High-quality nuclei isolation from postmortem human heart muscle tissues for single-cell studies

Sarah Araten; Ronald Mathieu; Anushka Jetly; Hoon Shin; Nazia Hilal; Bo Zhang; Katherine Morillo; Deepa Nandan; Indu Sivankutty; Ming Hui Chen; Sangita Choudhury

doi:10.1016/j.yjmcc.2023.03.010

High-quality nuclei isolation from postmortem human heart muscle tissues for single-cell studies

J Mol Cell Cardiol. 2023 Jun:179:7-17. doi: 10.1016/j.yjmcc.2023.03.010. Epub 2023 Mar 26.

Authors

Affiliations

¹ Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA.
² Flow Cytometry Core Facility, Boston Children's Hospital, Boston, MA, USA.
³ Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA; Harvard College, Cambridge, MA, USA.
⁴ Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA.
⁵ Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Biostatistics and Research Design Center, Institutional Centers for Clinical and Translational Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
⁶ Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA; Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA.
⁷ Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA. Electronic address: sangita.choudhury@childrens.harvard.edu.

PMID: 36977444
PMCID: PMC10192033 (available on 2024-06-01)
DOI: 10.1016/j.yjmcc.2023.03.010

Abstract

Single-cell approaches have become an increasingly popular way of understanding the genetic factors behind disease. Isolation of DNA and RNA from human tissues is necessary to analyze multi-omic data sets, providing information on the single-cell genome, transcriptome, and epigenome. Here, we isolated high-quality single-nuclei from postmortem human heart tissues for DNA and RNA analysis. Postmortem human tissues were obtained from 106 individuals, 33 with a history of myocardial disease, diabetes, or smoking, and 73 controls without heart disease. We demonstrated that the Qiagen EZ1 instrument and kit consistently isolated genomic DNA of high yield, which can be used for checking DNA quality before conducting single-cell experiments. Here, we provide a method for single-nuclei isolation from cardiac tissue, otherwise known as the SoNIC method, which allows for the isolation of single cardiomyocyte nuclei from postmortem tissue by nuclear ploidy status. We also provide a detailed quality control measure for single-nuclei whole genome amplification and a pre-amplification method for confirming genomic integrity.

Keywords: Heart; Postmortem tissue; RNA sequencing; Single cardiomyocyte; Single-nuclei; Whole genome amplification; Whole genome sequencing.

Publication types

Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural

MeSH terms

Cell Nucleus* / genetics
DNA
Humans
Myocardium*
Myocytes, Cardiac
RNA / genetics
Single-Cell Analysis / methods

Substances

DNA
RNA

Abstract

Publication types

MeSH terms

Substances

Grants and funding