Gene expression regulation mediating the activation and differentiation of cardiac fibroblasts and pulmonary fibroblasts after myocardial infarction

在组织损伤时，成纤维细胞被迅速激活，然后分化成肌成纤维细胞，其促进愈合过程。我们最近发现，在心肌梗死（MI）的小鼠模型中，肌成纤维细胞进一步分化为基质细胞，这是一种新发现的成纤维细胞分化状态，其可能有助于患有慢性纤维化的组织中的进行性硬化和功能降低。除了对MI经常发生的左心室的直接影响之外，左心室的功能降低还引起左心房中的压力超负荷，然后将其转移到肺中。肺中的压力积聚激活肺成纤维细胞（PF）并导致间质纤维化，这对心力衰竭的预后产生负面影响。有趣的是，我们的初步研究确定，与Ml后心脏成纤维细胞（CF）的瞬时MF状态不同，PF甚至在Ml后4周仍保持MF状态，表明两种成纤维细胞群体对Ml的反应存在差异，这可能涉及仍然未知的不同机制。我们推测，CF和PF响应MI的活化和分化与差异基因表达和染色质辅助相关，并涉及特异性转录因子。由于成纤维细胞在MI后心脏和肺重塑中的重要和复杂作用，CF和PF中基因表达调控的研究将是至关重要的，因为它可以允许成纤维细胞活性的微调，这可以有助于开发新的治疗策略。在目标#1中，将进行单细胞RNA-seq（scRNA-seq）和scATAC-seq以在单细胞水平研究CF中的基因表达谱和染色质可及性。结果将与我们初步研究中产生的大量RNA-seq和ATAC-seq数据相结合，以揭示Ml后CF中染色质可及性在基因表达调控中的作用。RNA-seq和ATAC-seq数据的基序富集分析将通过CUT&RUN实验进行验证。 验证的结果将用于构建Ml后介导CF活化和分化的基因调控网络。在目标#2中，将使用相同的策略来研究染色质可及性在MI后PF的基因表达调控中的作用。本研究还将通过构建基因调控网络来探讨MI后PF活化和分化的信号通路。将对这两个目标产生的数据进行比较，以确定共同和独特的特征。

Upon tissue injury, fibroblasts are rapidly activated and then differentiate into myofibroblasts, which facilitate the healing process. We recently identified that in a mouse model of myocardial infarction (Ml), myofibroblasts further differentiated to matribrocytes, a newly discovered fibroblasts differentiation state which may contribute to the progressive stiffening and function reduction in tissue suffering from chronic fibrosis. In addition to the direct impact on the left ventricle, where Ml often occurs, the reduced function of the left ventricle also causes pressure overload in the left atrium, which is then transferred into the lung. Pressure buildup in the lung activates pulmonary fibroblasts (PFs) and leads to interstitial fibrosis, which negatively impacts the prognosis of heart failure. Interestingly, our preliminary study identified that unlike the transient MF state of cardiac fibroblasts (CFs) after Ml, PFs remain in the MF state even 4 weeks after Ml, suggesting a difference in the response of two fibroblast populations to Ml, which may involve distinct mechanisms that are still unknown. We hypothesize that the activation and differentiation of CFs and PFs in response to Ml are associated with differential gene expression and chromatin accessibilities and involve specific transcription factors. Due to the important and complex role of fibroblasts in post-Ml cardiac and pulmonary remodeling, the study of the gene expression regulation in CFs and PFs will be critical as it may allow the fine-tuning of fibroblast activities, which can contribute to the development of novel treatment strategies. In Aim #1, single-cell RNA-seq (scRNA-seq) and scATAC-seq will be performed to study the gene expression profile and chromatin accessibility in CFs at the single-cell level. Results will be combined with bulk RNA-seq and ATAC-seq data generated in our preliminary study to reveal the role of chromatin accessibility in gene expression regulation in CFs after Ml. The motif enrichment analysis of RNA-seq and ATAC-seq data will be validated by CUT&RUN experiments. Validated results will be used in the construction of a gene regulatory network mediating CF activation and differentiation after Ml. In Aim #2, the same strategy will be used to study the role of chromatin accessibility in the gene expression regulations of PFs after MI. Gene regulatory network construction will also be performed to explore the signaling pathways mediating PF activation and differentiation after MI. Data generated in the two aims will be compared to identify common and unique features.