Integrated next-generation sequencing and avatar mouse models for personalized cancer treatment

Abstract

Background: Current technology permits an unbiased massive analysis of somatic genetic alterations from tumor DNA as well as the generation of individualized mouse xenografts (Avatar models). This work aimed to evaluate our experience integrating these two strategies to personalize the treatment of patients with cancer.

Methods: We performed whole-exome sequencing analysis of 25 patients with advanced solid tumors to identify putatively actionable tumor-specific genomic alterations. Avatar models were used as an in vivo platform to test proposed treatment strategies.

Results: Successful exome sequencing analyses have been obtained for 23 patients. Tumor-specific mutations and copy-number variations were identified. All samples profiled contained relevant genomic alterations. Tumor was implanted to create an Avatar model from 14 patients and 10 succeeded. Occasionally, actionable alterations such as mutations in NF1, PI3KA, and DDR2 failed to provide any benefit when a targeted drug was tested in the Avatar and, accordingly, treatment of the patients with these drugs was not effective. To date, 13 patients have received a personalized treatment and 6 achieved durable partial remissions. Prior testing of candidate treatments in Avatar models correlated with clinical response and helped to select empirical treatments in some patients with no actionable mutations.

Conclusion: The use of full genomic analysis for cancer care is encouraging but presents important challenges that will need to be solved for broad clinical application. Avatar models are a promising investigational platform for therapeutic decision making. While limitations still exist, this strategy should be further tested.

Figure 1

Study design schema.

Figure 2

A, structural models of PI3K. Kinase domain in yellow. Mutated aa in blue. Right, original protein with original aa. Left, predictive model of structural changes caused by the mutation. Severity of the mutation estimated to be high by computational analysis. B, total and activated ERK and AKT were evaluated by Western blot (WB) analysis in total protein extracts of the high-grade pancreatic neuroendocrine (PGDX7) and the glioblastoma (PGDX30) xenografted tumors. Left, total ERK and AKT proteins; right, phosphorylated forms of ERK and AKT, in the analyzed samples. GAPDH was used in all cases as loading control (P = phospho). C and D, representative tumor growth curve of Avatar PGDX7 treated with the studied agents. PI3i: 20 mg/kg per os; everyday, Monday–Friday (M–F), for 28 days. MEKi: 4 mg/kg per os; everyday, M–F, for 28 days. PI3Ki + MEKi: 20 mg/kg per os + 4 mg/kg per os; everyday, M–F, for 28 days. PI3Ki+Gemcitabine: 20 mg/kg per os; everyday, M–F, for 28 days + 100 mg/kg i.p.; twice a week for 28 days. E and F, representative tumor growth curve of Avatar PGDX30 treated with the studied agents. OSI774 (erlotinib): 50 mg/kg i.p.; daily for 28 days. Rapamycin: 4 mg/kg per os; daily, for 10 days. FTS: 100 mg/kg per os; daily, for 28 days. OSI774 (erlotinib) + rapamycin: 50 mg/kg i.p.; daily, for 28 days + 4 mg/kg per os; daily for 28 days. PI3Ki: 20 mg/kg per os; daily M–F, for 28 days. MEKi: 4 mg/kg per os; daily M–F, for 28 days. PI3Ki + MEKi: 20 mg/kg per os; daily M–F + 4 mg/kg per os; daily M–F for 28 days.