Metadata record supporting files in the related publication: “SET(ER/PR) - A robust 18-gene Predictor for Sensitivity to Endocrine Therapy for Metastatic Breast Cancer”
Creators: name: Valentin Sinn, Bruno
name: Fu, Chunxiao
name: Lau, Rosanna
name: Litton, Jennifer
name: Tsai, Tsung-Heng
name: Murthy, Rashmi
name: Tam, Alda
name: Andreopoulou, Eleni
name: Gong, Yun
name: Murthy, Ravi
name: Gould, Rebekah
name: Zhang, Ya
name: King, Tari A
name: Viale, Agnes
name: Andrade, Victor
name: Giri, Dilip
name: Salgado, Roberto
name: Laios, Ioanna
name: Sotiriou, Christos
name: Marginean, Esmeralda C
name: Kwiatkowski, Danielle N
name: Layman, Rachel M
name: Booser, Daniel
name: Hatzis, Christos
name: V, Vicente Valero
name: Fraser Symmans, W
Publisher: name: figshare
Year: 2019
Subjects: subject: Cancer
subject: Cell Biology
subject: Gene Expression (incl. Microarray and other genome-wide approaches)
subject: Genetics
subject: FOS: Biological sciences
subject: Medicine
subject: Cancer Cell Biology
subject: Cancer Diagnosis
subject: Cancer Genetics
subject: Cancer Therapy (excl. Chemotherapy and Radiation Therapy)

description: This metadata record
describes the gene expression data supporting the figures and tables in the related
manuscript: “SET<sub>ER/PR</sub> - A robust 18-gene Predictor for Sensitivity
to Endocrine Therapy for Metastatic Breast Cancer”<br><b>Study aims, design and methodology:</b>The study used microarrays and a customized RNA sequencing assay to measure sensitivity to endocrine therapy (SET) of hormone receptor positive (HR+), HER2-negative metastatic breast cancers, based on expression signatures of estrogen receptor (<i>ESR1</i>)- and progesterone receptor (<i>PGR</i>)-related gene transcripts. The SET<sub>ER/PR</sub> index can be used as a diagnostic tool to measure the transcription of genes associated with <i>ESR1</i> and <i>PGR</i> expression and thus to predict sensitivity to endocrine therapy for metastatic breast cancer.<br><br>The discovery cohort of Affymetrix U133A microarrays consisted of a total of 389 samples of invasive hormone-receptor-positive breast cancers. RNA was extracted from a total of 140 HR+/HER2-negative metastatic breast cancer patient samples, processed and hybridised to the Affymetrix U133A microarrays. Eighteen gene transcripts, correlated with both <i>ESR1</i> and <i>PGR</i> expression, and 10 reference gene transcripts were selected for inclusion in the SET<sub>ER/PR</sub> index. Additionally, the ligand binding domain (LBD) of <i>ESR1</i> was sequenced using droplet-based targeted RNAseq, to determine whether <i>ESR1</i> mutations are associated with endocrine resistance and SET<sub>ER/PR</sub> status<br><b>Data files:</b>All the data supporting the figures and tables of the related manuscript can be accessed from the NCBI Gene Expression Omnibus (GEO) repository. These include microarray and RNAseq data from patients with metastatic hormone receptor-positive (HR+), HER2-negative breast cancer.<br><b>Data supporting
figures and tables:</b>

<b>Data supporting
figure 2: </b>Data showing the progression-free (A) and overall
survival (B) in patients with HR+/HER2-negative metastatic breast cancer with high and
low SET<sub>ER/PR </sub>index who received endocrine therapy as next treatment.
<br>

<b>Data supporting
figure 3</b>: Correlation of SET<sub>ER/PR</sub> measurements derived from
the RNAseq assay with SET<sub>ER/PR</sub> measurements from the Affymetrix
U133A microarray assays in hormone receptor positive (HR+), HER2-negative
metastatic breast cancers with and without a mutation (WT) in the LBD of <i>ESR1</i> (A).
Correlation of SET<sub>ER/PR</sub> measurements with <i>ESR1</i> mutant allele frequency (B). Data showing the
progression free (C) and overall survival (D) for patients with HR+/HER2-negative metastatic breast cancer who received endocrine therapy as next treatment and
had a high SET<sub>ER/PR</sub>, low high SET<sub>ER/PR </sub>and a mutated <i>ESR1</i> gene, respectively. <br>

<b>Data supporting Table
1: </b>The table describes the characteristics of 140 patients with HR+, HER2-negative metastatic breast cancers. <br>

<b>Data supporting Tables
2 and 3 show </b>cox regression analyses data for prediction of progression-free
and overall survival respectively,<b> </b>in
patients with HR+, HER2-negative metastatic breast
cancer, using the dichotomized SET<sub>ER/PR</sub>. <br>Data supporting Figures 2 and 3 and Tables 1, 2 and 3 can be accessed from the GEO repository using the accession number GSE124647 (<b>http://identifiers.org/geo:GSE124647</b>).<br><br><b>Data supporting Supplementary Figure S1:</b> Data showing the expression levels of <i>ESR1</i>- and <i>PGR</i>- associated genes (A) and reference genes (B) from the hormone receptor-positive discovery cohort of Affymetrix U133A microarrays. In C, mean (gene expression) of target genes is plotted against the mean (gene expression) of reference genes for breast cancer cases with different receptor status. In D, breast cancer cases associated with different receptor status were assigned a SET<sub>ER/PR </sub>score. Data supporting Supplementary Figure S1 can be accessed from the GEO repository using the accession number GSE129551 (<b>http://identifiers.org/geo:GSE129551</b>).<br><br><b>Data supporting Supplementary Figure S2: </b>The intraclass correlation coefficient was used to evaluate intra-assay reproducibility of SET<sub>ER/PR</sub> values by performing six technical replicates for each sample (A, GSE129558, <b>http://identifiers.org/geo:GSE129558</b>). Intra-tumoral reproducibility was evaluated by performing three technical replicates for each tumor sample (B, GSE129557, <b>http://identifiers.org/geo:GSE129557</b>). Tissue type reproducibility (cytology vs. surgical tissue) of SET<sub>ER/PR</sub> was also evaluated (C, GSE129559, <b>http://identifiers.org/geo:GSE129559</b>). SET<sub>ER/PR</sub> reproducibility between two different types of microarray platform (Plus2.0 and U133A) was also evaluated (D, GSE129556, <b>http://identifiers.org/geo:GSE129556</b>).<br><br><b>Data supporting Supplementary Figure S3:</b> Effect on SET<sub>ER/PR </sub>of contamination of cancer tissue with different percentages of liver tissue (A, GSE33116, <b>http://identifiers.org/geo:GSE33116</b>) and normal breast tissue (B, GSE124646, <b>http://identifiers.org/geo:GSE124646</b>). Effect of cold ischemic time and RNA stabilization method on SET<sub>ER/PR</sub> measurements (C, GSE25011, <b>http://identifiers.org/geo:GSE25011</b>). Inter-platform reproducibility of SETER/PR was validated on an independent dataset of 32 cases (D, GSE17700, <b>http://identifiers.org/geo:GSE17700</b>). Inter-laboratory reproducibility of SET<sub>ER/PR</sub> values was validated by plotting SET<sub>ER/PR</sub> values from U133A and Plus2.0 microarray platforms obtained from the JBI laboratory, against SET<sub>ER/PR</sub> values from U133A and Plus2.0 microarray platforms obtained from the MDACC laboratory (E, GSE17700, <b>http://identifiers.org/geo:GSE17700</b>). To validate the technical reproducibility of U133A microarrays, SET<sub>ER/PR</sub> values from two technical replicates of an independent dataset of 63 cases, were plotted against each other (F, GSE129560, <b>http://identifiers.org/geo:GSE129556</b>).<br><b>Data supporting Supplementary Figure S4</b>: For 140 patients with HR+, HER2-negative metastatic breast cancers, the range of SET<sub>ER/PR </sub>was compared in samples from different sites of metastasis (A). The range of SET<sub>ER/PR</sub> was compared between samples with different progesterone receptor (<i>PGR</i>) status (B). The range of SET<sub>ER/PR</sub> was compared between cases with prior or no prior sensitivity to endocrine therapy (C). Hazard ratios and 95 % confidence intervals of Cox regression analyses for disease-free survival in metastatic breast cancer patients that received endocrine therapy as next treatment are shown in part D. Data supporting Supplementary Figure S4 can be accessed from the GEO repository using the accession number GSE124647 (<b>http://identifiers.org/geo:GSE124647</b>).<br><br><b>Data supporting
Supplementary Figure S5: </b>SET<sub>ER/PR </sub>values from U133A microarrays
were plotted against SET<sub>ER/PR </sub>values obtained from a customized
RNA-seq assay (A). The microarray replicates
were used to validate the technical reproducibility of SET<sub>ER/PR</sub> (B).
Data supporting Supplementary Figure S5 can be accessed from the GEO
repository using the accession number GSE129560 (<b>http://identifiers.org/geo:GSE129560</b>).<br><b>Data supporting Supplementary Table S1</b>: Table S1 describes the sample characteristics of the discovery dataset. Data supporting Supplementary Table S1 can be accessed from the GEO repository using the accession number GSE129551 (<b>http://identifiers.org/geo:GSE129551</b>).<br><br><b>Data supporting Supplementary Table S2:</b> List of target genes, whose transcription is associated with the expression of Estrogen (<i>ESR1</i>) and the Progesterone receptors (<i>PGR</i>), and a list of reference genes, all of which have been used for the calculation of the SET<sub>ER/PR</sub> index. The table can be found in the supplementary information of the related manuscript. <br><b>Data supporting Supplementary Table S3</b>: The table shows the mixed-effects analysis of the effect of tissue preservation method (snap frozen vs. RNAlater) and prolonged cold ischemic delay (0 vs. 40 min) on SET<sub>ER/PR</sub> measurements and the mixed-effects analysis of the effect of prolonged cold ischemic delay (0, 20, 40, 60, 120, 180 min) on SET<sub>ER/PR</sub> measurements. Data supporting Supplementary Table S3 can be accessed from the GEO repository using the accession number GSE25011 (<b>http://identifiers.org/geo:GSE25011</b>).<br><b>Data supporting Supplementary Table S4:</b> The table shows Cox regression analyses, including the variables used for prediction of progression-free and overall survival in patients with hormone receptor positive (HR+), HER2-negative metastatic breast cancer who received chemotherapy and endocrine therapy, respectively, as the next treatment. Data supporting Supplementary Table S3 can be accessed from the GEO repository using the accession number GSE124647 (<b>http://identifiers.org/geo:GSE124647</b>). <br><b>Name of IRB
that approved the study</b>: All patients gave informed written consent for the use
of tissue material for research purposes. Protocols were approved by the MD
Anderson Institutional Review Board (IRB).

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