Unsupervised clustering analysis with expression data of the processed 2,854 genes in the 60 ESCC samples treated with definitive CRT.

<p>Expression data in all of the 60 samples (A: 30 pre-treatment biopsy samples, B: 30 post-treatment biopsy samples) were analyzed by the Cluster and Treeview programs. Three patient clusters (box) were identified. Among them, one cluster (red) was a good responder with 73% CR.</p

Overall survival in the <i>CDH2</i>-negative epithelial-type cases and <i>CDH2</i>-positive mesenchymal-type cases in 117 cases of the second cohort.

<p>(A) In all of the 117 cases, 82 <i>CDH2</i>-negative cases showed better overall survival (OS) compared with 35 <i>CDH2</i>-positive cases (56% vs 21% in 5 year OS rate). (B) Especially, in 33 I-type cases, 15 <i>CDH2</i>-negative cases showed much better OS compared with 18 <i>CDH2</i>-positive cases (64% vs 12% in 5 year OS rate). (C) In 84 non I-type cases, 67 <i>CDH2</i>-negative cases showed better OS compared with 17 <i>CDH2</i>-positive cases (54% vs 31% in 5 year OS rate).</p

Supervised clustering analysis with expression data of the 234 immune-related genes in the 60 ESCC samples.

<p>In accordance with supervised clustering analyses with expression data of the 999 genes (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0143804#pone.0143804.g001" target="_blank">Fig 1A</a>), the dendrograms reproducibly showed the presence of a good responder cluster (CR: 56% and 68%) in each pre- and post- treatment samples. We designated the immune-activated ESCC subtype as I-type. </p

Supervised clustering analysis with expression data of the 999 genes induced by CRT in a good responder cluster.

<p>(A) In accordance with the unsupervised clustering analysis with expression data of the processed 2,854 genes, the dendrograms reproducibly showed the presence of a good responder cluster (CR: 56% and 68%) in both pre- and post- treatment samples. (B) Comparison of immune-related gene expression levels between pre- and post- treatment samples. Key genes (<i>PRF1</i>, <i>GZMB</i>, <i>IFNG</i>, <i>CASPs</i>, <i>TNFs</i>) for the CTL activation, which were included in 234 immune-related genes of the above 999 genes, were upregulated in post-treatment samples especially with CR cases. Pre-treatment samples (blue), post-treatment samples (red). CR: cases with complete response, non CR: cases with non CR (partial response, PR). * <i>p</i><0.05, **<i>p</i><0.01, ***<i>p</i><0.001.</p

Overall survival in the I-type cases and non I-type cases in 117 cases of the second cohort.

<p>The I-type cases did not show better overall survival in both all of the 117 cases (A) and the 59 CR cases (B).</p

Cumulative incidences of metachronous esophageal squamous cell carcinoma in the esophagus according to HRA score.

<p>Hazard ratio was adjusted for age and LVL grades.</p

Prediction of metachronous SCC in the esophagus based on Cox proportional hazards models.

<p>Prediction of metachronous SCC in the esophagus based on Cox proportional hazards models.</p

Time-dependent receiver operating characteristic curve according to HRA score at 24 months for predicting metachronous esophageal squamous cell carcinoma (SCC) in patients who had undergone endoscopic mucosectomy for early esophageal SCC.

<p>Time-dependent receiver operating characteristic curve according to HRA score at 24 months for predicting metachronous esophageal squamous cell carcinoma (SCC) in patients who had undergone endoscopic mucosectomy for early esophageal SCC.</p

Clinical characteristics of subjects according to HRA score.

<p>Clinical characteristics of subjects according to HRA score.</p