SE-driven metabolic reprogramming in ADPKD (ChIP-Seq). SE-driven metabolic reprogramming in ADPKD (ChIP-Seq)

Metabolic reprogramming is emerging as a key pathological contributor to the progression of autosomal dominant polycystic kidney disease (ADPKD), but the molecular mechanisms underlying dysregulated cellular metabolism in cystic cells remain elusive. Super-enhancers (SEs) are large clusters of transcriptional enhancers that drive robust expression of cell identity and disease genes. Here, we establish a prominent role for SEs in regulating metabolic gene expression and ADPKD progression. Characterization of cis-acting SE landscapes in cystic renal epithelial cells reveals extensive remodeling of SEs during cystogenesis. Gene ontology analysis indicates that SE-associated transcripts in the metabolic pathway category are most significantly enriched in cystic cells. Cystic cells are highly sensitive to the inhibition of cyclin-dependent kinase 7 (CDK7), a critical component of the trans-acting SE complex. THZ1, a specific CDK7 inhibitor, exerts a potent anti-cystogenesis effect in ADPKD cells and mouse models. Integrative analyses of transcriptomics and SE profiling identify AMP deaminase 3 (AMPD3) as a SE-driven metabolic gene. Up-regulation of AMPD3 in cystic cells results in reduced AMP level and decreased AMPK activity, while inhibition of AMPD3 suppresses cyst development in a zebrafish ADPKD model. In a cohort of ADPKD patients, CDK7 expression is frequently elevated, and its expression is significantly correlated with AMPD3 expression and disease severity. Taken together, our findings elucidate a mechanism by which SE controls metabolic gene transcription during cystogenesis, and identifies SE-driven metabolic reprogramming as a promising therapeutic target for ADPKD treatment. Overall design: ChIPmentation sequencing with H3K27ac antibody in pkd1 and null cell lines.

代谢重编程已成为常染色体显性遗传性多囊肾病（autosomal dominant polycystic kidney disease, ADPKD）进展的关键病理驱动因素，但囊性细胞代谢失调的潜在分子机制仍有待阐明。超级增强子（super-enhancers, SEs）是一类大型转录增强子簇，可强效驱动细胞身份基因与疾病相关基因的表达。本研究明确了SEs在调控代谢基因表达及ADPKD进程中的核心作用。对囊性肾上皮细胞中顺式作用SE调控图谱的表征分析显示，囊肿形成过程中SEs发生广泛重编程。基因本体（gene ontology, GO）富集分析表明，囊性细胞中与SEs关联的转录本在代谢通路类别中富集最为显著。作为反式作用SE复合物的关键组分，细胞周期蛋白依赖性激酶7（cyclin-dependent kinase 7, CDK7）的抑制可对囊性细胞产生强效作用。特异性CDK7抑制剂THZ1在ADPKD细胞与小鼠模型中均展现出显著的抗囊肿形成活性。转录组与SE图谱整合分析证实，腺苷酸脱氨酶3（AMP deaminase 3, AMPD3）是受SE调控的代谢基因。囊性细胞中AMPD3的上调会导致腺苷一磷酸（AMP）水平降低与AMP活化蛋白激酶（AMPK）活性下降，而抑制AMPD3可在斑马鱼ADPKD模型中抑制囊肿发育。在ADPKD患者队列中，CDK7的表达常出现上调，且其表达水平与AMPD3表达量及疾病严重程度显著相关。综上，本研究阐明了SEs在囊肿形成过程中调控代谢基因转录的分子机制，并证实SE介导的代谢重编程是ADPKD治疗的潜在靶向策略。实验整体设计：在pkd1缺失型与正常对照细胞系中，使用H3K27ac抗体开展ChIPmentation测序。