Additional file 1: Figure S1. of Monocarboxylate Transporter 1 (MCT1) is an independent prognostic biomarker in endometrial cancer

Kaplan-Meier survival analysis for grade I/II endometrial tumours. (PDF 309 kb

Characterisation of a head and neck squamous cell carcinoma (HNSCC) cell line cohort.

<p><b>A)</b> Graph showing the mean SF2 (log10) (y-axis) for each of the 11 cervix cancer cell lines (x-axis). Error bars show the standard error of mean of 2–3 independent experiments. <b>B)</b> Graph showing that there is no difference in TP63 expression between the SF2 high and low groups. Bar shows the median expression. <b>C)</b> Unsupervised hierarchical clustering of the top 1000 genes ranked by coefficient of variation (from U133 array data). Heatmap colouring is by log₂ expression value. Rows represent genes and columns are cell lines. x-axis dendrogram (clusters) indicates the similarity of the cell lines and y-axis dendrogram the similarity of genes. Cluster 1 represents two samples with the lowest TP63 values (p63 negative). Cluster 2 shows the grouping of the other p63− cell line, along with low TP63 expressing lines. Cluster 3 groups together all HNSCC lines with >6.0 (log2 expression) TP63 expression. <b>D)</b> Diagram to represent the integrated SF2 analysis of the cervix and HNSCC cell lines. Rank product analysis (FDR <0.05) identified 96 genes in the cervix cohort differentially expressed between SF2 low and high cell lines. An identical analysis in the HNSCC cell lines identifies 97 probesets (42 genes) differentially expressed between SF2 low and high cell lines. PCA of the cervix genes shows that they are capable of separating the cell lines by SF2. PCA of the HNSCC genes is equally capable of separating the samples based on SF2. The Venn diagram shows that only 4/138 genes are common between the two cohorts and of these only 2/138 are “congruent” and associated with the same directionality (high SF2/low SF2 in both HNSCC and cervix). PCA shows probeset expression of these two “common” and “congruent” genes (MGST1 and TFPI) in the NCI-60 dataset. The NCI-60 upper PCA shows data-points coloured for median SF2 and lower PCA coloured for 0.2, used previously to partition radiosensitive and radioresistant cell lines in this cohort.</p

Assessment of established radiosensitivity gene signatures.

<p><b>A)</b> PCA of the Tewari radiosensitivity gene signature. The original signature consists of 49 genes, with mapping to the NCI-60 (60 Plus2 probesets) HNSCC (60 Plus2 probesets) and cervix cell line (48/49 genes) datasets. The x-axis shows PC1, accounting for the largest amount of variation in the experiment and the y-axis shows the second principal component (PC2). Colouring based on median SF2, blue data-points are radiosensitive cell lines (below the median SF2) with red data-points being the radioresistant lines (above the median SF2). <b>B)</b> Implementation of the Eschrich radiosensitivity model <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086329#pone.0086329-Eschrich2" target="_blank">[12]</a>. Applied to a training set of 16 samples from the NCI-60 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086329#pone.0086329-Eschrich3" target="_blank">[13]</a>. xy-scatterplot with the x-axis showing reported SF2 values, generated with these cell lines on a earlier array type (U95) against values generated by implementing the model in the current U133 plus 2.0 dataset (y-axis). Line indicates perfect correlation. <b>C)</b> Applied to the HNSCC and cervix cancer cell line cohorts. The y-axis indicates the predicted SF2 determined from the radiosensitivity model. The x-axis shows the empirically derived SF2 values. <b>D)</b> Principal component analysis of the Amundson radiosensitivity gene signature <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086329#pone.0086329-Amundson1" target="_blank">[10]</a>. The original signature consists of 22 genes (33 Plus2 probesets), with mapping to the NCI-60 (33 Plus2 probesets), HNSCC (33 Plus2 probesets) and cervix cell line (21/22 genes) datasets. The x-axis shows PC1, accounting for the largest amount of variation in the experiment and the y-axis shows the second principal component (PC2). In the NCI-60 data colouring is based a threshold of 0.2 (previously defined <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086329#pone.0086329-Hall1" target="_blank">[21]</a> where the HNSCC and cervix cell line datasets are coloured by median SF2. In all cases blue data-points are radiosensitive cell lines (below the median SF2) with red data-points being the radioresistant lines (above the median SF2).</p

Radiobiological characterisation of cervix carcinoma cell lines.

<p><b>A)</b> Radiation survival curves showing surviving fraction (log10) (y-axis) following irradiation with 2, 4, 6, 8 and 10 Gy for 14 cervix cancer cell lines. Data points are the mean and standard error of 2–3 independent experiments (3–6 replicates per experiment). Data-points are fitted with the linear quadratic equation and coloured by below (blue) or above (red) the median SF2.</p

ZeptoMARK protein profiling of the cervix cancer cell lines.

<p><b>A)</b> Histogram displaying the ZeptoMARK protein-array derived abundance for the 16 cervix cancer cell lines. The y-axis displays E-cadherin protein level (relative fluorescent intensity (RFI) for each of the cell lines (x-axis). Cell lines are ranked based on TP63 expression. Grouping into p63 negative and p63 positive cell lines confirms the association of E-cadherin with p63. The p value is T-test derived comparing the difference in E-cadherin expression between the p63 positive and negative groups, error bars display standard deviation of two biological replicates. <b>B)</b> x–y scatterplot showing E-cadherin gene expression (Exon array) on the y-axis against E-cadherin protein expression on the x-axis. Dashed line represents perfect correlation. Exon array data-points represent the average of multiple exonic probesets (n = 19) from a single Exon expression array, where protein data are the mean of two biological replicates. <b>C)</b> Heatmap showing clustering of proteins with similar expression (y-axis) in the ZeptoMARK protein profiling data. Cell lines ranked by SF2. Heatmap colouring is based on row Z-score. <b>D)</b> xy-scatter plot showing the expression (y-axis) of the top 5 proteins from LIMMA against SF2 (x-axis). Table summarises the results of Limma differential protein expression analysis between high and low SF2 groups and Pearson correlation of protein expression (RFI) against SF2. p values denote those proteins with differential expression (* p<0.05 or ** p<0.01) between SF2 low and high groups according to LIMMA analysis. However these fail to pass false discovery rate correction.</p

Summary characteristics of the cervix cell lines.

*<p>Provenance information from ATCC, JCRB or <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086329#pone.0086329-Fertil1" target="_blank">[17]</a>.</p>$<p>HPV genotype from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086329#pone.0086329-Marples1" target="_blank">[20]</a>.</p>†<p>p63 expression from Western analysis and Exon derived array expression values from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086329#pone.0086329-Brady1" target="_blank">[19]</a>.</p