Targeting transcriptional machinery to inhibit enhancer-driven gene expression in heart failure

The Current Therapeutic Role of Chromatin Remodeling for the Prognosis and Treatment of Heart Failure

Cardiovascular diseases are a major cause of death globally, with no cure to date. Many interventions have been studied and suggested, of which epigenetics and chromatin remodeling have been the most promising. Over the last decade, major advancements have been made in the field of chromatin remodeling, particularly for the treatment of heart failure, because of innovations in bioinformatics and gene therapy. Specifically, understanding changes to the chromatin architecture have been shown to alter cardiac disease progression via variations in genomic sequencing, targeting cardiac genes, using RNA molecules, and utilizing chromatin remodeler complexes. By understanding these chromatin remodeling mechanisms in an injured heart, treatments for heart failure have been suggested through individualized pharmaceutical interventions as well as biomarkers for major disease states. By understanding the current roles of chromatin remodeling in heart failure, a potential therapeutic approach may be discovered in the future.

Identification of hub genes and transcription factor regulatory network for heart failure using RNA-seq data and robust rank aggregation analysis

Background

Heart failure (HF) is the end stage of various cardiovascular diseases with a high mortality rate. Novel diagnostic and therapeutic biomarkers for HF are urgently required. Our research aims to identify HF-related hub genes and regulatory networks using bioinformatics and validation assays.

Methods

Using four RNA-seq datasets in the Gene Expression Omnibus (GEO) database, we screened differentially expressed genes (DEGs) of HF using Removal of Unwanted Variation from RNA-seq data (RUVSeq) and the robust rank aggregation (RRA) method. Then, hub genes were recognized using the STRING database and Cytoscape software with cytoHubba plug-in. Furthermore, reliable hub genes were validated by the GEO microarray datasets and quantitative reverse transcription polymerase chain reaction (qRT-PCR) using heart tissues from patients with HF and non-failing donors (NFDs). In addition, R packages “clusterProfiler” and “GSVA” were utilized for enrichment analysis. Moreover, the transcription factor (TF)–DEG regulatory network was constructed by Cytoscape and verified in a microarray dataset.

Results

A total of 201 robust DEGs were identified in patients with HF and NFDs. STRING and Cytoscape analysis recognized six hub genes, among which ASPN, COL1A1, and FMOD were confirmed as reliable hub genes through microarray datasets and qRT-PCR validation. Functional analysis showed that the DEGs and hub genes were enriched in T-cell-mediated immune response and myocardial glucose metabolism, which were closely associated with myocardial fibrosis. In addition, the TF–DEG regulatory network was constructed, and 13 significant TF–DEG pairs were finally identified.

Conclusion

Our study integrated different RNA-seq datasets using RUVSeq and the RRA method and identified ASPN, COL1A1, and FMOD as potential diagnostic biomarkers for HF. The results provide new insights into the underlying mechanisms and effective treatments of HF.

Gene Therapy With the N-Terminus of Junctophilin-2 Improves Heart Failure in Mice

BACKGROUND

Transcriptional remodeling is known to contribute to heart failure (HF). Targeting stress-dependent gene expression mechanisms may represent a clinically relevant gene therapy option. We recently uncovered a salutary mechanism in the heart whereby JP2 (junctophilin-2), an essential component of the excitation-contraction coupling apparatus, is site-specifically cleaved and releases an N-terminal fragment (JP2NT [N-terminal fragment of JP2]) that translocates into the nucleus and functions as a transcriptional repressor of HF-related genes. This study aims to determine whether JP2NT can be leveraged by gene therapy techniques for attenuating HF progression in a preclinical pressure overload model.

METHODS

We intraventricularly injected adeno-associated virus (AAV) (2/9) vectors expressing eGFP (enhanced green fluorescent protein), JP2NT, or DNA-binding deficient JP2NT (JP2NTΔbNLS/ARR) into neonatal mice and induced cardiac stress by transaortic constriction (TAC) 9 weeks later. We also treated mice with established moderate HF from TAC stress with either AAV-JP2NT or AAV-eGFP. RNA-sequencing analysis was used to reveal changes in hypertrophic and HF-related gene transcription by JP2NT gene therapy after TAC. Echocardiography, confocal imaging, and histology were performed to evaluate heart function and pathological myocardial remodeling following stress.

RESULTS

Mice preinjected with AAV-JP2NT exhibited ameliorated cardiac remodeling following TAC. The JP2NT DNA-binding domain is required for cardioprotection as its deletion within the AAV-JP2NT vector prevented improvement in TAC-induced cardiac dysfunction. Functional and histological data suggest that JP2NT gene therapy after the onset of cardiac dysfunction is effective at slowing the progression of HF. RNA-sequencing analysis further revealed a broad reversal of hypertrophic and HF-related gene transcription by JP2NT overexpression after TAC.

CONCLUSIONS

Our prevention- and intervention-based approaches here demonstrated that AAV-mediated delivery of JP2NT into the myocardium can attenuate stress-induced transcriptional remodeling and the development of HF when administered either before or after cardiac stress initiation. Our data indicate that JP2NT gene therapy holds great potential as a novel therapeutic for treating hypertrophy and HF.

Genomic enhancers in cardiac development and disease

The Human Genome Project marked a major milestone in the scientific community as it unravelled the ~3 billion bases that are central to crucial aspects of human life. Despite this achievement, it only scratched the surface of understanding how each nucleotide matters, both individually and as part of a larger unit. Beyond the coding genome, which comprises only ~2% of the whole genome, scientists have realized that large portions of the genome, not known to code for any protein, were crucial for regulating the coding genes. These large portions of the genome comprise the 'non-coding genome'. The history of gene regulation mediated by proteins that bind to the regulatory non-coding genome dates back many decades to the 1960s. However, the original definition of 'enhancers' was first used in the early 1980s. In this Review, we summarize benchmark studies that have mapped the role of cardiac enhancers in disease and development. We highlight instances in which enhancer-localized genetic variants explain the missing link to cardiac pathogenesis. Finally, we inspire readers to consider the next phase of exploring enhancer-based gene therapy for cardiovascular disease.