Molecular Characterization of the Pediatric Preclinical Testing Panel

Abstract

Purpose Identifying novel therapeutic agents for the treatment of childhood cancers requires preclinical models that recapitulate the molecular characteristics of their respective clinical histotypes. Experimental Design and Results Here, we have applied Affymetrix HG-U133Plus2 profiling to an expanded panel of models in the Pediatric Preclinical Testing Program. Profiling led to exclusion of two tumor lines that were of mouse origin and five osteosarcoma lines that did not cluster with human or xenograft osteosarcoma samples. We compared expression profiles of the remaining 87 models with profiles from 112 clinical samples representing the same histologies and show that model tumors cluster with the appropriate clinical histotype, once “immunosurveillance” genes (contributed by infiltrating immune cells in clinical samples) are eliminated from the analysis. Analysis of copy number alterations using the Affymetrix 100K single nucleotide polymorphism GeneChip showed that the models have similar copy number alterations to their clinical counterparts. Several consistent copy number changes not reported previously were found (e.g., gain at 22q11.21 that was observed in 5 of 7 glioblastoma samples, loss at 16q22.3 that was observed in 5 of 9 Ewing’s sarcoma and 4 of 12 rhabdomyosarcoma models, and amplification of 21q22.3 that was observed in 5 of 7 osteosarcoma models). We then asked whether changes in copy number were reflected by coordinate changes in gene expression. We identified 493 copy number – altered genes that are nonrandom and appear to identify histotype-specific programs of genetic alterations. Conclusions These data indicate that the preclinical models accurately recapitulate expression profiles and genetic alterations common to childhood cancer, supporting their value in drug development.

Transcriptional Profiling Identifies the Signaling Axes of IGF and Transforming Growth Factor-β as Involved in the Pathogenesis of Osteosarcoma

“…Patient specimens obtained after preoperative chemotherapy usually contain at least partly necrotic tissue. Cultured cell lines and xenograft tissues are more reproducible and can be expanded, but transcriptome differences from the primary material are likely [23]. We therefore used a more stringent criterion for statistical analysis, only genes that were commonly deregulated in all osteosarcoma SAGE libraries were selected.…”

Anthrax toxin receptor 1 is the cellular receptor for Seneca Valley virus

“…Normalized gene expression data for cancer cell lines was downloaded from the Cancer Cell Line Encyclopedia (CCLE) or from the Pediatric Preclinical Testing Program (PPTP) (30,35). Custom content descriptor files (CDFs) were used for both gene expression data sets.…”

Osteosarcoma

“…With a consortium of laboratories in the United States and abroad, the program is able to quickly screen a large number of agents using in vitro and in vivo models. (65,(69)(70)(71) The in vitro models are cell lines, with the in vivo models typically human patient-derived tumors grown as heterotopic xenografts in severe combined immunodeficiency mice. Although osteosarcoma can be grown in orthotopic as well as heterotopic sites, the heterotopic site permits frequent tumor size measurements using a caliper, which is feasible and cost-effective.…”

“…This program has generated a large amount of data, including characterizations of the model systems, that has rapidly been published or made available through Web-based applications (http://home.ccr.cancer.gov/oncology/oncogenomics/). (65,(69)(70)(71) Canine Models…”