Abstract 1515: Tracking the origins and drivers of metastatic expansion in osteosarcoma
Authors: Kinnaman Michael David , Makohon-Moore Alvin , Glodzik Dominik , Levine Max , Bouvier Nancy , Dela Cruz Filemon , Hameed Meera , Meyers Paul , Papaemmanuil Elli , Kung Andrew , Iacobuzio-Donahue Christine 
Published: September 2020

Objective: Outcomes for patients with osteosarcoma with metastatic or relapsed disease remain poor. Multiple large-scale tumor genomic profiling efforts have been undertaken, however little is known about its spatial intermetastic heterogeneity and temporal clonal evolutionary processes.

Methods: To address this issue, we performed 30-80x whole genome sequencing of nine metastases, three pre-treatment samples, and three on-therapy resection samples from three patients with osteosarcoma. Each patient (OSCE1, OSCE2, OSCE3) had a pre-treatment and on therapy resection of primary site sample as well as at least two sites of metastatic disease sequenced. OSCE1 has multiply relapsed disease and had tissue sequenced from relapse one, two, and four, while OSCE2 and OSCE3 had lethal refractory osteosarcoma. A set of high confidence single nucleotide variants (SNV), copy number alterations (CNA), structural variations (SV), and mutational signatures were called for each sample and an evolutionary analysis was performed using the Treeomics pipeline.

Results: There was diversity in the evolutionary patterns observed across the three patients. OSCE1 and OSCE2 demonstrated linear evolutionary patterns during progression to metastatic disease while OSCE3 demonstrated parallel evolution. Whole-genome duplication events were truncal in all three samples with an average ploidy of 3.3, 3.0, and 3.3 per sample in OSCE1, OSCE2, and OSCE3 respectively. Regarding SNVs, OSCE1 had a clonal TP53, OSCE2 had a clonal SUZ12 mutation, and OSCE3 had a clonal ATRX mutation which was present in all samples. Subclonal mutations in consensus cancer genes were typically private to the individual sample. Copy number changes were a source of genomic diversity in consensus driver genes and between primary and metastatic sites. OSCE1 had persistent KEAP1 and CCNE1 amplification in relapse specimens that were not present in the pretreatment biopsy. OSCE2 had gains or amplifications in MECOM and KRAS which were truncal to all samples however gains in RUNX2 and KDR were private to the metastatic samples. In OSCE3 had focal amplifications in chromosome 7p were truncal to all samples, however focal amplifications in chromosome 12q involving CDK4 and GLI1 were present in only the pretreatment biopsy and one of four metastatic sites. Structural variants involving consensus driver genes were typically truncal to all samples for each patient.

Conclusion: Our study confirms that copy number alterations in osteosarcoma are key oncogenic drivers of treatment resistance and are the largest contributor to intertumoral genetic heterogeneity in consensus driver genes, especially when comparing primary to metastatic samples. Our findings demonstrate the dynamic nature of genomic instability processes, highlighting the importance of longitudinal sampling at the time of recurrence to define treatment effect and the changing mutational landscape in these tumors.

Citation Format: Michael David Kinnaman, Alvin Makohon-Moore, Dominik Glodzik, Max Levine, Nancy Bouvier, Filemon Dela Cruz, Meera Hameed, Paul Meyers, Elli Papaemmanuil, Andrew Kung, Christine Iacobuzio-Donahue. Tracking the origins and drivers of metastatic expansion in osteosarcoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1515.