Top matches for both BLBC and TNBC in the SCAN-B dataset were extracted, E 0.05. motifs in promoter region DEGs in SCAN-B data sets Supplemental Fig. 4. Protein and mRNA levels of ERR / mRNA levels in SCAN-B patients, sorted into TNBC subtypes. d, e. mRNA levels in cell lines representing the TNBC cell lines Supplemental Fig. 5. IHC optimization and localization. a. Negative and positive controls used for antibody optimization of ERRsf ERR2. Scale bar = 100m b. High magnification view representing subcellular staining of tumor cores staining for ERRsf or ERR2. Selected panels for ERRsf from tumor cores identified by Vectra3 as 90% nuclear and cytoplasmic staining, or 90% cytoplasmic staining. Arrows in left panels show positive nuclei. Supplemental Table 2. ERR isoform expression and subcellular localization. Mean (sd) and median (IQR) expression of ERR2 receptor, ERRsf receptor, and total ERR2:total ERRsf expression (S2.1) and nuclear/ cytoplasmic localization of ERR2 receptor and ERRsf (S2.2) in three IHC breast cancer subtypes Supplemental Table 3. ERR isoform expression and clinical features. Analysis of ERR2 and ERRsf receptor expression in the IHC subtypes and lymph node status, race, and age, with and without interaction NIHMS1543814-supplement-10549_2019_5485_MOESM1_ESM.pdf (4.1M) GUID:?C3C79869-077B-4459-844B-2AE3207CF812 Sup_Tab_Fig. NIHMS1543814-supplement-Sup_Tab_Fig.pdf (4.1M) GUID:?7FC6700C-A061-44DE-8BE1-F235A039E8B9 Abstract Purpose Triple negative breast cancer (TNBC)/ basal-like breast cancer (BLBC) is a highly aggressive form of breast cancer. We previously reported that a small molecule agonist ligand for the orphan nuclear receptor estrogen-related receptor beta (ERR or mRNA, copy number levels, and protein expression with demographic, clinicopathological, and gene expression features in breast tumor clinical specimens. Methods mRNA level expression and clinical associations were analyzed using RNAseq data. Array-based comparative genomic hybridization determined copy number in AA and Caucasian women. Transcription factor activity was measured using promoter-reporter luciferase assays in TNBC cell lines. Semi-automatic quantification of immunohistochemistry measured ERR protein expression on a 150-patient tissue microarray series. Results mRNA expression is significantly lower in TNBC/BLBC vs. other breast cancer subtypes. There is no evidence of copy number loss. mRNA expression is correlated with the expression of genes associated with neuroactive ligand-receptor interaction, metabolic GR-203040 pathways, and ENAH deafness. These genes contain G/C-rich transcription factor binding motifs. The message is alternatively spliced into three isoforms, which we show have different transcription factor activity in basal-like vs. other TNBC cell lines. We further show that the ERR2 and ERRsf isoforms are broadly expressed in breast tumors at the protein level. Conclusions Decreased mRNA expression, and distinct patterns of ERR isoform subcellular localization and transcription factor activity are key features in TNBC/BLBC. mRNA expression have significantly improved distant-metastases free, and recurrence- free survival in comparison to patients with low expression [11]. Previous publications have shown that patients with BLBC overall have tumors with significantly lower mRNA expression in comparison to other breast cancer subtypes [12, 13]. The goal of the present study is to: (1) define expression levels in breast cancer, specifically in BLBC and TNBC; (2) determine how DNA copy number and protein levels are modulated GR-203040 in various data sets to determine if the previously observed decrease in is caused by copy number loss, and the effects of decreased mRNA on protein expression and function; (3) characterize clinical correlations found in breast cancer. We show that mRNA expression is significantly lower in patients with BLBC/ TNBC and GR-203040 that there is no observed decrease in DNA copy number. ERR splice variants have differential transcription factor activity in TNBC cell lines. Lastly, we also show that ERR splice variant protein levels are different in.