups are boxed.</p

Clinical and pathological features of 123 invasive breast tumor specimens.

<p>P-values listed as NS (not significant) >0.05.</p>a<p>Other included histological types including tubular, medullary, apocrine, and mucinous carcinomas.</p>b<p>IHC markers were used as surrogates to define subtype as follows: luminal A = ER and/or PR+/HER2−; luminal B = ER and/or PR+/HER2+; HER2-enriched = ER and PR−/HER2+ and triple negative = ER, PR and HER2−.</p

Extended survival curves (>60 months) for patients with AI at chromosome 13q14.

<p>The survival curves between patients with and without AI begin to separate only after 60 months (P = 0.0159), suggesting that alteration of 13q14 is associated with long-term mortality.</p

Characteristics of the 87 women included in this study, drawn from the Clinical Breast Care Project.

1<p>Percentages may not add up to 100 due to missing values.</p

Average percent-methylation in leukocyte and mammary tissue DNA from women with benign breast disease and invasive breast cancer.

<p>N corresponds to the number of samples for which methylation values are available for both blood and mammary tissue. Values are means ± standard deviations. Spearman's ρ was calculated excluding pairs with unknown values.</p

Comparisons of methylation values between blood and matching mammary tissue in different subgroups of patients.

<p>Black circles correspond to the methylation value for an individual participant.</p

Comparisons between blood and mammary tissue DNA methylation.

<p>Axes correspond to percent-methylation observed in blood and mammary tissue, respectively. Crosses correspond to non-cancerous cases, and circles to invasive cases.</p

Inhibition of migration of MDA-MB-231 and HCC1806.

<p>MDA-MB-231 (A) or HCC1806 (B) cells were harvested, washed and resuspended in RPMI1640-serum free media. Migration assays were performed using type I collagen (10 µg/ml) as an adhesive substrate in the lower compartment of Transwell by incubating at 37°C for 4 hours. The aptamers were added in both upper and lower chambers at the indicated concentrations. Experiments were performed in triplicate. Statistical significance was calculated by Student’s two-tailed paired <i>t</i>-test.</p

CD44 associated with EphA2 on breast cancer cells.

<p>(A) HCC38 cells were lysed with 100 mM Tris-HCl (pH 7.5) containing 1% Brij35, 0.14 M NaCl, 1 mM CaCl₂, 1 mM MnCl₂, and a protease inhibitor cocktail by scraping and pipetting. The cell lysates were precleared and immunoprecipitated with anti-CD44 antibody clone (clone 156-3C11)-, anti-EphA2- or control IgG-protein G beads for 4 hours at 4°C. The bound proteins were released by boiling at 95°C in SDS-sample buffer under reducing conditions and separated on SDS-PAGE followed by western blotting with anti-EphA2 antibody followed by HRP-secondary antibody. The proteins are visualized with enhanced chemiluminescence (ECL) reaction. (B) Cells were harvested using 5 mM EDTA in PBS and were lysed in 100 mM Tris-HCL (pH 7.5) containing 1% Brij35, 0.14 M NaCl, 1 mM CaCl₂, 1 mM MnCl₂, and a protease inhibitor cocktail. The lysates were precleared with anti-FLAG (M2) agarose beads for 4 hours by shaking at 4°C. The cleared lysates were incubated with recombinant protein CD44v10 P-FLAG-anti-FLAG (M2) antibody-agarose beads (CD44v10) or anti-FLAG (M2) antibody-agarose beads (Con.) in the presence or absence of aptamers (Apt#4 and Apt#7) by shaking at 4°C for 4 hours. The beads were washed extensively with the lysis buffer. The bound proteins were released by boiling at 95°C in SDS-sample buffer under reducing conditions and separated on SDS-PAGE followed by western blotting with anti-EphA2 followed by HRP-secondary antibody or HRP-conjugated anti-FLAG (M2) antibody. The proteins are visualized with enhanced chemiluminescence (ECL) reaction. CD44 exon v10 peptide was used as a loading control for ensuring the same amount of proteins was loaded in each lane.</p