Variations in GATA3 and ER expression in node-positive luminal breast tumors and matched lymph node metastases.

<p>A majority of node-positive luminal-phenotype primary breast cancer cases maintains or increases the expression levels of ER and GATA3 in their matched lymph node metastases, independent of histological grade. A 20% decrease in Hscores from PM to its matched LNM was considered a downregulation (DN), a 20% increase an upregulation (UP) and Hscore variations inferior to 20% were considered as not altered (NA).</p

Expression levels of selected genes that discriminate between node-positive and node-negative breast cancer samples.

<p>(A) Hierarchical clustering based on QRT-PCR values for 61 genes in whole tissue samples. All but one PNM tumors were correctly segregated from PM tumors. (B) Hierarchical clustering based on QRT-PCR values for 61 genes in microdissected samples. Ductal carcinoma in situ (DCIS) samples were analyzed in addition to the sample categories shown in (A). Both analyses show that, among other genes, GATA3 is intensely expressed both in primary tumors and LNM samples. </p

Metastasis-free survival curves for luminal phenotype cases as a function of GATA3 expression status.

<p>(A) Kaplan-Meier metastasis-free survival actuarial curves for PNM vs. PM cases. (B) Metastasis-free survival actuarial curves according to GATA3 status. (C) Metastasis-free survival actuarial curves according to molecular phenotype (luminal, HER2(+), TN).</p

Additional file 1: Table S1. of Response and survival of breast cancer intrinsic subtypes following multi-agent neoadjuvant chemotherapy

Cox model DRFS analyses including intrinsic subtype in all patients from the MDACC-based cohort (GSE25066). Table S2. Cox model DRFS analyses including ROR-P in all patients from the MDACC-based cohort (GSE25066). Table S3. Cox model DRFS analyses including intrinsic subtype in patients that achieved a pCR from the MDACC-based cohort (GSE25066). Table S4. Cox model DRFS analyses including ROR-P in patients that achieved a pCR from the MDACC-based cohort (GSE25066). Table S5. Cox model DRFS analyses including ROR-P in patients with residual disease from the MDACC-based cohort (GSE25066). Table S6. Distribution of the PAM50 subtypes within the TNBCtype groups and vice versa. Table S7. Association of the TNBCtype subtypes with chemotherapy response in triple-negative breast cancer. Figure S1. CONSORT diagram of the various cohorts evaluated in this study. Figure S2. Kaplan-Meier distant relapse-free survival analysis in MDACC-based (GSE25066 [13]) dataset set. (A) Survival outcomes of the ROR-P groups in all patients. (B) Survival outcomes of the ROR-P groups in patients with clinically node-negative disease. Figure S3. Levels of ESR1 across TNBCtype ESR1-low group, TNBCtype ESR1-high group and ER+ group. Median expression of ESR1 in the PAM50 training dataset reported in Parker et al. [24] has been set to zero. Figure S4. Distribution of the TNBCtype subtypes and ESR1-high group within the PAM50 subtypes in TNBC. Figure S5. Distribution of the TNBCtype subtypes and ESR1-high group within the PAM50 + Claudin-low subtypes in TNBC. Figure S6. Training and testing gene expression-based models predictive of pCR in all patients. Figure S7. Training and testing gene expression-based models predictive of pCR in patients with Basal-like disease. Figure S8. Training and testing gene expression-based models predictive of pCR in patients with luminal (A/B) disease. (DOCX 819 kb

Distribution WCRF/AICR score and individual recommendations and other baseline characteristics for cases and controls.

<p>Distribution WCRF/AICR score and individual recommendations and other baseline characteristics for cases and controls.</p

Association of WCRF/AICR score and individual recommendations with breast cancer risk by menopausal status.

<p>¹ Adjusted for total calorie intake, smoking habit, age at first delivery, education, history of breast problems, family history of BC and menopausal status.</p><p>²</p><p></p><p></p><p></p><p></p><p><mi>P</mi><mi>A</mi><mi>F</mi><mo>=</mo></p><p></p><p><mo stretchy="false">[</mo><mi>P</mi></p><p><mi>F</mi></p><p></p><p><mo>[</mo></p><p><mn>6</mn><mo>−</mo><mn>9</mn></p><mo>]</mo><p></p><p></p><p></p><mo>⋅</mo><p><mo>(</mo></p><p><mi>O</mi></p><p><mi>R</mi></p><p></p><p><mo>[</mo></p><p><mn>6</mn><mo>−</mo><mn>9</mn></p><mo>]</mo><p></p><p></p><p></p><mo>−</mo><mn>1</mn><p></p><mo>)</mo><p></p><p><mo>]</mo><mo>+</mo><mo>[</mo></p><mi>P</mi><p><mi>F</mi></p><p></p><p><mo>[</mo></p><p><mn>5</mn><mo>−</mo><mn>6</mn></p><mo>]</mo><p></p><p></p><p></p><mo>⋅</mo><p><mo>(</mo></p><p><mi>O</mi></p><p><mi>R</mi></p><p></p><p><mo>[</mo></p><p><mn>5</mn><mo>−</mo><mn>6</mn></p><mo>]</mo><p></p><p></p><p></p><mo>−</mo><mn>1</mn><p></p><mo>)</mo><p></p><mo stretchy="false">]</mo><mo>+</mo><mo stretchy="false">[</mo><mi>P</mi><p><mi>F</mi></p><p></p><p><mo>[</mo></p><p><mn>4</mn><mo>−</mo><mn>5</mn></p><mo>]</mo><p></p><p></p><p></p><mo>⋅</mo><p><mo>(</mo></p><p><mi>O</mi></p><p><mi>R</mi></p><p></p><p><mo>[</mo></p><p><mn>4</mn><mo>−</mo><mn>5</mn></p><mo>]</mo><p></p><p></p><p></p><mo>−</mo><mn>1</mn><p></p><mo>)</mo><p></p><p><mo>]</mo><mo>+</mo><mo>[</mo></p><mi>P</mi><p><mi>F</mi></p><p></p><p><mo>[</mo></p><p><mn>3</mn><mo>−</mo><mn>4</mn></p><mo>]</mo><p></p><p></p><p></p><mo>⋅</mo><p><mo>(</mo></p><p><mi>O</mi></p><p><mi>R</mi></p><p></p><p><mo>[</mo></p><p><mn>3</mn><mo>−</mo><mn>4</mn></p><mo>]</mo><p></p><p></p><p></p><mo>−</mo><mn>1</mn><p></p><mo>)</mo><p></p><mo stretchy="false">]</mo><mo>+</mo><mo stretchy="false">[</mo><mi>P</mi><p><mi>F</mi></p><p></p><p><mo>[</mo></p><p><mn>0</mn><mo>−</mo><mn>3</mn></p><mo>]</mo><p></p><p></p><p></p><mo>⋅</mo><p><mo>(</mo></p><p><mi>O</mi></p><p><mi>R</mi></p><p></p><p><mo>[</mo></p><p><mn>0</mn><mo>−</mo><mn>3</mn></p><mo>]</mo><p></p><p></p><p></p><mo>−</mo><mn>1</mn><p></p><mo>)</mo><p></p><p></p><p><mn>1</mn><mo>+</mo><mo stretchy="false">[</mo><mi>P</mi></p><p><mi>F</mi></p><p></p><p><mo>[</mo></p><p><mn>6</mn><mo>−</mo><mn>9</mn></p><mo>]</mo><p></p><p></p><p></p><mo>⋅</mo><p><mo>(</mo></p><p><mi>O</mi></p><p><mi>R</mi></p><p></p><p><mo>[</mo></p><p><mn>6</mn><mo>−</mo><mn>9</mn></p><mo>]</mo><p></p><p></p><p></p><mo>−</mo><mn>1</mn><p></p><mo>)</mo><p></p><p><mo>]</mo><mo>+</mo><mo>[</mo></p><mi>P</mi><p><mi>F</mi></p><p></p><p><mo>[</mo></p><p><mn>5</mn><mo>−</mo><mn>6</mn></p><mo>]</mo><p></p><p></p><p></p><mo>⋅</mo><p><mo>(</mo></p><p><mi>O</mi></p><p><mi>R</mi></p><p></p><p><mo>[</mo></p><p><mn>5</mn><mo>−</mo><mn>6</mn></p><mo>]</mo><p></p><p></p><p></p><mo>−</mo><mn>1</mn><p></p><mo>)</mo><p></p><mo stretchy="false">]</mo><mo>+</mo><mo stretchy="false">[</mo><mi>P</mi><p><mi>F</mi></p><p></p><p><mo>[</mo></p><p><mn>4</mn><mo>−</mo><mn>5</mn></p><mo>]</mo><p></p><p></p><p></p><mo>⋅</mo><p><mo>(</mo></p><p><mi>O</mi></p><p><mi>R</mi></p><p></p><p><mo>[</mo></p><p><mn>4</mn><mo>−</mo><mn>5</mn></p><mo>]</mo><p></p><p></p><p></p><mo>−</mo><mn>1</mn><p></p><mo>)</mo><p></p><p><mo>]</mo><mo>+</mo><mo>[</mo></p><mi>P</mi><p><mi>F</mi></p><p></p><p><mo>[</mo></p><p><mn>3</mn><mo>−</mo><mn>4</mn></p><mo>]</mo><p></p><p></p><p></p><mo>⋅</mo><p><mo>(</mo></p><p><mi>O</mi></p><p><mi>R</mi></p><p></p><p><mo>[</mo></p><p><mn>3</mn><mo>−</mo><mn>4</mn></p><mo>]</mo><p></p><p></p><p></p><mo>−</mo><mn>1</mn><p></p><mo>)</mo><p></p><mo stretchy="false">]</mo><mo>+</mo><mo stretchy="false">[</mo><mi>P</mi><p><mi>F</mi></p><p></p><p><mo>[</mo></p><p><mn>0</mn><mo>−</mo><mn>3</mn></p><mo>]</mo><p></p><p></p><p></p><mo>⋅</mo><p><mo>(</mo></p><p><mi>O</mi></p><p><mi>R</mi></p><p></p><p><mo>[</mo></p><p><mn>0</mn><mo>−</mo><mn>3</mn></p><mo>]</mo><p></p><p></p><p></p><mo>−</mo><mn>1</mn><p></p><mo>)</mo><p></p><p></p><p></p><mo>•</mo><mn>100</mn><p></p><p></p><p></p><p></p><p></p><p></p><p></p><p></p><p></p><p>PAF=PopulationAtributableFraction</p><p></p><p></p><p>PF=Proportionofpopulationinthespecificexposurecategory</p><p></p><p></p><p>OR=Oddsratiofortheespecificexposurecategory</p><p></p><p></p><p></p><p></p><p></p><p><mrow></mrow></p><p></p><p></p><p></p><p></p><p></p><p></p><p></p><p></p><p>³ Number of controls and cases that do not accomplish the specific recommendation.</p><p>⁴ OR per unit decrease (recommendation met vs not met). Adjusted for total calorie intake, smoking habit, age at first delivery, education, history of breast problems, family history of BC, menopausal status and score excluding the recommendation under study.</p><p>⁵ OR per unit decrease (recommendation met vs not met). Adjusted for total calorie intake, smoking habit, age at first delivery, education, history of breast problems, family history of BC and score excluding the recommendation under study.</p><p>Association of WCRF/AICR score and individual recommendations with breast cancer risk by menopausal status.</p