Abstract 484: Fidelity of subclonal representation in human neuroblastoma-derived cell line and patient-derived xenograft models: A report from the NCI-TARGET project

Abstract Patient-derived xenografts and cell lines have been the underpinning of functional characterization and drug discovery efforts in cancer. The use of these models is often under the assumption that these systems are renewable, faithful representations of original progenitor tumor cell populations. To test this assumption, we performed whole exome (92X median coverage) and genome sequencing (36X median coverage) analysis of cell line and patient-derived mouse xenografts (PDXs) originating from 7 neuroblastoma patients. Data are from1 primary tumor, 3 PDXs, and 15 neuroblastoma cell lines cultured from tumor, bone marrow, or blood. The cell lines consisted of 4 pre-/post-therapy pairs and 3 pairs established and maintained in either hyperoxia (room air i.e. “standard” cell culture) or physiologic (bone marrow hypoxia = 5%) oxygen. 7 lymphoblastoid or fibroblast cell lines were used as matched normals to identify somatic mutations. Subclonal population structures were inferred from somatic mutation calls calibrated for copy number state and tumor purity. In all cell lines and xenografts, we observed 1-2 additional subclonal populations, primarily supported by deep coverage from exome sequencing. In nearly every case, we observed shifts in the proportional representation of genetic subclones and many subclones showed additional mutations not evident in the progenitor tissue or cancer line derived in parallel. Comparison of three cell line pairs established in bone marrow level hypoxia versus room air found only ∼40% of coding mutations in each line were shared (average 82 mutations per line), suggesting significant genetic impact of growing tumor cells in the two different culture conditions. Matched PDXs from these cases had only ∼17% of coding mutations shared across all three models. The greatest genetic similarity was seen between paired cell lines established from tissue obtained pre-/post-therapy from the same patient (36 coding mutations shared, 14 private to diagnosis and 13 private to progression). However, a second pre/post-therapy cell line pair did not share any coding mutations, although they did have 585 non-coding mutations in common (of 4,033 and 2,480 in each line), assuring that the relapse was derived from a diagnostic tumor clone. These results highlight a need for comprehensive subclonal analysis of human cancer laboratory models to better inform design and interpretation of biological and preclinical therapeutic studies. Citation Format: Maya Schonbach, Arnavaz Danesh, Jeff Bruce, Tito Woodburn, Tanja Davidsen, Leandro Hermida, Patee Gesuwan, Jaime Guidry Auvil, Oliver Hampton, David Wheeler, Julie Gastier-Foster, Malcolm Smith, Daniela Gerhard, John M. Maris, Patrick Reynolds, Trevor J. Pugh. Fidelity of subclonal representation in human neuroblastoma-derived cell line and patient-derived xenograft models: A report from the NCI-TARGET project. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 484. doi:10.1158/1538-7445.AM2015-484

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