A sweeping single-nucleus atlas reveals how human hearts lose cellular balance with age and points to PRDM16 as a potential molecular target for future cardiac aging research.
Study: Life-span–dependent transcriptional dynamics of the human heart. Image Credit: Vishal Bhaskar Nagtilak / Shutterstock
In a recent study published in the journal Science Advances, researchers conducted a comprehensive analysis to map the single-nucleus transcriptomic landscape of the human heart from fetal development to older adulthood. The study analyzed 442,239 single nuclei from nonfailing hearts and identified age-associated transcriptional states in heart muscle cells linked to progressive loss of gene-expression homeostasis, stress responses, and inflammatory signaling.
Most notably, the study identified a candidate transcriptional regulator, PRDM16. PRDM16 activity and expression declined with age, and PRDM16 knockdown in human cardiomyocyte models induced senescence-like, metabolic, and stress-response phenotypes. Encouragingly, study findings revealed that Prdm16 overexpression in aged mouse hearts improved systolic function and partially reversed aging-associated transcriptional programs, thereby indicating a potential molecular target for future research into age-associated cardiac decline.
Background
Decades of cardiac research have established that the human heart relies on an intricate network of specialized cells working in harmony to maintain constant circulation. However, more recent research indicates that the cardiac system undergoes a progressive structural and functional shift that compromises its former circulatory performance.
As a result, aging is now recognized as a major risk factor for cardiovascular disease. Unfortunately, while science has elucidated the macro-level changes that occur as the heart ages, the underlying cellular dynamics and molecular pathways governing this process remain understudied.
Reviews on the topic attribute these knowledge gaps to previous research facing difficulties in isolating fragile adult heart muscle cells. Scientists still have a limited understanding of the mechanisms underlying how gene expression shifts between the left ventricle (LV) and right ventricle (RV) across development, adulthood, and aging affect the temporal performance of the cardiovascular system and contribute to progressive heart disease.
About the Study
The present study aimed to address these knowledge gaps and inform future mechanistic and preclinical research by conducting a comprehensive evaluation of nonfailing transmural tissue across multiple donor life stages.
The study specifically collected 54 nonfailing transmural tissue samples from 29 individual donors across six distinct life stages spanning the chronological (calendar age) spectrum from early fetal development (13 gestational weeks) to older adulthood (75 years).
The study primarily utilized high-throughput single-nucleus RNA sequencing (snRNA-seq) to analyze individual nuclei and capture transcriptional states in fragile adult cardiomyocytes and other cardiac cells. The final analytical dataset comprised 442,239 single nuclei. Statistical analysis leveraged principal components analysis (PCA) to track broader transcriptional similarities across multiple human heart life stages.
The study further utilized human-induced pluripotent stem cell (hiPSC) models to test the impacts of targeted genetic manipulations in vitro. Finally, the study investigated the effects of using intramyocardial adenoviral delivery to overexpress Prdm16 in 23-month-old mice, with cardiac function assessed over approximately two weeks.
The study’s key readouts included shifts in cellular proportions, SASP activation scores, and mitochondrial respiratory capacity. Study findings were subsequently used to build machine-learning models using the XGBoost (Extreme Gradient Boosting) algorithm to calculate transcriptomic heart age.
Study Findings
The study showed cardiac aging as a temporally dynamic, coordinated, and multicellular process, highlighting that during early life, the heart rapidly loses its proliferative cell (ProC) population (from 7.2% to 1.1% between early fetal stages and late gestation). This suggests that cardiomyocyte-like proliferative potential is largely reduced before birth.
In contrast, aging hearts revealed a prominent, stress-induced state in cardiomyocytes (CMs), termed CM4, which dominated the hearts of individuals aged 60 to 75. Statistical analyses indicate that the CM4 state is characterized by increased CRYAB expression in cardiomyocytes and aged heart samples (P < 2.28 × 10-16), a known biomarker of cellular stress. This CM4 state was also associated with elevated cardiomyocyte aging and SASP scores (P < 2.28 × 10-16).
The study’s most important finding was likely the identification of PRDM16, a TF whose regulatory activity was observed to decline markedly with chronological age. PRDM16 expression was shown to be inversely associated with aging scores (R = -0.6, P < 0.0001).
Furthermore, knocking down PRDM16 in human cell models triggered senescence-associated cellular dysfunction, leading to a significant increase in the cell cycle inhibitor p21 (P < 0.01) and an overproduction of the inflammatory marker interleukin-8 (P < 0.001).
Conversely, when researchers overexpressed Prdm16 in aged mouse hearts, it significantly improved cardiac systolic function by increasing ejection fraction and fractional shortening relative to aged controls, while simultaneously attenuating cardiomyocyte hypertrophy.
Conclusions
The present study establishes a novel, detailed, single-nucleus-derived resource detailing how the human heart changes over a lifetime. The identification of PRDM16 suggests that some molecular features of age-related cardiac decline may be modifiable in experimental models, rather than proving that human cardiac aging can be reversed.
The study used its findings to generate transcriptomic aging clocks. These clocks were shown to be accurate, showing a near-perfect correlation with gestational age in fetal samples (Pearson correlation coefficient = 0.997). When applied to diseased hearts, these clocks revealed deviations consistent with accelerated or dysregulated transcriptional aging in patients with cardiomyopathies, supporting future work toward age-aware precision cardiovascular research.
However, the authors note several limitations. Sex-specific effects were not systematically analyzed, the study focused on nonfailing hearts, and future spatial and longitudinal datasets will be needed to investigate region-specific and time-dependent aspects of cardiac aging.
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