Abstract B002: Profiling intra-tumor heterogeneity and chromosomal instability in malignant peripheral nerve sheath tumors
Authors: Yixiao Cheng, Haixi Yan, Maxime Tarabichi, Zhihui Zhang, Chunxu Gao, Tom Lesluyes, Adrienne Flanagan, Peter Van Loo
Journal: Cancer Research (2024)

Abstract Malignant peripheral nerve sheath tumors (MPNSTs) are rare soft-tissue sarcomas that manifest on peripheral nerves, constituting 2% of all sarcomas. They arise both sporadically and in 8% to 13% of individuals with neurofibromatosis type 1 (NF1), where they represent the major cause of morbidity and mortality. While previous genomic analyses of MPNSTs have been conducted on small cohorts, often limited to single samples per patient and lacking comprehensive resolution, the extent of intra-tumor heterogeneity and the contribution of chromosomal instability to MPNST development remain unclear. To address these limitations, we developed a multi-omics integration pipeline and applied it to integrate bulk Next Generation Sequencing (NGS), single-cell RNA sequencing, single-cell DNA sequencing, spatial transcriptomics (ST), and Laser Capture Microsection (LCM) information. 35 tumor samples were collected from 10 patients with MPNST, and for each sample, data were generated using the above five techniques. Overall, we detected copy-number aberrations recurrently found in MPNSTs, including events such as loss of heterozygosity (LOH), whole genome doubling (WGD) and chromosome 7 and 8 amplifications. Subclonal copy number alterations were called by the Battenberg algorithm, followed by SNV clustering using Dirichlet Process-based methods. Applying the pigeonhole principle, we constructed tumor phylogenetic trees. Intriguingly, our findings indicate that for patient 2.3, primary tumor samples PT_1 and PT_2 displayed a close phylogenetic relationship, while local recurrences LR_2 and LR_3 represent a different branch of the phylogenetic tree. Following stringent quality control and cell type annotation, we leveraged normal cells identified within the snRNA data as controls to infer copy number changes in tumor cells through inferCNV. Notably, in patient 2.16, we identified significant copy number gains on chromosomes 5, 7, 8, and 15. Comparing the inferred copy number changes derived from snRNA with those obtained through Battenberg copy number profiles showed a remarkable congruence, thereby reinforcing the robustness of our results. To reveal communication networks among tumor microenvironment (TME) cells, we used iTalk to visualize ligand-receptor interactions between distinct cell types. For Patient 2.3, macrophages emerged as key players, releasing cytokines such as IL-16 and IL-18, which exerted their influence on receptors in tumor cells. Additionally, T cells engaged in checkpoint factors, including TNFSF4 and CD28, interacting with receptors on tumor cells, such as TRAF2 and LGALS9. Our research revealed that MPNSTs are primarily driven by chromosomal instability and intra-tumor heterogeneity is shaped by TME interactions. We enhanced our understanding of the tumors' evolutionary histories and intra-tumor heterogeneity down to single-cell resolution. By shedding light on the genomic landscape of MPNSTs, we aspire to make profound contributions to the field of sarcoma research, ultimately improving patient outcomes. Citation Format: Yixiao Cheng, Haixi Yan, Maxime Tarabichi, Zhihui Zhang, Chunxu Gao, Tom Lesluyes, Adrienne Flanagan, Peter Van Loo. Profiling intra-tumor heterogeneity and chromosomal instability in malignant peripheral nerve sheath tumors [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Cancer Evolution and Data Science: The Next Frontier; 2023 Dec 3-6; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_2):Abstract nr B002.