Derepressing nuclear pyruvate dehydrogenase induces therapeutic cancer cell reprogramming (RNA-seq_1)

Metabolites are essential substrates for epigenetic modifications. Although nuclear acetyl-CoA constitutes a small fraction of the whole cell pool, it regulates cell fate by locally providing histone acetylation substrate. Here, we report a nucleus-specific acetyl-CoA regulatory mechanism that can be modulated to achieve therapeutic cancer cell reprogramming. Combining phenotypic chemical screen, genome-wide CRISPR screen, and proteomics, we identified that the nucleus-localized pyruvate dehydrogenase complex (nPDC) is constitutively inhibited by the nuclear protein ELMSAN1 through direct interaction. Pharmacologic inhibition of the ELMSAN1-nPDC interaction derepressed nPDC activity, enhancing nuclear acetyl-CoA generation and reprograming cancer cells to a postmitotic state with diminished cell-of-origin signatures. Reprogramming was synergistically enhanced by histone deacetylase 1/2 inhibition, resulting in inhibited tumor growth, durably suppressed tumor-initiating ability, and improved survival in multiple cancer types in vivo, including therapy-resistant sarcoma patient-derived xenografts and carcinoma cell line xenografts. Our findings highlight the potential of targeting ELMSAN1-nPDC as epigenetic cancer therapy. Overall design: We used RNA-seq to study the effect of small molecule treatment on transcriptomic changes in sarcoma cells.

代谢物是表观遗传修饰的必需底物。尽管细胞核乙酰辅酶A仅占细胞总乙酰辅酶A库的极小部分，但其可通过局部提供组蛋白乙酰化底物调控细胞命运。本研究报道了一种细胞核特异性乙酰辅酶A调控机制，通过调控该机制可实现治疗性癌细胞重编程。研究结合表型化学筛选、全基因组CRISPR筛选与蛋白质组学分析，发现核蛋白ELMSAN1可通过直接相互作用，持续性抑制定位于细胞核的丙酮酸脱氢酶复合物（nucleus-localized pyruvate dehydrogenase complex, nPDC）。靶向抑制ELMSAN1与nPDC的相互作用，可解除nPDC的活性抑制，增强细胞核乙酰辅酶A的生成，并将癌细胞重编程为有丝分裂后状态，同时减弱其起源细胞特征。联合组蛋白去乙酰化酶1/2（histone deacetylase 1/2）抑制可协同增强重编程效果，在多种癌症的体内模型中抑制肿瘤生长、持久抑制肿瘤起始能力并改善宿主生存期，其中包括治疗抵抗性肉瘤患者来源异种移植瘤与癌细胞系异种移植瘤模型。本研究结果表明，靶向ELMSAN1-nPDC通路可作为表观遗传癌症治疗的潜在策略。整体实验设计：本研究通过RNA测序（RNA-seq）探究小分子化合物处理对肉瘤细胞转录组变化的影响。