A method for cryopreservation and single nucleus RNA-sequencing of normal adult human interventricular septum heart tissue reveals cellular diversity and function

• Published in: BMC medical genomics Vol. 14; no. 1; pp. 161 - 8
• Main Authors: Larson, Amy, Chin, Michael T
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 15-06-2021; BioMed Central; BMC
• Subjects: Adult; Analysis; Animals; Cardiomyocytes; Cardiomyopathy; Cardiovascular disease; Cell Nucleus - genetics; Composition; Cryopreservation; Cryopreservation - methods; Cryopreservation of organs, tissues, etc; Datasets; Fibroblasts; Functional genomics; Gene expression; Gene expression and regulation; Genetic aspects; Genomes; Genomic analysis; Genomics; Health aspects; Heart; Heart cells; Heart septum; Homogenization; Human heart tissue; Humans; Identification and classification; Laboratories; Methods; Myocardial biology; Myocardium - cytology; Myocardium - metabolism; Nuclei; Organ donors; Ribonucleic acid; RNA; RNA sequencing; Septum; Sequence Analysis, RNA; Single nucleus RNA-sequencing; Single-Cell Analysis - methods; Software; Swine; Technical Advance; Transcription; Transcriptomics; Ventricular Septum - cytology; United States; Myocardial biology; Single nucleus RNA-sequencing; Cardiovascular disease; Human heart tissue; Functional genomics; Gene expression and regulation
• ISSN: 1755-8794; 1755-8794
• DOI: 10.1186/s12920-021-01011-z

Single cell sequencing of human heart tissue is technically challenging and methods to cryopreserve heart tissue for obtaining single cell information have not been standardized. Studies published to date have used varying methods to preserve and process human heart tissue, and have generated interesting datasets, but development of a biobanking standard has not yet been achieved. Heart transcription patterns are known to be regionally diverse, and there are few single cell datasets for normal human heart tissue.
Using pig tissue, we developed a rigorous and reproducible method for tissue mincing and cryopreservation that allowed recovery of high quality single nuclei RNA. We subsequently tested this protocol on normal human heart tissue obtained from organ donors and were able to recover high quality nuclei for generation of single nuclei RNA-seq datasets, using a commercially available platform from 10× Genomics. We analyzed these datasets using standard software packages such as CellRanger and Seurat.
Human heart tissue preserved with our method consistently yielded nuclear RNA with RNA Integrity Numbers of greater than 8.5. We demonstrate the utility of this method for single nuclei RNA-sequencing of the normal human interventricular septum and delineating its cellular diversity. The human IVS showed unexpected diversity with detection of 23 distinct cell clusters that were subsequently categorized into different cell types. Cardiomyocytes and fibroblasts were the most commonly identified cell types and could be further subdivided into 5 different cardiomyocyte subtypes and 6 different fibroblast subtypes that differed by gene expression patterns. Ingenuity Pathway analysis of these gene expression patterns suggested functional diversity in these cell subtypes.
Here we report a simple technical method for cryopreservation and subsequent nuclear isolation of human interventricular septum tissue that can be done with common laboratory equipment. We show how this method can be used to generate single nuclei transcriptomic datasets that rival those already published by larger groups in terms of cell diversity and complexity and suggest that this simple method can provide guidance for biobanking of human myocardial tissue for complex genomic analysis.