Abstract 868: A novel unsupervised machine learning model applied to neuroblastoma single-cell RNA-seq data reveals a drug-induced mesenchymal-like gene expression program

Abstract

Abstract High-risk neuroblastoma is one of the most difficult to treat pediatric cancers, with a survival rate of only about 50% and significant long-term consequences from current chemotherapy. Preclinical models such as cell lines and mice are the backbone of drug development and experimental-mechanistic oncology, but the development of new treatments is hampered in part by a lack of understanding of the direct clinical relevance of such data collected in preclinical models. Despite this, few formal methods have been developed to determine how these various models represent/resemble primary patient tumors. Here, we present the first comprehensive single-cell RNA-seq analysis of neuroblastoma across an extensive cohort of patient tumors and a variety of preclinical model systems (n = 126 total samples assembled - the largest cohort of its kind). By building an innovative unsupervised machine learning method, which we term “automatic consensus nonnegative matrix factorization” (acNMF), we have integrated and contrasted the transcriptional landscapes of patient tumors with those of cell lines, patient-derived xenografts (PDX), and genetic mouse models (GEMM).Using these tools, we discovered the dominant adrenergic gene expression programs found in neuroblastoma patient tumors were preserved across all preclinical models. However, the presumptive chemo-resistant mesenchymal-like programs, while identifiable in cell lines, were primarily restricted to subpopulations of cancer-associated fibroblasts and Schwann-like cells in vivo. Surprisingly, a mesenchymal-like program could be acutely chemotherapy-induced in GEMM and was evident in pre-treated patient and PDX samples, suggesting a previously uncharacterized mechanism of therapy escape. In addition to these core findings, our computational tools were able to further delineate the classical neuroblastoma adrenergic and mesenchymal gene expression programs, discovering for example, novel subpopulations of cancer associated fibroblasts. These behaviors were conserved across tumors and most preclinical models, which we validated by RNA in situ hybridization, which is a high resolution ultra sensitive spatial transcriptomics technology. Our work cautions against overreliance on traditional preclinical models without recognizing their limitations and we offer a nuanced, high-resolution view of neuroblastoma pre-clinical systems for advancing therapeutic development. We have launched an open-source web resource, featuring this integrated map to aid the scientific community in further exploration of these data and hypothesis generation (available at http://pscb.stjude.org). Citation Format: Rich Chapple, Xueying Liu, Sivaraman Natarajan, Margaret I. Alexander, Yuna Kim, Anand Patel, Christy W. LaFlamme, Min Pan, William C. Wright, Hyeong-Min Lee, Yinwen Zhang, Meifen Lu, Selene C. Koo, Courtney Long, John Harper, Chandra Savage, Melissa D. Johnson, Thomas Confer, Walter J. Akers, Michael A. Dyer, Heather Sheppard, John Easton, Paul Geeleher. A novel unsupervised machine learning model applied to neuroblastoma single-cell RNA-seq data reveals a drug-induced mesenchymal-like gene expression program [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 868.