Single-Cell RNA-seq of Human Cardiomyocytes Revealed DNA Damage Response as a Novel Predictor for Therapeutic Prognosis in Heart Failure Patients with Dilated Cardiomyopathy

Purpose Patients with dilated cardiomyopathy (DCM) who achieved left ventricular reverse remodeling (LVRR) have a favorable prognosis, but it is still difficult to precisely predict LVRR in the clinical setting. Methods We conducted single-cell RNA-seq (scRNA-seq) analysis of cardiomyocytes from both normal subjects and patients with DCM (n=10). We also obtained heart tissue specimens from patients with DCM (n=58) who underwent endomyocardial biopsy before optimal medical therapy and conducted immunofluorescence staining of DNA damage markers including poly(ADP-ribose) (PAR) and γH2A.X. Immunofluorescence staining of DNA damage markers was quantitatively assessed using image measurement software, and their utility for the prediction of LVRR and prognosis were statistically analyzed. Results Single-cell transcriptome analysis of 71 normal and 340 DCM cardiomyocytes separated normal and DCM cardiomyocytes and revealed DCM-specific transcriptional heterogeneity, which can be explained by DNA damage response gene module. By integrating these transcriptomic data with clinical information, we found that the patients without LVRR had cardiomyocytes in which DNA damage response genes were highly expressed. Patients with LVRR showed a significantly smaller percentage of DNA damage markers in biopsy specimens compared with those without LVRR (%PAR: 3.7% vs. 16.3%, p<0.0001, %γH2A.X: 3.5% vs. 11.7%, p<0.0001). Multivariate analysis showed that the percentage of DNA damage markers were an independent risk factor for both major adverse cardiovascular events and LVRR, after adjustment for important confounding factors. Furthermore, %PAR nuclei predicted LVRR with high sensitivity (77.8%) and specificity (87.1%). Conclusion scRNA-seq of human cardiomyocytes revealed DNA damage response as one of the key signatures in failing cardiomyocytes. We further demonstrated the utility of DNA damage staining of myocardial biopsy to predict the probability of LVRR. Our study not only revealed a novel prognostic predictor of medical therapy for DCM, but also promoted more effective utilization of endomyocardial biopsy. Patients with dilated cardiomyopathy (DCM) who achieved left ventricular reverse remodeling (LVRR) have a favorable prognosis, but it is still difficult to precisely predict LVRR in the clinical setting. We conducted single-cell RNA-seq (scRNA-seq) analysis of cardiomyocytes from both normal subjects and patients with DCM (n=10). We also obtained heart tissue specimens from patients with DCM (n=58) who underwent endomyocardial biopsy before optimal medical therapy and conducted immunofluorescence staining of DNA damage markers including poly(ADP-ribose) (PAR) and γH2A.X. Immunofluorescence staining of DNA damage markers was quantitatively assessed using image measurement software, and their utility for the prediction of LVRR and prognosis were statistically analyzed. Single-cell transcriptome analysis of 71 normal and 340 DCM cardiomyocytes separated normal and DCM cardiomyocytes and revealed DCM-specific transcriptional heterogeneity, which can be explained by DNA damage response gene module. By integrating these transcriptomic data with clinical information, we found that the patients without LVRR had cardiomyocytes in which DNA damage response genes were highly expressed. Patients with LVRR showed a significantly smaller percentage of DNA damage markers in biopsy specimens compared with those without LVRR (%PAR: 3.7% vs. 16.3%, p<0.0001, %γH2A.X: 3.5% vs. 11.7%, p<0.0001). Multivariate analysis showed that the percentage of DNA damage markers were an independent risk factor for both major adverse cardiovascular events and LVRR, after adjustment for important confounding factors. Furthermore, %PAR nuclei predicted LVRR with high sensitivity (77.8%) and specificity (87.1%). scRNA-seq of human cardiomyocytes revealed DNA damage response as one of the key signatures in failing cardiomyocytes. We further demonstrated the utility of DNA damage staining of myocardial biopsy to predict the probability of LVRR. Our study not only revealed a novel prognostic predictor of medical therapy for DCM, but also promoted more effective utilization of endomyocardial biopsy.