Figure 2.
Transcriptional Profiling Detects a Signature of CTVT Regression
(A) Heatmap showing differential expression of the 1,016 significant genes (FC > 10 and adj-p < 0.01) relative to the geometric mean of CTVT-5 B1 and CTVT-6 B1 (mean of the logs). Genes are sorted by expression of B3/geometric mean of (CTVT-5 B1, CTVT-6 B1). B1, first biopsy; B2, second biopsy; B3, third biopsy.
(B) qPCR on DNA extracted from biopsies obtained before (B1, day 0) and after (B2, day 28) vincristine administration of the 7xx CTVTs. Specific primers were used to amplify LINE-MYC DNA (tumor specific), DLA DQA-1 (tumor specific), and DLA DQA-1 (common to both host and tumor). All quantifications are relative to β-actin.
(C) Heatmap showing differential expression of the 1,350 significant genes in the 7xx CTVTs (FC > 10 and adj-p < 0.01) relative to the geometric mean of the five B1 samples. Genes are sorted by expression of B2/geometric mean of 7xx B1s. Each row represents an individual gene. RNA-seq data were not available for CTVT-774 B1. The red lines next to each row indicate genes that reached statistical significance in the R-B2/R-B1 versus NR-B2/NR-B1 comparison.
(D) Venn diagram showing the degree of overlap between CTVT-5 R versus P genes (1,016 genes), the 7xx CTVTs B2 versus B1 genes (1,350 genes) and genes that reached statistical significance in the R-B2/R-B1 versus NR-B2/NR-B1 comparison (189 genes).