We present a whole-blood isoform ratio QTL (irQTL) resource by analyzing genome-wide isoform-to-gene expression ratios using sequencing data. In Framingham Heart Study (FHS, n = 2622) discovery, we identify over 1.1 million cis -irQTLs (minor allele frequency [MAF] ≥ 0.01, ±1 Mb of 10,883 isoform transcripts, P < 5 × 10 ⁻⁸ ) across 4,971 genes. Among 11,425 sentinel cis -irQTLs, 72% replicate ( P < 1 × 10 ⁻⁴ ) in the Women’s Health Initiative (WHI; n = 2005). Notably, 20% of cis -irQTLs have no significant association with overall gene expression, indicating isoform-specific regulation. These variants are enriched at splice donor/acceptor sites and genome-wide association study loci ( P < 1 × 10 ⁻¹⁰ ). We also identify 1870 sentinel trans -irQTLs (MAF ≥ 0.01, P < 1.5 × 10 ⁻¹³ ) for 1,084 isoforms across 590 genes, and 2327 rare cis -irQTLs (0.003 < MAF < 0.01) for 2467 isoforms of 1428 genes in FHS, with external replication rates of 61% and 41% in WHI, respectively. We highlight rs12898397 in ULK3 , which alters splice site usage and reduces expression of a full-length isoform. Mendelian randomization supports a causal role between this isoform shift and reduced diastolic blood pressure. These findings highlight the power of irQTL mapping to uncover transcript-specific regulatory mechanisms underlying complex traits.

Investigating the interplay between mitochondrial DNA (mtDNA) variations and epigenetic aging metrics may elucidate biological mechanisms associated with age‐related diseases. We estimated epigenetic age acceleration (EAA) metrics from DNA methylation data and derived mtDNA metrics, including heteroplasmic variants and mtDNA copy number (mtDNA CN) from whole genome sequencing. Linear regressions and meta‐analyses were conducted to assess associations between EAA and mtDNA metrics, adjusting for chronological age, self‐identified sex, and other covariates in 6,316 participants (58% female, 41% non‐White Americans). Mediation analysis was conducted to examine whether EAA mediated the relationship between mtDNA CN and metabolic traits. A higher burden of rare heteroplasmic variants was associated with accelerations of first‐generation EAA metrics, while a lower level mtDNA CN was associated with accelerations of second‐ and third‐generation EAA metrics. For example, one standard deviation (SD) higher MSS, a score based on the predicted functions of rare heteroplasmic variants, was associated with a 0.22‐year higher EAA by the Hannum method ( p = 1.3E‐6) among all participants, while one SD lower mtDNA CN was associated with higher DunedinPACE ( β = −0.005, p = 6.0E‐4). No significant association was observed between the heteroplasmy burden of common variants and EAAs. Furthermore, we observed DunedinPACE mediated 11.1% and 10.8% of the associations of mtDNA CN with obesity and T2DM in older FHS participants, respectively. Our analysis indicated that higher levels of heteroplasmy burden of rare variants and lower mtDNA CN were associated with accelerated epigenetic aging, and these associations showed stronger magnitudes among older participants.

Background: Alcohol use patterns influence health outcomes. This study examined sex-specific drinking trajectories and their associations with all-cause mortality and coronary heart disease (CHD) in the US-based Framingham Heart Study. Method: Among 6570 participants (mean age: 55 ± 13; 55% women) followed for 15 years, a growth mixture model identified four sex-specific alcohol consumption trajectories. Cox models examined associations of alcohol trajectories with CHD and mortality over 10 years of follow-up, adjusting for covariates. Results: This study identified four distinct, sex-specific alcohol consumption trajectories: the Moderate-Decreasing group (1179 women, 0–14 g/day; 1534 men, 0–28 g/day) showed a declining moderate intake, The Low-to-None group included light or non-drinkers (992 women, 826 men), the Inverse-U group (606 women, 199 men) showed variable intake over time, while the High-Decreasing group (858 women, 376 men) had high initial consumption (women > 14 and men > 28 g/day) that declined over time. Compared with the Moderate-Decreasing group, women in other groups had higher CHD risks (HRs 1.58–1.61) and greater mortality risk in the Low-to-None (HR 1.25) and Inverse-U (HR 1.28) groups. Men in Low-to-None had higher mortality (HR 1.17) and CHD (HR 1.60), while High-Decreasing showed the highest mortality (HR 1.27). Low-to-moderate drinking was associated with lower mortality and CHD risks; however, these findings do not confirm the protective effects of alcohol use. Discussion: Our findings suggest that sustained low to moderate drinking was associated with lower risks of mortality and CHD in both women and men, compared to high-level or fluctuating patterns. Although these associations may not confirm causality, our findings emphasize the importance of investigating long-term drinking patterns in public health. Nevertheless, we caution against promoting moderate alcohol use as a strategy to reduce mortality risk or prevent CHD.

We analyze 10,986 participants (mean age 77; 63% women; 54% non-White) across seven U.S. cohorts to study the relationship between mitochondrial DNA (mtDNA) heteroplasmy and nuclear DNA methylation. We identify 597 CpGs associated with heteroplasmy burden, generally showing lower methylation. These CpGs are enriched in dynamically regulated island shores and depleted in CpG islands, indicating involvement in context-specific rather than constitutive gene regulation. In HEK293T cells, we introduce a truncating mtDNA mutation (MT-COX3, mt.9979) and observe a positive correlation between variant allele fraction and methylation at cg04569152, supporting a direct mtDNA–nDNA epigenetic link. Many heteroplasmy-associated CpGs overlap with known methylation-trait associations for metabolic and behavioral traits. Composite CpG scores predict all-cause mortality and incident CVD, with one-unit increases associated with 1.27-fold and 1.12-fold higher hazards, respectively. These findings suggest an mtDNA–nDNA epigenetic connection in aging and disease, though its direction and mechanisms remain to be studied.

Background: Alcohol use patterns influence health outcomes. This study examined sex-specific drinking trajectories and their associations with all-cause mortality and coronary heart disease (CHD) in the US-based Framingham Heart Study. Method: Among 6,570 participants (mean age: 55±13; 55% women) followed for 15 years, a growth mixture model identified four sex-specific alcohol consumption trajectories. Cox models examined associations of alcohol trajectories with CHD and mortality over 10 years of follow-up, adjusting for covariates. Results: The Moderate-Decreasing group (1,179 women, 0–14 g/day; 1,534 men, 0–28 g/day) showed a declining moderate intake. The Low-to-None group included light or non-drinkers (992 women, 826 men). The Inverse-U group (606 women, 199 men) showed variable intake, while the High-Decreasing group (858 women, 376 men) had high (women >14 and men >28 g/day) but declining consumption. Compared with Moderate-Decreasing, women in other groups had higher CHD risks (HRs 1.58-1.61) and greater mortality in Low-to-None (HR 1.25) and Inverse-U (HR 1.28) groups. Men in Low-to-None had higher mortality (HR 1.17) and CHD (HR 1.60), while High-Decreasing showed the highest mortality (HR 1.27). Low-to-moderate drinking was associated with lower mortality and CHD risks; however, these findings do not confirm the protective effects of alcohol use. Discussion: Our findings suggest that sustained low to moderate drinking was associated with lower risks of mortality and CHD in both women and men, compared to high-level or fluctuating patterns. These results emphasize the importance of understanding long-term drinking patterns in public health, but we caution against interpreting moderate use as a means to lower mortality risk or prevent CHD.