Article Impact Level: HIGH Data Quality: STRONG Summary of Journal of Molecular and Cellular Cardiology, 179, 7–17. https://doi.org/10.1016/j.yjmcc.2023.03.010 Dr. Sarah Araten et al.
Points
- The SoNIC method is introduced for isolating single cardiac nuclei from postmortem human heart tissues, enabling whole-genome amplification and RNA sequencing.
- The Qiagen EZ1 instrument and kit consistently yield high-quality genomic DNA from postmortem heart tissues, serving as a reliable measure of DNA quality before single-cell experiments.
- The study involves 106 individuals, including those with myocardial disease, diabetes, or smoking history, and controls, highlighting the relevance of single-cell approaches in understanding genetic factors related to diseases.
- A negative correlation is observed between DNA integrity number (DIN) and postmortem interval (PMI) or age, emphasizing the significance of considering DIN alongside RNA integrity number (RIN) for tissue quality assessment.
- DIN values exceeding 5.8 are deemed suitable for WGA and RNAseq analysis, ensuring the preservation of crucial biological signals for further investigations.
Summary
This research paper presents a novel SoNIC method for isolating single cardiac nuclei from human postmortem tissue to facilitate whole-genome amplification (WGA) and RNA sequencing (RNAseq). The authors emphasize the importance of single-cell approaches in understanding disease-related genetic factors. To analyze multi-omic datasets, the isolation of DNA and RNA from human tissues is necessary for studying the single-cell genome, transcriptome, and epigenome. The study involved the collection of postmortem human heart tissues from 106 individuals, including 33 with a history of myocardial disease, diabetes, or smoking and 73 controls without heart disease.
The authors conducted experiments to validate the effectiveness of the Qiagen EZ1 instrument and kit for consistently isolating high-yield genomic DNA from postmortem heart tissues. This genomic DNA can be used to assess DNA quality before conducting single-cell experiments. The SoNIC method introduced in this study enables the isolation of single cardiomyocyte nuclei from postmortem cardiac tissue based on their nuclear ploidy status. Additionally, the researchers present a comprehensive quality control measure for single-nuclei whole genome amplification and a pre-amplification method to ensure genomic integrity.
The study findings indicate a negative correlation between DNA integrity number (DIN) and postmortem interval (PMI) or age, suggesting that DIN, along with RNA integrity number (RIN), should be considered as a measure of tissue quality. DIN values above 5.8 were identified as suitable for WGA and RNAseq analysis without compromising the essential signals required for biological investigations. This research contributes to the advancement of single-cell genomic analysis by providing a robust method for single cardiac nuclei isolation and offering insights into quality control measures for DNA and RNA analysis in postmortem human heart tissues.
Link to the article: https://www.jmcc-online.com/article/S0022-2828(23)00055-X/fulltext
References Araten, S., Mathieu, R., Jetly, A., Shin, H., Hilal, N., Zhang, B., Morillo, K., Nandan, D., Sivankutty, I., Chen, M. H., & Choudhury, S. (2023). High-quality nuclei isolation from postmortem human heart muscle tissues for single-cell studies. Journal of Molecular and Cellular Cardiology, 179, 7–17. https://doi.org/10.1016/j.yjmcc.2023.03.010
