Feb 14, 2023 / Immunology

A single cell and spatial map of how the heart heals

Jeanene Swanson

American Heart Month in February was instituted to help bring awareness to heart disease, which is the leading cause of death across the world (1). Gaps in treating chronic heart failure after a heart attack—often a result of scar tissue formation—are reflected in our lack of understanding of the process behind how the heart heals.

Fortunately, cardiovascular research has benefited of late from single cell technologies, which continue to push new ideas and novel findings to the fore. To honor the importance of understanding more about heart disease, its progression, and potential new therapies, in this blog we feature a publication that digs into the mechanisms behind heart attack at the single cell level. Combining single cell gene expression, chromatin accessibility mapping, and spatial transcriptomics to describe the landscape of the recovering heart, the publication demonstrates the discovery power of integrating multiple 10x Genomics assays.

Cardiac remodeling after a heart attack is a process that involves many moving parts, primarily immune cells tracking to the site of damage, activation of myofibroblasts, and formation of scar tissue and new vasculature (2).

With an ongoing interest in the study of how cardiac tissue repairs itself after such injury, Christoph Kuppe, PhD, (the very first winner of our Visium Spatial Gene Expression Scientific Challenge back in 2019 and now head of his own lab at Germany’s RWTH Aachen University) led research that integrated multiomic analyses to create a single cell, spatial atlas of the heart as it recovers from myocardial infarction (MI). Applying Chromium Single Cell Gene Expression, Chromium Single Cell ATAC (Assay for Transposase Accessible Chromatin), and Visium Spatial Gene Expression, the researchers characterized cellular states in spatial context during various stages of MI compared to healthy controls (3). As a foundational reference, this publication lays the groundwork for further in-depth studies of cardiac injury, repair, and fibrosis, the authors believe.

Building a multiomic spatial map

Proper cellular function doesn’t only depend on individual cellular activity; how cells interact with those around them matters, too. So, while single cell technologies can characterize cellular heterogeneity, knowing the spatial context during states of disease is key to identifying pathways involved in progression that can be therapeutically targeted.

In this work, Dr. Kuppe’s team took a total of 31 heart samples from 23 patients with acute myocardial infarction, including necrotic areas (ischemic [or, blood-deprived] zone and border zone) and the unaffected left ventricular myocardium (remote zone), and controls, at different time points after a heart attack. They also took samples from human hearts at a later stage (fibrotic zone), which showed ischemic heart disease. For each cardiac sample, they performed Visium Spatial gene expression analysis, single nuclei RNA sequencing (snRNA-seq), and single nuclei ATAC sequencing (snATAC-seq).

Integrating their data, they uncovered 10 major cardiac cell types (including cardiomyocytes, or heart muscle cells, but also fibroblast, lymphoid, and cycling cells, to name a few) and were able to identify different cell states of cardiomyocytes, endothelial cells, myeloid cells, and fibroblasts that are associated with heart disease progression after MI.

Combining spatial transcriptomic and snATAC-seq data, they delved deeper into pathway and transcription factor binding activity, which provided additional layers of biological information. With their spatial transcriptomics data, they identified nine cell-type clusters, or niches, based on their cell-type compositions (including myogenic, inflammatory, and fibrotic cell-type niches). Spatial data also allowed them to see heterogeneity in cardiomyocyte function. For example, they observed that key pathways in fibrosis are colocalized, including TGFβ and NFκB in fibroblasts, and JAK–STAT and NFκB in immune cells.

By taking samples from not only different time points after the heart attack began but also from different tissues surrounding the site of infarction, Dr. Kuppe and team were able to create a comprehensive map of cell-type differences across time, tissue types, and individual patients.

Cardiomyocyte state is disease specific

Combining snRNA-seq and snATAC-seq data from cardiomyocytes, they discovered five cell states of ventricular cardiomyocytes (vCM1–5). Using differential gene expression analysis, they uncovered upregulation of ANKRD1 in both vCM2 and vCM3, while NPPB was upregulated and showed increased chromatin accessibility in vCM3 cells. Their findings suggest that these cardiomyocyte states can be described as “distinct cellular stress states within the acute myocardial infarction phase,” (as in, vCM1 is “non-stressed,” vCM2 is “pre-stressed,” and vCM3 is “stressed”).

Cardiomyocyte state is variable

Paired snRNA-seq and snATAC-seq data also allowed them to identify major transcription factors. For example, the mineralocorticoid receptor (NR3C2), which is a common target for heart failure, acts as a major regulator of the vCM1 state. Because decreased NR3C2 expression has been associated with the development of severe heart failure and cardiac fibrosis (4), it’s possible that targeting this gene or its downstream targets could be therapeutically relevant. They also found that the stressed cardiomyocyte vCM3 is localized in distinct cell-type neighborhoods filled with different mixes of vascular smooth muscle cells, fibroblasts, adipocytes, and myeloid cells—possibly pointing to the importance of interactions between cardiac and immune cells.

Read more about their extensive multiomic analyses in their publication.

Mapping the future: Improved therapies for heart attack and cardiac disease

By employing a multiomic approach, this work allows us to see how cell state changes over the progression of MI and cardiac remodeling, based on where the cell is in relation to other cell types. It also reveals how gene regulation affects cellular states in different tissue zones and stages of disease. As a reference for the field, Dr. Kuppe’s single cell and spatial map can be used as a starting point for other more advanced mechanistic and therapeutic studies of cardiac disease.


  1. Wong ND. Epidemiological studies of CHD and the evolution of preventive cardiology. Nat Rev Cardiol 11: 276–89 (2014).
  2. Prabhu SD & Frangogiannis NG. The biological basis for cardiac repair after myocardial infarction. Circ Res 119: 91–112 (2016).
  3. Kuppe C, et al. Spatial multi-omic map of human myocardial infarction. Nature 608: 766–777 (2022).
  4. Beggah AT, et al. Reversible cardiac fibrosis and heart failure induced by conditional expression of an antisense mRNA of the mineralocorticoid receptor in cardiomyocytes. Proc Natl Acad Sci USA 99: 7160–7165 (2002).