Molecular differences between patients’ tumors and BCXs.

<p>(A) Unsupervised clustering of proteomic profile of patient tumors and BCXs as determined by RPPA. Each protein tested represents a column: Red, high expression; green, low expression. Samples are listed on the right side. Left, cluster trees of sample groups; top, cluster trees of proteins. Each BCX model’s P1-3 generation clustered together, demonstrating relative stability of the proteomic profile once growth in mouse is established. However, all P0 generations clustered together, suggesting that differences between patient tumor-xenograft proteomic profiles is greater than inter-tumoral differences. (B) Selected proteins and phosphoproteins that are differentially expressed between patient tumors (P0) and the first-generation of BCXs passaged through nude mice (P1). Protein levels were compared between the two groups with RPPA; all shown have a FDR 0.1 or less. (C) Copy number analysis determined PTEN loss in MDA-BCX-002. Top panel shows the chromosome 10 ideogram and the PTEN gene. Deletions are plotted in red below the 0% baseline, and dark red indicates homozygous loss. The lowest portion of the top panel separates out P0 and P3. A heterozygous PTEN loss is detected in P0, and in the P3, the second PTEN allele is lost, resulting in a homozygous PTEN loss. Bottom panel shows the PTEN gene ideogram followed by the copy number aberration plot and the allele frequency plot for P0 and P3. A heterozygous PTEN loss is detected in P0 (single red line), and a homozygous PTEN loss is detected in P3 (double red line). Each blue dot corresponds to an individual probe on the array. The brown and purple lines mark the thresholds for loss of heterozygosity (LOH) and allelic imbalance regions, respectively. (D) PCR confirmed PTEN deletion in genomic DNA from Patient 2 tumor and BCX-002 P3. PTEN was undetectable in P3 but present in P0. RB1, another tumor suppressor gene, is detected in both samples and included for comparison. (E) PTEN loss demonstrated by next generation sequencing in BCX-024. P0 on the left, P1 on the right.