NSD2 p.E1099K（EK）突变在复发性急性淋巴细胞白血病（ALL）患者中富集，表明其在克隆演化和药物耐受中发挥作用。为揭示与药物耐受相关的三维染色质结构机制，我们对三株NSD2 EK杂合的B-ALL细胞系进行Hi-C实验。NSD2突变导致3D基因组的广泛重塑，其中最明显的是在A区域转移方面的偏向性。将Hi-C数据与先前发布的ATAC-seq，RNA-seq和ChIP-seq数据进行系统整合，显示A区域内H3K36me2扩张、H3K27me3收缩以及基因表达和染色质可及性的增加。这些结果表明NSD2 EK通过丰富H3K36me2在染色质脱臼中发挥重要作用。相比之下，在区域内关联域活动中，我们鉴定出很少的变化。虽然区域的变化在不同的细胞系中存在差异，但有一组共享的部分区域变化，驱动以前已涉及药物耐受的基因/通路的表达。此外，我们对一组携带复发特异性NSD2 EK突变的诊断/复发ALL患者进行了RNA测序。与复发前相比，患者基因表达的变化显著与核心区域变化相关，在进一步说明NSD2 EK在基因组脱臼中的作用。尽管EK介导的细胞环境依赖性变化存在差异，但表现差异可解释EK细胞系之间的表型差异。这个核心程序是治疗干预的一个有吸引力的目标。 © 2023.作者。

The NSD2 p.E1099K (EK) mutation is shown to be enriched in patients with relapsed acute lymphoblastic leukemia (ALL), indicating a role in clonal evolution and drug resistance.To uncover 3D chromatin architecture-related mechanisms underlying drug resistance, we perform Hi-C on three B-ALL cell lines heterozygous for NSD2 EK. The NSD2 mutation leads to widespread remodeling of the 3D genome, most dramatically in terms of compartment changes with a strong bias towards A compartment shifts. Systematic integration of the Hi-C data with previously published ATAC-seq, RNA-seq, and ChIP-seq data show an expansion in H3K36me2 and a shrinkage in H3K27me3 within A compartments as well as increased gene expression and chromatin accessibility. These results suggest that NSD2 EK plays a prominent role in chromatin decompaction through enrichment of H3K36me2. In contrast, we identify few changes in intra-topologically associating domain activity. While compartment changes vary across cell lines, a common core of decompacting loci are shared, driving the expression of genes/pathways previously implicated in drug resistance. We further perform RNA sequencing on a cohort of matched diagnosis/relapse ALL patients harboring the relapse-specific NSD2 EK mutation. Changes in patient gene expression upon relapse significantly correlate with core compartment changes, further implicating the role of NSD2 EK in genome decompaction.In spite of cell-context-dependent changes mediated by EK, there appears to be a shared transcriptional program dependent on compartment shifts which could explain phenotypic differences across EK cell lines. This core program is an attractive target for therapeutic intervention.© 2023. The Author(s).