Epigenetic and transcriptional heterogeneity define osteosarcoma subtypes and establish targetable vulnerabilities [multiomics]

Osteosarcoma is a genomically complex tumor with structural rearrangements, aneuploidy, and chromosomal alterations, resulting in significant intertumoral heterogeneity. This complexity hampers the identification of key oncogenic pathways and subtypes. We hypothesized that chromatin accessibility could uncover molecular features to clarify their transcriptional programs, suggesting new therapies. Using ATAC-seq, H3K27ac profiling, and single-cell multiome analysis, we identified two distinct cellular states in osteosarcoma driven by unique transcription factor networks linked to normal bone development. These subtypes can be detected in patient samples via a specific gene expression signature with prognostic value. We utilized multiomic analysis single-nucleus (snRNAseq + snATACseq) on five samples from patient-derived xenografts to investigate the heterogeneity and transcriptional/epigenetic landscape of osteosarcoma. This study specifically aimed to address the enrichment of early osteoblast derived (EOD) and late osteoblast derived (LOD) clusters.骨肉瘤(Osteosarcoma)是一种基因组结构复杂的肿瘤，存在结构重排、非整倍体及染色体变异等特征，进而导致显著的瘤间异质性。这种复杂性极大阻碍了关键致癌通路及肿瘤亚型的鉴定。我们提出假说：染色质可及性可揭示骨肉瘤的分子特征，阐明其转录程序，进而为新型治疗策略的开发提供方向。本研究通过ATAC测序（ATAC-seq）、H3K27ac谱分析及单细胞多组学分析，在骨肉瘤中鉴定出两种独特的细胞状态，这两种状态由与正常骨发育相关的特异性转录因子网络驱动。上述两种亚型可通过具有预后价值的特定基因表达特征在患者样本中被检测到。我们对5份患者来源异种移植样本开展单细胞核多组学分析（单细胞核RNA测序（single-nucleus RNA sequencing, snRNAseq）与单细胞核ATAC测序（single-nucleus ATAC sequencing, snATACseq）），以探究骨肉瘤的异质性及其转录与表观遗传图谱。本研究特别旨在解析早期成骨细胞衍生（early osteoblast derived, EOD）与晚期成骨细胞衍生（late osteoblast derived, LOD）细胞簇的富集特征。