5 research outputs found
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