Genome-wide DNA hypermethylation opposes healing in patients with chronic wounds by impairing epithelial-mesenchymal transition.
Genome-wide DNA hypermethylation opposes healing in patients with chronic wounds by impairing epithelial-mesenchymal transition.
复制标题
全基因组DNA高甲基化通过损害上皮 - 间质转变，反对慢性伤口患者的愈合。
DOI：
10.1172/jci157279
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发表时间：
2022-09-01
影响因子：
15.9
通讯作者：
Sen, Chandan K.
中科院分区：
文献类型：
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作者：
Singh, Kanhaiya;Rustagi, Yashika;Abouhashem, Ahmed S.;Tabasum, Saba;Verma, Priyanka;Hernandez, Edward;Pal, Durba;Khona, Dolly K.;Mohanty, Sujit K.;Kumar, Manishekhar;Srivastava, Rajneesh;Guda, Poornachander R.;Verma, Sumit S.;Mahajan, Sanskruti;Killian, Jackson A.;Walker, Logan A.;Ghatak, Subhadip;Mathew-Steiner, Shomita S.;Wanczyk, Kristen E.;Liu, Sheng;Wan, Jun;Yan, Pearlly;Bundschuh, Ralf;Khanna, Savita;Gordillo, Gayle M.;Murphy, Michael P.;Roy, Sashwati;Sen, Chandan K.
极端的慢性伤口组织微环境导致表观遗传基因沉默。在慢性创面患者的创缘组织中研究了无偏倚的全基因组甲基组。与未受伤的人皮肤相比，慢性创口边缘皮肤中总共发现了4689个差异甲基化区域(DMR)。在慢性创缘组织中，高甲基化(3,661个DMR)比低甲基化(1,028个DMR)更常见。26例DMR高甲基化参与了上皮-间充质转化(EMT)。亚硫酸氢盐测序证实了预测的特定上游调控因子TP53的超甲基化。进行RNA-Seq分析以确认甲基组分析的结果。对下调基因的分析发现，TP53信号通路显著沉默。直接比较高甲基化和下调的基因确定了4个基因，ADAM17，Noch，Twist1和SMURF1，它们在功能上代表了EMT途径。单细胞RNA-Seq研究表明，这些对基因表达的影响仅限于角质形成细胞间。小鼠实验研究证实，组织缺血可有效地诱导伤口边缘基因甲基化，甲基化抑制剂5‘-氮杂胞苷可改善伤口闭合。为了明确TP53甲基化的重要性，通过基于组织纳米转染法的CRISPR/dCas9方法实现了创伤边缘角质形成细胞特异性的TP53甲基化编辑。这项工作证实，逆转甲基化依赖的角质形成细胞基因沉默是改善伤口闭合的有效治疗策略。
An extreme chronic wound tissue microenvironment causes epigenetic gene silencing. An unbiased whole-genome methylome was studied in the wound-edge tissue of patients with chronic wounds. A total of 4,689 differentially methylated regions (DMRs) were identified in chronic wound-edge skin compared with unwounded human skin. Hypermethylation was more frequently observed (3,661 DMRs) in the chronic wound-edge tissue compared with hypomethylation (1,028 DMRs). Twenty-six hypermethylated DMRs were involved in epithelial-mesenchymal transition (EMT). Bisulfite sequencing validated hypermethylation of a predicted specific upstream regulator TP53. RNA-Seq analysis was performed to qualify findings from methylome analysis. Analysis of the downregulated genes identified the TP53 signaling pathway as being significantly silenced. Direct comparison of hypermethylation and downregulated genes identified 4 genes, ADAM17, NOTCH, TWIST1, and SMURF1, that functionally represent the EMT pathway. Single-cell RNA-Seq studies revealed that these effects on gene expression were limited to the keratinocyte cell compartment. Experimental murine studies established that tissue ischemia potently induces wound-edge gene methylation and that 5′-azacytidine, inhibitor of methylation, improved wound closure. To specifically address the significance of TP53 methylation, keratinocyte-specific editing of TP53 methylation at the wound edge was achieved by a tissue nanotransfection-based CRISPR/dCas9 approach. This work identified that reversal of methylation-dependent keratinocyte gene silencing represents a productive therapeutic strategy to improve wound closure.