Deep Functional and Molecular Characterization of a High-Risk Undifferentiated Pleomorphic Sarcoma

Figures

• 

  Figure 1. RNA-seq and histology of PCB-209. RNA-seq data for PTIM identified targets and multiple staining images of PCB-209. RNA-seq and histology data were used to partially guide cohorts of the in vivo PDX trial. (a) RNA-seq expression of PCB-209 vs. PCB-209 PDX. (b) H&E stain. (c) PDX H&E stain. (d) Staining for COX2. (e) Staining for GLI2. (f) Staining for ki67. (g) Staining for pERK. (h) Staining for PRKCA. (i) RNA-seq RPKM reported in log2 format for targets identified by the PTIM analysis informed with RNA-seq data. Red indicates high expression, and green indicates low expression. The left column is the expression for the original cell culture, and the right column is the expression for the culture created from the xenograft mice.

• 

  Figure 2. Circos plot of PCB-209 RNA sequencing and whole genome sequencing data. The outermost data circle represents log2-scaled gene expression (green represents negative, red represents positive) for genes with identified mutations or copy number variations. The middle circle represents genes with identified mutations or indels (black) or lack thereof (white). The innermost circle represents copy number variations (pink is amplification, light blue is deletion, and white is no variation). Genes which carry both mutations and amplifications (TNS3, BRINP1, RABEP1, and CDH4) are written in blue around the circle, as are genes relevant to in vivo studies (HDAC1, ALK, GL1, HDAC3, FLT4, PSMB8, HDAC2, JAK2, PSMB5, MAP2K1, PRKCA, BCL2, MAP2K2, AKT2, BCL2L1, and MAPK1).

• 

  Figure 3. Probabilistic Target Inhibitor Map (PTIM) model of the PCB209 xenograft-derived chemical screen. Orange text indicate targets inhibited by ABY-737; blue text indicates targets inhibited by midostaurin. (a) Pediatric preclinical testing initiative (PPTI) 60 chemical screen informed PTIM. (b) RNA-seq + PPTI chemical screen informed PTIM. PTIM models were used to guide a portion of the larger PDX in vivo trial shown in Figure 2. Numbers listed in the individual boxes represent scaled sensitivity values, 1 being a highly sensitive target combination and 0 being an ineffective/resistant target combination.

• 

  Figure 4. PCB-209 xenograft-derived in vivo trial results. Mean tumor volume of all treatment cohorts of the Jackson Lab-based PCB-209 patient-derived xenograft (PDX) model in vivo preclinical studies. (a) Tumor growth of crizotinib-treated PDX mice (n = 6) versus control (n = 4). (b) Tumor growth of carfilzomib-treated PDX mice (n = 7) versus control (n = 4). (c) Tumor growth of panobinostat-treated PDX mice (n = 8) versus control (n = 4). (d) Tumor growth of celecoxib- (n = 5), trametinib- (n = 5), and celecoxib + trametinib-treated (n = 4) PDX mice versus control (n = 4). (e) Tumor growth of ABT-737 (n = 7), midostaurin (n = 8), and ABT-737 + midostaurin-treated PDX mice (n = 2) versus control (n = 4). The p value was calculated without the midostaurin + ABT-737 due to low sample population, noted by the asterisk. The low number of models for the combination experiment is due to microbiological considerations at the Jackson Laboratory. In (a–e), the endpoint was treatment days 30–32.