Abstract 5671: 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. 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 remains unclear. To address these limitations, we developed a multi-omics integration pipeline and applied it to bulk Whole Genome Sequencing (WGS), single-cell RNA sequencing(scRNA-seq), single-cell DNA sequencing (scDNA-seq), spatial transcriptomics (ST), and Laser Capture Microsection (LCM) sequencing data. 60 tumor samples were collected from 17 patients with MPNST, and the above five techniques were applied to each sample. Overall, tumors harbor a high degree of chromosomal instability and evidence of whole-genome doubling (WGD). We reconstructed tumor phylogenetic trees from WGS data using Dirichlet Process-based methods. Intriguingly, our findings indicated 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 represented a different branch of the phylogenetic tree. Moreover, scRNA-seq analysis of patient 2.16 highlighted an enrichment of immune cells, including macrophages, B cells, and T cells. To infer copy number alterations (CNA) of tumor cells from scRNA-seq data, we leveraged inferCNV, with normal cells identified within the same sample as controls. Significant copy number gains were identified on chromosomes 5, 7, 8, and 15 in patient 2.16. The inferred copy number changes derived from scRNA-seq were validated against copy number profiles obtained through WGS using Battenberg, revealing a remarkable congruence. In the scDNA analysis of patient 2.12, we observed that all tumor cells exhibited biallelic loss of CDKN2A, with a majority showcasing WGD and chromosome 7 amplification. This finding underscored the potential significance of CDKN2A in the pathogenesis of this tumor, in keeping with the observation that CDKN2A is recurrently mutated and lost in MPNSTs. Our research profiled the tumors' evolutionary histories and intra-tumor heterogeneity down to single-cell resolution, highlighting the genotype and phenotype differences between tumor subclones. 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 American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5671.