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

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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.