PO.CL06.02 · 临床研究
多组学分析揭示神经母细胞瘤治疗耐药背后的细胞异质性与微环境重塑
Multi-omic profiling of cellular heterogeneity and microenvironmental remodeling underlying treatment resistance in neuroblastoma
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摘要 Abstract
中文摘要
背景：高危神经母细胞瘤（NBL）的复发与治疗耐药仍是重大的临床挑战。神经母细胞及其肿瘤微环境（TME）在治疗过程中的动态演变尚未得到充分阐明。我们建立了一个多组学、纵向队列，以剖析驱动治疗失败的细胞与分子机制。
方法：我们建立了一个高危神经母细胞瘤的多组学纵向队列。该队列包括对18例肿瘤（7例治疗前、5例治疗后、6例复发）进行单细胞RNA测序（scRNA-seq），并辅以匹配的Xenium空间转录组学进行空间定位。同时对一个纵向NBL队列进行了Nanopore测序，以界定其基因组与表观基因组图谱。使用一个包含76例bulk RNA-seq样本的验证队列，将研究结果与临床结局进行关联。
结果：我们的scRNA-seq分析鉴定出一个独特的ADRN_proliferating（ADRN增殖型）神经母细胞亚型。在我们的验证队列（n=76）中，该亚型的特征标志与不良预后显著相关，并与对诱导化疗最差的反应相关。纵向取样显示，诱导化疗驱动神经母细胞发生以ADRN向MES为主的转变，而复发肿瘤则表现出ADRN样细胞的再度出现。然而，这种再度出现伴随着显著增加的空间异质性。
甲基化分析揭示复发时存在一种表观遗传学上后印记的ADRN程序；这些细胞在关键转录因子（如GATA3）中保留了治疗后样的甲基化模式，与其未治疗（治疗初治）状态不同。TME经历了从化疗前到化疗后的渐进性重塑，趋向更不利的、免疫抑制的状态，其特征是SPP1⁺巨噬细胞及其他髓系细胞群的富集。这种不利的TME在复发时基本得以维持，即使MES样肿瘤细胞回复至ADRN表型，从而形成一个高度治疗难治的生态系统。配体-受体分析提示，源自单核细胞和中性粒细胞、作用于神经母细胞的RTN4R信号，以及源自施万细胞的NOTCH信号，可能是这一易复发生态位的潜在介导因素。
结论：我们的多组学分析表明，NBL复发并非简单的回复，而是一种新的、表观遗传学上预启动的ADRN状态的出现，并与持续存在的免疫抑制性TME共同演化。
查看英文原文 English abstract
Background: Relapse and therapy resistance in high-risk neuroblastoma (NBL) remain major clinical challenges. The dynamic evolution of neuroblasts and their tumor microenvironment (TME) during treatment is not fully characterized. We established a multi-omic, longitudinal cohort to dissect the cellular and molecular mechanisms driving therapeutic failure.
Methods: We established a multi-omic longitudinal cohort of high-risk neuroblastoma. This included single-cell RNA sequencing (scRNA-seq) on 18 tumors (7 pre-treatment, 5 post-treatment, 6 relapsed), complemented by matched Xenium spatial transcriptomics for spatial mapping. Parallel Nanopore sequencing was conducted on a longitudinal NBL cohort to define the genomic and epigenomic landscape. A validation cohort of 76 bulk RNA-seq samples was used to correlate findings with clinical outcomes.
Results: Our scRNA-seq analysis identified a distinct ADRN_proliferating neuroblast subtype. In our validation cohort (n=76), the signature of this subtype was significantly associated with poor prognosis and correlated with the poorest response to induction chemotherapy. Longitudinal sampling showed that induction chemotherapy drives a predominant ADRN to MES shift in neuroblasts, while relapsed tumors exhibit the re-emergence of ADRN-like cells. However, this re-emergence was accompanied by markedly increased spatial heterogeneity.
Methylation profiling revealed an epigenetically post-imprinted ADRN program at relapse; these cells retained post-treatment-like methylation patterns in key TFs, such as GATA3, distinct from their treatment-naïve state. The TME underwent progressive remodeling from pre- to post-chemotherapy toward a more unfavorable, immunosuppressive state characterized by enrichment of SPP1⁺ macrophages and other myeloid populations. This unfavorable TME was largely maintained at relapse, even as MES-like tumor cells reverted toward an ADRN phenotype, creating a highly treatment-refractory ecosystem. Ligand-receptor analysis implicated monocyte- and neutrophil-derived RTN4R signaling to neuroblasts and NOTCH signaling from Schwann cells as potential mediators of this relapse-prone niche.
Conclusion: Our multi-omic analysis demonstrates that NBL relapse is not a simple reversion but the emergence of a novel, epigenetically primed ADRN state co-evolving with a sustained, immunosuppressive TME.
利益披露 Disclosure
E. Seo,
Geninus Employment.
I. Hwang, None..
J. Kim, None..
K. Sung, None.