Longitudinal molecular analysis of tumor exome and transcriptome to evaluate clonal evolution and identify novel therapeutic targets in thymoma.

Abstract

e20624 Background: The rarity of thymic epithelial tumors has limited mechanistic understanding of tumor biology and the rational identification of potential therapeutic targets for patients with advanced disease. While the Cancer Genome Atlas Project enabled multi-omic profiling of thymic epithelial tumors, the majority of samples were early-stage and chemotherapy-naïve. Furthermore, next generation sequencing for patients with advanced disease often provides only a limited breadth of genome coverage. The genetic changes in thymic epithelial tumors that evolve through disease progression and treatment represent a current knowledge gap and opportunity for reassessment of new therapeutic targets. Methods: To address these points, we conducted whole exome and bulk RNA transcriptome sequencing for serially-collected FFPE archival tumor samples from a patient with Stage IVA, WHO B2/B3 thymoma using the BostonGene Tumor Portrait Test version 1.3. Samples analyzed include the initial primary tumor resected without induction treatment; two subsequent, metachronous pleural recurrences resected without any induction treatment; and a third pleural metastasis resected following two cycles of induction chemotherapy with Cisplatin/Adriamycin/Cyclophosphamide without interval radiographic evidence of treatment response. Results: Tumor characteristics were largely consistent with prior molecular studies, and without significant evidence of major clonal evolutionary changes based on single nucleotide polymorphisms, insertions/deletions or copy number alterations. Tumor mutational burden was recurrently low (< 1 mutation per megabase) with stable microsatellite status. EGFR copy number gain was observed (+1 copy) across recurrent pleural resection specimens. While the degree of copy number gain did not change with disease progression, increasing EGFR transcript counts were observed and evaluated by IHC. Other notable therapeutic biomarkers included absent TGFB1 and present VEGFA expression. Collective RNA-based gene expression changes were compared with the Thymic TCGA cohort for reference. Conclusions: Our analysis illustrates the narrow clonal evolution of a thymic epithelial tumor through treatment—both with and without the selective pressures of induction chemotherapy. This suggests that the genomic features of advanced thymoma may reflect the treatment-naïve state as described in the TCGA, one marked by a low mutational burden but with recurrent copy number alterations in select genes. Complementary transcriptome sequencing identified EGFR expression as a promising therapeutic target for further study. Taken together, these findings illustrate the hypothesis-generating potential for deep molecular analysis with whole exome and transcriptome sequencing to improve the understanding of rare tumors.