Table 1.

Multi-omics studies in cardiac aging.

Omics	Techniques Used	Aging Hallmarks	Samples	Major Findings of Aging Impact	Ref.
Epigenomics	ChIP-seq, Hi-C seq	Epigenetic alteration	murine whole hearts (6, 12, 18 months)	Disruption of nuclear lamina and chromatin architecture leads to the misexpression of genes lacking CpG islands, contributing to chronic inflammation, physiological deterioration, and the loss of functional identity during cardiac aging.	[12]
	ChIP-seq, RNA-seq		male murine left ventricles (6, 24 months)	Changes in chromatin accessibility and histone modifications, active marks (H3K27ac) and repressive marks (H3K27me3), are prominent in the aging cardiomyocytes, with relatively stable transcriptomes but significant epigenetic alterations.	[13]
	ChIP-seq, Hi-C seq, RNA-seq, UHPLC-MS/MS *		murine cardiomyocytes (2, 6, 18 months)	The enhancer activation of glycolysis genes via p300/CBP is a key driver of metabolic remodeling in cardiac aging, and the pharmacological inhibition of p300/CBP can blunt age-related cardiac dysfunction.	[14]
	snATAC-seq		murine hearts, brains, bone marrow, skeletal muscle (3, 10, 18 months)	Cardiac ECs showed uniquely more accessible promoter of Nhp2 during aging, while cardiac cells in general showed fewer age-related changes to accessibility of cCREs than other tissues tested.	[15]
Transcriptomics	Bulk RNA-Seq	Oxidative stress, disrupted metabolism, cellular senescence, chronic inflammation, mitochondrial dysfunction, disabled macroautophagy	zebrafish ventricles (7, 48 months)	Aging hearts showed the upregulation of genes of immune response and chemotaxis, downregulation of genes of metabolism and tissue regeneration, and impaired regenerative capacity to cardiac injury.	[16,17]
	Bulk RNA-Seq MS *		hearts from male and female mice (4, 20 months)	Heart tissues showed sex-specific changes to gene expression with age impacting mitochondrial metabolism, translation, autophagy, etc., and rewiring of RNA splicing programs in exon usage and splice patterns.	[18]
	Bulk RNA-Seq		rat hearts (6, 12, 17, 36 months)	Aging hearts showed upregulation of circadian, senescence and cellular stress genes, and conserved aging-related gene expression patterns across species.	[19]
	Bulk RNA-Seq		zebrafish (2, 7, 16, 39 months); rat (6, 12, 17, 36 months) hearts	Identified conserved and distinctive aging-related changes to gene expression across tissues and species. Cardiac specific changes in fish involved immune response genes, while those in rats involved wound healing and heart development genes.	[20]
	Bulk RNA-Seq		human atrial tissue (adult: 18–65 years and aged: >65 years); rat CMs (6, 24 months)	Increased ROS production in both mitochondrial and extramitochondrial pathways, altered ROS clearance, and reduced antioxidant pathways in both species.	[21]
	Bulk RNA-Seq		rat left ventricular CMs with/without relaxin treatment (9, 24 months)	Aging enhanced inflammation and fibrosis, while relaxin helped to reverse markers. More pronounced aging effects in female hearts can be reduced by relaxin.	[22]
	Bulk RNA-Seq, scRNA-Seq		murine ECs (3, 24 months)	Endothelial Apelin receptor-enriched subtype reduced in aged hearts, downregulation of endothelial barrier function and calcium signaling, upregulation of diabetes and metabolism pathways, and altered receptor-ligand interactions.	[23]
	snRNA-seq		cynomolgus monkey left ventricles (adult: 4–6 years and aged: 18–21 years)	Aged hearts showed upregulated Senescence-Associated Secretory Phenotype (SASP) gene expression, upregulated transcription factors (TFs), FOXP1 and FOXP2, and diminished cytokine production of anti-inflammatory M2 macrophages.	[24]
	snRNA-seq		murine hearts (3, 18 months)	Aged fibroblasts showed increased transcriptional heterogeneity, disrupted interactions with endothelial cells, antiangiogenic properties, and adoption of osteogenic traits.	[25]
	Bulk RNA-Seq, snRNA-Seq		murine hearts (3–7, 18–20 months)	Aging reduces nerve density and dysregulates vascular-derived neuroregulatory genes. Accumulation of senescent cells and downregulation of miR-145 increase semaphorin-3A. Treating aged mice with senolytic drugs could help reverse these effects.	[26]
	scRNA-seq		cynomolgus monkey aortic and coronary arteries (adult: 4–6 years and aged: 18–21 years)	Arterial aging leads to downregulation of FOXO3A, leading to the disruption of vascular homeostasis. Aging also causes the inflammatory response, increased wall thickness, calcification, fibrous cap formation, and fragmentation of elastic lamina.	[27]
	scRNA-seq ATAC-seq		utilized publicly available data for murine and primate aging models	Endothelial cell aging leads to the upregulation of BACH1 in both mouse and monkey vasculature, leading to endothelial dysfunction and senescence; BACH1 binds to open chromatin regions, particularly at the enhancer of the CDKN1A gene, promoting its transcription in senescent endothelial cells.	[28]
Proteomics	UHPLC-MS RNA-seq	Disrupted metabolism loss of proteostasis	male diabetic murine hearts (13 weeks)	LAV-BPIFB4 gene therapy reprograms rather than reverses the diabetic heart phenotype, offering potential cardioprotective effects through subtle metabolic changes.	[29]
Metabolomics	NMR spectroscopy	Dysregulated metabolism	murine hearts, brains, kidneys, livers, lungs and spleens (2–3, 24–26 months)	Aging showed increased GABA in modulating heart rhythm and branched-chain amino acids (BCAAs), such as leucine, isoleucine, valine, and the change in purine metabolites.	[30]
	NMR spectroscopy		female and male murine heart, brain, liver, lung and skeletal muscle tissues (3, 6, 12, 24 months)	Aging process showed biphasic patterns of acetic acid and BCAAs, and sex differences in metabolic alterations.	[31]
			murine hearts and blood with/without mitoxantrone treatment (19 months)	MTX treatment in aged mice led to long-lasting cardiac metabolic adaptations, including increased fatty acid oxidation, reduced glucose metabolism, and amino acid oxidation.	[32]
Multi-Omics	scRNA-seq scATAC seq	All cardiac aging hallmarks	murine aortas (4, 26, 86 weeks)	Aortic aging in mice leads to cell-type specific transcriptional and chromatin accessibility changes. The EC subtype EC1 showed higher involvement in senescence and inflammation, while EC2 was more associated with vascular tone regulation. Key transcription factors, Atf3 and Stat3, were identified as regulators of these processes.	[33]
			male and female human heart left ventricle and/or apex (25–60 years)	Identified sex-and-age-linked molecular signatures, e.g., increased immune activation, metabolic shifts, and pathways changes, such as TGF-β signaling and epithelial-to-mesenchymal transition (EMT), particularly affecting fibroblasts, macrophages, and cardiomyocytes in the human heart.	[34]
	snATAC-Seq snRNA-Seq		male and female mice (6, 12, 18 months)	Aging in the mouse heart is associated with changes in immune response, protein homeostasis, and cellular transport, with significant impacts on protein folding, fatty acid oxidation, and autophagy.	[35]
	RNA-seq LC/MS *		murine hearts (2–3 months, 18 months); human engineered heart tissue	The lncRNA Sarrah is a conserved anti-apoptotic regulator that is downregulated during cardiac aging and promotes cardiomyocyte survival after ischemic injury.	[36]
	RNA-seq LC/MS		male and female murine cardiac and skeletal muscle (4, 20 months)	Cardiac aging showed a significant shift in gene expression from mitochondrial metabolism and protein synthesis towards immune activation and extracellular matrix remodeling. About 48% of the aging-associated transcriptomic changes in the heart is predictive of protein-level changes.	[37]

* UHPLC–MS/MS: ultra–performance liquid chromatography–mass spectrometry; MS: mass spectrometry; LC/MS: liquid chromatography/mass spectrometry.