Single-cell analysis of chromatin and expression reveals age- and sex-associated alterations in the human heart

Sex differences and age-related changes in the human heart at the tissue, cell, and molecular level are well-documented, but how molecular programs within individual cell types vary with age and sex across individuals remains poorly characterized. To address this, the authors performed single-nucleus combinatorial indexing (sci) ATAC- and RNA-sequencing on heart samples from nine donors. They identified hundreds of differentially expressed genes by age and sex and corresponding epigenetic signatures, including metabolic alterations by sex and immune changes by age, as well as sex- and age-associated changes in cardiomyocyte abundance. Comparison of adult-derived ATAC-seq profiles with fetal counterparts revealed developmental-stage-specific regulatory factors. Predictive models leveraging ATAC-seq-derived promoter and distal motif features accounted for approximately a quarter of variation in cell-type-specific RNA expression and identified cell-type-specific transcription factors. This constitutes the largest single-cell analysis of cardiac age- and sex-associated variation to date and provides a resource for studying healthy cardiac transcriptional regulation at single-cell resolution.