Identification of IL-34 and Slc7al as potential key regulators in MASLD progression through epigenomic profiling

Epigenetic alterations are critical regulators in the progression of metabolic dysfunction-associated steatotic liver disease (MASLD); however, the dynamic epigenomic landscapes are not well defined. Our previous study found that H3K27ac and H3K9me3 play important roles in regulating lipid metabolic pathways in the early stages of MASLD. However, the epigenomic status in the inflammation stages still needs to be determined. C57BL/6 male mice were fed with the methionine- and choline-deficient (MCD) or normal diet, and their serum and liver samples were collected after 6 weeks. Serum alanine aminotransferase (ALT), aspartate amino transferase (AST), total cholesterol (TC), triglyceride (TG), high-density lipoprotein cholesterol (HDL-C), and low-density lipoprotein cholesterol (LDL-C) levels were measured. Chromatin immunoprecipitation sequencing (ChIP-Seq) for H3K27ac and H3K9me3 was performed together with RNA sequencing (RNA-seq) and key regulators were analyzed. The target genes of enhancers with increased H3K27ac and decreased H3K9me3 signals are enriched in lipid metabolism and immuno-inflammatory pathways. <i>Il-34</i> and <i>Slc7al</i> are identified as potential regulators in MASLD. Our study reveals that active enhancers and heterochromatin associated with metabolic and inflammatory genes are extensively reprogrammed in MCD-diet mice, and <i>Il-34</i> and <i>Slc7al</i> are potentially key genes regulating the progression of MASLD.

表观遗传改变是代谢功能障碍相关脂肪性肝病（metabolic dysfunction-associated steatotic liver disease, MASLD）进展过程中的关键调控因子，但其动态表观基因组景观尚未得到清晰阐释。我们既往研究发现，H3K27ac与H3K9me3在MASLD早期阶段的脂质代谢通路调控中发挥重要作用，但炎症阶段的表观基因组状态仍有待明确。本研究将C57BL/6雄性小鼠饲喂蛋氨酸胆碱缺乏（methionine- and choline-deficient, MCD）饲料或正常饲料，并于6周后采集其血清与肝脏样本；检测血清丙氨酸氨基转移酶（alanine aminotransferase, ALT）、天冬氨酸氨基转移酶（aspartate amino transferase, AST）、总胆固醇（total cholesterol, TC）、甘油三酯（triglyceride, TG）、高密度脂蛋白胆固醇（high-density lipoprotein cholesterol, HDL-C）及低密度脂蛋白胆固醇（low-density lipoprotein cholesterol, LDL-C）水平；针对H3K27ac与H3K9me3开展染色质免疫沉淀测序（chromatin immunoprecipitation sequencing, ChIP-Seq），并联合RNA测序（RNA-seq）对关键调控因子进行分析。结果显示，H3K27ac信号上调且H3K9me3信号下调的增强子其靶基因显著富集于脂质代谢与免疫炎症通路，同时鉴定出<i>Il-34</i>与<i>Slc7al</i>为MASLD潜在调控因子。本研究表明，饲喂MCD饲料的小鼠中，与代谢及炎症基因相关的活性增强子与异染色质发生了广泛重编程，且<i>Il-34</i>与<i>Slc7al</i>是调控MASLD进展的潜在关键基因。