nuclei isolation from cardiac progenitor cells

Nuclei Isolation from Mouse Cardiac Progenitor Cells at Single-Cell Resolution

Among birth defects, congenital heart defects (CHDs) are the most common, occurring in about 1% of live births each year1,2. Genetic mutations are identified in only a minority of cases, implying that other causes, such as abnormalities in gene regulation, are involved in the etiology of CHD2,3. Cardiac development is a complex process of diverse and interacting cell types, making the identification of causal noncoding mutations and their effects on gene regulation challenging. Organogenesis of the heart begins with cellular progenitors that give rise to different subtypes of cardiac cells, including myocardial, fibroblast, epicardial, and endocardial cells4,5.&#160;Single-cell genomics is emerging as a key method for studying heart development and assessing the impact of cellular heterogeneity in health and disease6. The development of multi-omics methods for the simultaneous measurement of different parameters and the expansion of computational pipelines has facilitated the discovery of cell types and subtypes in the normal and diseased heart6. This article describes a reliable single-nucleus isolation protocol for frozen cardiac progenitor cells obtained from mouse embryos that is compatible with downstream snRNA-seq and snATAC-seq (as well as snRNA-seq and snATAC-seq combined)7,8,9.
ATAC-seq is a robust method that allows the identification of regulatory open chromatin regions and the positioning of nucleosomes10,11. This information is used to draw conclusions about the location, identity, and activity of transcription factors. The activity of chromatin factors, including remodelers, as well as the transcriptional activity of RNA polymerase, can, thus, be analyzed since the method is highly sensitive for measuring quantitative changes in chromatin structure1,2. Thus, ATAC-seq provides a robust and impartial approach to uncovering the mechanisms controlling transcriptional regulation in a specific cell type. ATAC-seq protocols have also been validated to measure chromatin accessibility in single cells, revealing variability in the chromatin architecture within cell populations10,12,13.
Although there have been notable advances in the field of single cells in recent years, the main difficulty is the processing of the fresh samples needed to perform these experiments14. To circumvent this difficulty, various tests have been carried out with the aim of conducting analyses such as snRNA-seq and snATAC-seq with frozen cardiac tissue or cells15,16.
Several platforms have been used to analyze single-cell genomics data17. The widely used platforms for single-cell gene expression and ATAC profiling are platforms for multiple microfluidic droplet encapsulation17. As these platforms use microfluidic chambers, debris or aggregates can clog the system, resulting in non-usable data. Thus, the success of single-cell studies depends on the accurate isolation of individual cells/nuclei.
The protocol presented here uses a similar approach to recent studies using snRNA-seq and snATAC-seq to understand congenital heart defects18,19,20,21,22,23. This procedure utilizes the enzymatic dissociation of freshly microdissected cardiac tissue followed by the cryopreservation of mouse cardiac progenitor cells. After thawing, the viable cells are purified and processed for nuclear isolation. In this work, this protocol was successfully used to obtain snRNA-seq and snATAC-seq data from the same nuclear preparation of mouse cardiac progenitor cells.

Author Spotlight: Nuclei Isolation from Mouse Cardiac Progenitor Cells for Epigenome and Gene Expression Profiling at Single-Cell Resolution  

Nuclei Isolation from Mouse Cardiac Progenitor Cells for Epigenome and Gene Expression Profiling at Single-Cell Resolution

The main objective of this protocol is to study the interaction of genetic and environmental factors in the context of heart development and their contribution to congenital heart defects. Single nuclei approaches such as single nuclei RNA-seq and single nuclei ataxic are emerging as key methods to study cellular heterogeneity in health and disease during heart development. One limiting step of these experiments is that all the sample have to be run simultaneously.While working with all the experimental conditions, collecting fresh enough material is for all the condition simultaneously could be challenging. Although there have been a significant progress in the field in single cell for recent years, the main difficulty is processing free samples. Avoiding the difficulty is extremely benefit to identify the molecular mechanism underlying congenital heart disease defects.This protocol describes the steps to follow for successfully isolating high quality nuclei from frozen cardiac cell suspension obtained from mouse embryos. And our protocol is compatible with downstream single nuclei RNA-seq and single nuclei ataxic. We hope that this procedure will help interested researchers and encourage them to use this powerful method for their research.

Watch this Scientific Journal Video about Nuclei Isolation from Cardiac Progenitor Cells at JoVE.com

Nuclei Isolation from Cardiac Progenitor Cells  

To begin, clean the working place and materials with 70%ethanol and RNase removing solution. Freshly prepare lysis buffer, lysis dilution buffer, 0.1 x lysis buffer, and wash buffer and maintain the buffers on ice. Pre-chill swinging bucket centrifuges to four degrees Celsius.Centrifuge the cardiac progenitor cell suspension in a swinging bucket centrifuge. Gently remove all the supernatant without touching the bottom of the tube. Add 100 microliters of chilled 0.1 x lysis buffer to the cell suspension, and mix it by pipetting 10 times.After five minutes of incubation on ice, add one milliliter of chilled wash buffer and mix it. After centrifuging the suspension, remove the supernatant and repeat two more washes with chilled wash buffer. Prepare the diluted nuclei buffer.After resuspending the nuclei in the nuclei buffer, place the nuclei stock solution on ice. When the quality of the isolated nuclei was assessed by the evaluation of the nuclear membrane morphology, the isolated nuclei appeared smooth and uniformly round under Bright-field microscopy indicating an effective isolation process.

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JoVE Journal

Developmental Biology

187 Views.  Aix-Marseille University. To begin, clean the working place and materials with 70%ethanol and RNase removing solution. Freshly prepare lysis buffer, lysis dilution buffer, 0.1 x lysis buffer, and wash buffer and maintain the buffers on ice. Pre-chill swinging bucket centrifuges to four degrees Celsius.Centrifuge the cardiac progenitor cell suspension in a swinging bucket centrifuge. Gently remove all the supernatant without touching the bottom of the tube. Add 100 microliters of chilled 0.1 x lysis buffer to th...