The 682-gene signature expression pattern in mouse carcinomas is dependent on p53 expression.

<p><b>A</b>) SV40 Large-T antigen expression in mammary gland was analysed at various time-points during carcinoma formation in transgenic WAP-TNP8 mice. Heatmaps of 682-gene signature transcripts from normal mammary glands (green), primary breast carcinomas (red) and mammary samples with transgene expression at 1, 2, 3, 4 and 5 months (blue) are shown (upper panel). <b>B</b>) p53 expression was induced in lung adenomas and adenocarcinomas in the Kras^LA2/+;Trp53^LSL/LSL;Rosa26Cre^ERT2 mouse model. The heatmaps of the 682-gene signature transcripts from normal lungs (green), lung adenomas (orange) and adenocarcinomas (red) (treated and untreated) are shown (upper panel). In <b>A</b> and <b>B</b>, sample groups are ordered from left to right based on increasing Pearson correlation with the centroid template based on the 682-gene signature. Probesets are ordered from top to bottom based on T-values (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042494#s4" target="_blank">Materials and Methods</a>). The number of samples in each group is shown under the heatmap. The correlation values for individual samples with the centroid are shown in the middle panel. Values range from −1 (negative correlation, bluish background) to +1 (positive correlation, reddish background). The significance of the correlation for each sample is shown in the lower panel as –log₁₀(p-val). The red line indicates a p-val of 0.01.</p

Survival curves of human BC stratified using 40-gene test and depending on molecular subtypes.

<p>Kaplan-Meier curves of distant metastasis-free survival (DMFS) for patients with BC depending on ER, PR and HER2 status. Patients were stratified based on the 40-gene test as of low (green), intermediate (blue) or high (red) risk (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042494#s4" target="_blank">Materials and Methods</a>). p-val: significance of survival differences (log-rank test).</p

Survival curves of human LAd stratified using 36-gene genomic-clinic test and depending on molecular subtypes.

<p>Kaplan-Meier curves of overall survival for patients with LAd depending on EGFR and KRAS mutation status. Patients were stratified based on the 36-gene genomic-clinic test as of low (green), intermediate (blue) or high (red) risk (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042494#s4" target="_blank">Materials and Methods</a>). p-val: significance of survival differences (log-rank test).</p

Multivariate Cox regression including the 40-gene test and breast cancer clinical variables.

<p>Total number of samples is 668. Endpoint analyzed was distant metastasis at 10 years.</p><p>Cox analysis was done stratifying by dataset.</p>1<p>HR: Hazard ratio.</p>2<p>CI: confidence interval.</p>*<p>Significant p-values.</p

The mouse skin 682-gene signature is significantly present in mouse mammary and lung carcinoma models showing p53 inhibition.

<p>Heatmaps of the 682-gene signature transcripts from (<b>A</b>) primary breast carcinomas and normal mammary glands from different transgenic GEMMs (upper panel), and from (<b>B</b>) primary and metastatic lung adenocarcinomas and normal lungs from different transgenic GEMMs (upper panel) (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042494#pone.0042494.s011" target="_blank">Table S1</a>) are shown. The T-values returned by Student’s t-test comparisons between normal skin and carcinoma samples in which the 682-gene signature was determined (GSE11990) were used to build a centroid template. The Pearson correlation coefficient (and the corresponding p-value) with respect to the centroid was calculated for each mouse sample. Samples were ordered from left to right based on increasing correlation. Probesets are ordered from top to bottom based on T-values (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042494#s4" target="_blank">Materials and Methods</a>). Samples within blue rectangles are normal skin samples and skin tumour samples. The number of samples in each group is shown under the heatmaps. Pearson values are shown in the middle panel. Values range from −1 (negative correlation, bluish background) to +1 (positive correlation, reddish background). The significance value for the correlation is shown in the lower panel as –log₁₀(p-val). The red line indicates p-val = 0.01. Genotypes highlighted in red are models with p53 alterations significantly correlated with the 682-signature. Samples highlighted in pink are metastases. In (<b>B</b>), the Kras (1) and Kras/Lkb1^L/L (1) samples are from the GSE6135 dataset; the Kras (2) and Kras/Lkb1^L/L (2) samples are from the GSE21581 dataset.</p

Top 10 pertubagens identified through the Connectivity Map that induce a reverse 682-signature.

1<p>Ranking based upon permutation analysis of the same perturbagen made in the same cell line.</p>2<p>Arithmetic mean of the connectivity scores.</p>3<p>An estimate of the likelihood that the enrichment of a set of instances in the list of all instances in a given result would be observed by chance.</p

Human LAd patient stratification using the mouse-derived 36-gene genomic-clinical predictor test.

<p><b>A</b>) Kaplan-Meier curves for overall survival (OS) for the pooled population of patients with lung cancer in three datasets including patients with all disease stages. Patients were stratified based on the 36-gene test as of low (green), intermediate (blue) or high (red) risk (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042494#s4" target="_blank">Materials and Methods</a>). <b>B</b>) Kaplan-Meier curves for early stage patients (Stages IA and IB). Patients were stratified based on the 36-gene test as of low (green), intermediate (blue) or high (red) risk. <b>C</b>) Kaplan-Meier curves for patients profiled using qRT-PCR and FFPE samples. Patients were stratified based on the 36-gene test as of low (green), or high-intermediate (red) risks (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042494#s4" target="_blank">Materials and Methods</a>). Owing to the small sample size, the intermediate and high risk groups were pooled. p-val: significance of survival differences (log-rank test).</p

Human BC patient stratification using the mouse-derived 40-gene predictor test.

<p><b>A</b>) Kaplan-Meier curves of distant metastasis-free survival (DMFS) for a pooled population of 12 GE datasets of patients with BC. Patients were stratified based on the 40-gene test as of low (green), intermediate (blue) or high (red) risk (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042494#s4" target="_blank">Materials and Methods</a>). <b>B</b>) Kaplan-Meier curves of DMFS from ER+, tamoxifen-treated women with BC. Patients were stratified based on the 40-gene test as of low (green), intermediate (blue) or high (red) risk. <b>C</b>) Kaplan-Meier curves for ER+, tamoxifen-treated patients with breast cancer in the Miller dataset. Patients were stratified depending on the presence (red) or absence (green) of p53 mutations. p-val: significance of survival differences (log-rank test).</p

The Long-HER Study: Clinical and Molecular Analysis of Patients with HER2+ Advanced Breast Cancer Who Become Long-Term Survivors with Trastuzumab-Based Therapy

<div><p>Background</p><p>Trastuzumab improves survival outcomes in patients with HER2+ metastatic breast cancer. The Long-Her study was designed to identify clinical and molecular markers that could differentiate long-term survivors from patients having early progression after trastuzumab treatment.</p><p>Methods</p><p>Data were collected from women with HER2-positive metastatic breast cancer treated with trastuzumab that experienced a response or stable disease during at least 3 years. Patients having a progression in the first year of therapy with trastuzumab were used as a control. Genes related with trastuzumab resistance were identified and investigated for network and gene functional interrelation. Models predicting poor response to trastuzumab were constructed and evaluated. Finally, a mutational status analysis of selected genes was performed in HER2 positive breast cancer samples.</p><p>Results</p><p>103 patients were registered in the Long-HER study, of whom 71 had obtained a durable complete response. Median age was 58 years. Metastatic disease was diagnosed after a median of 24.7 months since primary diagnosis. Metastases were present in the liver (25%), lungs (25%), bones (23%) and soft tissues (23%), with 20% of patients having multiple locations of metastases. Median duration of response was 55 months. The molecular analysis included 35 patients from the group with complete response and 18 patients in a control poor-response group. Absence of trastuzumab as part of adjuvant therapy was the only clinical factor associated with long-term survival. Gene ontology analysis demonstrated that PI3K pathway was associated with poor response to trastuzumab-based therapy: tumours in the control group usually had four or five alterations in this pathway, whereas tumours in the Long-HER group had two alterations at most.</p><p>Conclusions</p><p>Trastuzumab may provide a substantial long-term survival benefit in a selected group of patients. Whole genome expression analysis comparing long-term survivors vs. a control group predicted early progression after trastuzumab-based therapy. Multiple alterations in genes related to the PI3K-mTOR pathway seem to be required to confer resistance to this therapy.</p></div

Signaling pathway annotation enrichment analysis for 858 genes related with trastuzumab resistance.

<p>This analysis was performed using SPEED software. PI3K pathway appeared as the most relevant pathway in relation with trastuzumab resistance.</p