Additional file 3: Figure S1. of Preclinical evaluation and reverse phase protein Array-based profiling of PI3K and MEK inhibitors in endometrial carcinoma in vitro

Endometrial cancer cell lines in which synergism was observed to the combination of pictilisib (PI3K), apitolisib (PI3K/mTOR), and cobimetinib (MEK) inhibitors. a) Eight cell lines in which synergism was observed to the combination of PI3K and MEK inhibition. b) Eight cell lines in which synergism was observed to the combination of PI3K/mTOR and MEK inhibition. (XLSX 158 kb

Germline single nucleotide polymorphisms in <i>ERBB3</i> and <i>BARD1</i> genes result in a worse relapse free survival response for HER2-positive breast cancer patients treated with adjuvant based docetaxel, carboplatin and trastuzumab (TCH) - Fig 3

<p>Reverse Phase Protein array analysis correlating differential expression and phosphorylation of proteins involved in either the A) AKT or B) MAPK pathway versus the presence or absence of the minor allele of the ERBB3 rs2229046 SNP. p-values <0.05 included on the graph demonstrate significantly differential protein expression between the presence of the reference allele or the presence of the minor allele and are corrected for multiple testing.</p

Germline single nucleotide polymorphisms in <i>ERBB3</i> and <i>BARD1</i> genes result in a worse relapse free survival response for HER2-positive breast cancer patients treated with adjuvant based docetaxel, carboplatin and trastuzumab (TCH)

<div><p>Breast cancer is the leading cause of cancer related deaths in women worldwide and is classified into subtypes based on the cancer’s receptor status. Of these subtypes, those expressing the human epidermal growth factor receptor 2 (HER2) receptor were traditionally associated with poor prognosis. Several advances have been made in the treatment of HER2-positive breast cancer, yet issues of resistance and poor response to therapy remains prevalent. In this study we explored the impact of HER-family and homologous recombination deficiency SNPs on response to patients who received TCH-based (docetaxel (T), carboplatin (C), and trastuzumab (H)) treatment versus those who received other treatment regimens. Using Cox regression analysis, we identified 6 SNPs that correlate with recurrence free survival in our patients and supported our findings using support vector machines. We also used reverse phase protein array analysis to examine the impact ERBB3 SNPs may have on both the PI3K/AKT and MAPK/ERK signaling pathways. Finally, using cell line models, we correlated SNP status with sensitivity to platinum based drugs and docetaxel. We found that patients on a TCH based regimen with the minor allele of the ERBB3 (rs2229046 and rs773123) and BARD1 (rs2070096) SNPs, were significantly more likely to relapse than those women who were not. Additionally, we observed that patients with these ERBB3 SNPs had shown elevated protein expression/phosphorylation of Src kinase, c-MET (Y1234/1235), GSK-3β (S9) and p27, indicating that these SNPs are associated with non-PI3K/AKT signaling. Finally, using cell line models, we demonstrate that the BARD1 SNP (rs2229571) is associated with greater sensitivity to both carboplatin and cisplatin. The BARD1 and ERBB3 SNPs can potentially be used to determine those patients that will have a worse response to TCH based treatment, an effect that may arise from the SNPs impact on altered cellular signaling.</p></div

Impact of HER-family and HRD SNPs on relapse free and overall survival of HER2-positive BC patients who have received either TCH based regimen or a non-TCH based regimen as part of their therapeutic regimen (n = 157).

<p>Impact of HER-family and HRD SNPs on relapse free and overall survival of HER2-positive BC patients who have received either TCH based regimen or a non-TCH based regimen as part of their therapeutic regimen (n = 157).</p

The prognostic role of RNF8-T448T SNP in TCH versus non-TCH treated primary tumours (n = 157).

<p>The blue, red and green lines represent the samples with the wild type (reference), heterozygous and minor alleles respectively. Kaplan Meier estimates where RFS is the survival endpoint (HR = 12.42 (2.00–77.19) p = 0.01) in non-TCH treated patients versus no-significant impact in TCH treated patients.</p

List of SNPs including Gene ID, accession number, mutant allele frequency and haplotype details which were detected by high depth next generation sequencing and selected for further analysis.

<p>List of SNPs including Gene ID, accession number, mutant allele frequency and haplotype details which were detected by high depth next generation sequencing and selected for further analysis.</p

Summary of patient characteristics used in the RPPA analysis (<i>n</i> = 60).

<p>Summary of patient characteristics used in the RPPA analysis (<i>n</i> = 60).</p

Analysis of the differential sensitivity of HER2-positive breast cancer cell lines to the platinum drugs cisplatin and carboplatin.

<p>We correlated the presence or absence of the minor allele of HER-family or BARD1 versus the GD₅₀ to either drug. GD₅₀ values were taken from the GDSC cell line analysis database [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0200996#pone.0200996.ref021" target="_blank">21</a>]. p-value of <0.05 indicates a significant p-value after multiple testing correction.</p

Germline single nucleotide polymorphisms in <i>ERBB3</i> and <i>BARD1</i> genes result in a worse relapse free survival response for HER2-positive breast cancer patients treated with adjuvant based docetaxel, carboplatin and trastuzumab (TCH) - Fig 4

<p>Reverse Phase Protein array analysis correlating differential expression and phosphorylation of proteins involved in either the A) AKT or B) MAPK pathway versus the presence or absence of the minor allele of the ERBB3 rs773123 SNP. p-values <0.05 included on the graph demonstrate significantly differential protein expression between the presence of the reference allele or the presence of the minor allele and are corrected for multiple testing.</p

The prognostic role of ERBB2, ERBB3 and BARD1 SNPs in TCH versus non-TCH treated primary tumours (n = 157).

<p>In each plot, the blue and red lines represent the samples with the wild type (reference) and heterozygous alleles respectively. Kaplan Meier estimates of (A) the ERBB2-rs1136201 SNP where RFS is the survival endpoint (HR = 2.67 (1.05–6.78), p = 0.05) in TCH treated patients versus no-significant impact in non-TCH treated patients, (B) the ERBB3 rs2229046 SNP, where RFS is the survival endpoint (HR = 4.95 (1.91–2.79), p = 1.51x10-3) in TCH treated patients versus no significant impact on non-TCH treated patients, (C) the ERBB3 rs773123 SNP, where RFS is the survival endpoint (HR = 2.67 (1.02–7.03), p = 0.05) in TCH treated patients versus no significant impact on non-TCH treated patients, and (D) the BARD1 rs2070096 SNP, where RFS is the survival endpoint (HR = 3.27 (1.16–9.17), p = 0.05) in TCH treated patients versus no significant impact in non-TCH treated patients. p-values <0.05 indicates a significant p-value after multiple testing correction.</p