The project

Heart failure is a global public health issue that affects more than 60 million people worldwide1. Despite substantial advances in research, heart failure remains the most intractable heart disease and the leading cause of death in the USA even during the COVID-19 pandemic2. Myocardial infarction, valve disease, genetic mutations, numerous infections (including COVID-19) and cardiotoxic cancer therapies are among the most frequent causes of heart failure3. Various ‘omics’ technologies provided insights into the roles of genetic mutations, epigenetics, the transcriptome, metabolome or proteome in the pathogenesis of heart failure due to different etiologies4. We applied cap analysis of gene expression (CAGE) technology to map the genome regulatory network that is responsible for gene transcription in the human heart. This approach enabled us to identify thousands of genes that were transcribed from alternative promoters or were dependent on specific enhancers in healthy versus failing hearts, which resulted in different transcriptomes driving cardiac remodeling during heart failure from different etiologies.

The discovery

We generated CAGE profiles of 109 samples from 4 cardiac chambers from 21 healthy and 10 failing adult human hearts (Fig. 1a). CAGE enables the precise mapping of the activity of genome regulatory elements, such as promoters and enhancers, that control gene transcription. After extraction of total RNA, sequencing of regulatory regions and extensive validation (Fig. 1b), we identified 17,668 promoters and 14,920 enhancers that control the expression of 14,519 genes in the human heart. On the basis of this atlas of transcribed regulatory elements, we demonstrated how these promoters and enhancers are differentially transcribed across different heart chambers, disease states, and in ischemic versus non-ischemic etiologies. We found that in many cases, alternative promoter usage (including in key genes that control heart function, such as PALLD, which encodes palladin) generates specific transcript isoforms in pathological states. This result sheds light on the etiology-specific molecular mechanisms of heart failure pathogenesis and the remodeling or reprogramming of the cardiac cells caused by the disease.

Fig. 1: An atlas of transcribed promoters and enhancers in healthy and failing human hearts.
figure 1

a, Experimental design, with donor demographics and tissues sampled. SAN, sinoatrial node. b, Data-processing workflow using FANTOM5 (functional annotation of the mammalian genome) pipelines for CAGE: decomposition peak identification and bidirectional enhancer pipelines result in unidirectional and bidirectional transcribed regulatory elements (TREs), which are then classified into promoters and enhancers. CTSS, CAGE transcription start site. c, Promoter-switching analysis using CAGE defines alternative unidirectional TRE usage in PALLD in healthy and failing heart samples. © 2023, Deviatiiarov, R. M. et al.

Many genome-wide association studies (GWAS) have identified thousands of cardiac-disease-related single-nucleotide polymorphisms5. With our atlas, we found that promoters and enhancers are enriched with such genomics variants, which often coincide with allele-specific transcription factor-binding sites and expression quantitative trait loci, and thereby affect cardiac state by modulating transcription. This finding points to a strategy for genome-editing therapy to target genome regulatory elements. To conclude, we developed an open-source heart CAGE atlas that will serve the cardiovascular community to improve the understanding of the mechanistic role of the cardiac gene regulatory networks in cardiovascular disease. The atlas will also offer new directions in the development of etiology-specific therapies for heart failure.

Future directions

The heart CAGE atlas offers a wealth of information about the human heart genome regulatory network, which dynamically controls transcription during our entire lifespan, in health and disease. We reported thousands of essential genes controlled by alternative promoters and enhancers on the basis of the pathological state. The atlas is open to all cardiovascular researchers, who can mine important information relevant to their research programs, whether focused on specific genes or proteins, signaling pathways, or cellular physiological systems.

Moreover, our data could shed light on the role of biological sex during heart failure pathogenesis. Such insight would be crucial because of the substantial disparities between men and women in cardiovascular health, disease and therapy delivery. Future studies based on our heart CAGE atlas could help to develop sex-specific diagnostics and therapy for heart failure. Finally, the aging human heart undergoes considerable remodeling that predisposes it to diseases, including atrial fibrillation and heart failure. Mining our atlas could help to build an improved understanding of the genome regulatory mechanisms that govern cardiac aging in health and disease, conceivably along different trajectories in men and women.

We will continue to extend our atlas by incorporating new data from human hearts with different heart disease etiologies, ages, ethnicities, and other factors known to affect cardiac health.

Igor R. Efimov

McCormick School of Engineering and Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.

Expert opinion

“In this study, the authors presented a new CAGE dataset from 31 healthy and failing human hearts and performed extensive analyses to show that this atlas of cardiac regulatory elements can be a helpful resource for studying cardiovascular diseases. Specifically, the authors identified many cardiac-specific regulatory elements, differentially active elements and pathways between healthy and failing hearts, and disease-specific pathways.” Dongwon Lee, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA

Behind the paper

Heart failure is one of the leading challenges of modern medicine. The worldwide research community is working on the mechanisms of heart failure pathogenesis, using an array of tools, from animal models to numerous ‘omics’ approaches. However, short of a heart transplant, therapies remain mostly ineffective. In this work, we aimed to close knowledge gaps in the genomic and transcriptomic bases of heart failure. We were fortunate to receive samples from donor hearts that were not accepted for transplantation and failing hearts from patients who had received transplantation. This approach enabled us to systematically study genome regulatory elements that control transcription — promoters and enhancers. We made several important observations that are likely to lead to new therapies. We found hundreds of important genes that are transcribed by alternative promoters in health versus disease, or in ischemic versus non-ischemic cardiomyopathy. I.R.E.

From the editor

“The authors take advantage of a relatively new sequencing technique (CAGE sequencing) and identify the actively transcribed regulatory elements in different regions of the human heart, in healthy versus failing hearts, and in two different types of heart failure. This atlas will provide an important reference to improve our understanding of cardiac gene regulation and how it could be differentially affected by mutations in the non-coding genome.” Elvira Forte, Associate Editor, Nature Cardiovascular Research.