Rare Genetic Variants in LDLR, APOB, and PCSK9 Are Associated With Aortic Stenosis

Abstract

Background: Despite a proposed causal role for LDL-C (low-density lipoprotein cholesterol) in aortic stenosis (AS), randomized controlled trials of lipid-lowering therapy failed to prevent severe AS. We aimed to assess the impact on AS and peak velocity across the aortic valve conferred by lifelong alterations in LDL-C levels mediated by protein-disrupting variants in 3 clinically significant genes for LDL (low-density lipoprotein) metabolism (LDLR, APOB, and PCSK9).

Methods: We used sequencing data and electronic health records from UK Biobank (UKB) and All of Us and magnetic resonance imaging data from UKB. We identified predicted protein-disrupting variants with the Loss Of Function Transcript Effect Estimator (LOFTEE) and AlphaMissense algorithms and evaluated their associations with LDL-C and peak velocity across the aortic valve (UK Biobank), as well as diagnosed AS and aortic valve replacement (UK Biobank and All of Us).

Results: We included 421 049 unrelated participants (5621 with AS) in UKB and 195 519 unrelated participants (1087 with AS) in All of Us. Carriers of protein-disrupting variants in LDLR had higher mean LDL-C (UKB: +42.6 mg/dL; P=4.4e-237) and greater risk of AS (meta-analysis: odds ratio, 3.52 [95% CI, 2.39-5.20]; P=2.3e-10) and aortic valve replacement (meta-analysis: odds ratio, 3.78 [95% CI, 2.26-6.32]; P=4.0e-7). Carriers of protein-disrupting variants in APOB or PCSK9 had lower mean LDL-C (UKB: -32.3 mg/dL; P<5e-324) and lower risk of AS (meta-analysis: odds ratio, 0.49 [95% CI, 0.31-0.75]; P=0.001) and aortic valve replacement (meta-analysis: odds ratio, 0.54 [95% CI, 0.30-0.97]; P=0.04). Among 57 371 UKB imaging substudy participants, peak velocities across the aortic valve were greater in carriers of protein-disrupting variants in LDLR (+12.2 cm/s; P=1.6e-5) and lower in carriers of protein-disrupting variants in PCSK9 (-6.9 cm/s; P=0.022).

Conclusions: Rare genetic variants that confer lifelong higher or lower LDL-C levels are associated with substantially increased and decreased risk of AS, respectively. Early and sustained lipid-lowering therapy may slow or prevent AS development.

Keywords: aortic valve stenosis; cholesterol; genetics; lipids; lipoproteins, LDL; magnetic resonance imaging; receptors, LDL.

Figure 1.. Association of loss-of-function variants in LDLR, APOB and PCSK9 with low-density lipoprotein cholesterol and aortic stenosis in UK Biobank.

Panel A depicts the distributions of directly measured low-density lipoprotein cholesterol (LDL-C) taken at the UK Biobank baseline visit for participants who carried a predicted truncating variant (tv) in APOB (blue; 388 carriers), PCSK9 (magenta; 483 carriers) or LDLR (orange; 91 carriers), and participants who did not carry a predicted truncating variant in any of the aforementioned genes (noncarriers; grey; 384907 individuals). Statistical differences between variant carriers and noncarriers were evaluated using linear regression with variant carrier status, age, age², sex, genotyping array, and the first 10 genomic principal components as independent variables. Panel B depicts the distributions of directly measured LDL-C for carriers of variants that were predicted to be damaging by AlphaMissense (AM) in APOB (blue; 606 carriers), PCSK9 (magenta; 510 carriers) or LDLR (orange; 559 carriers). In panel C, the odds ratio for aortic stenosis is shown on the y axis and the mean difference in directly measured LDL-C (mg/dl) compared with noncarriers is shown on the x-axis for truncating variants. Odds ratios for aortic stenosis were estimated using Firth’s logistic regression with variant carrier status, age, age², sex, genotyping array and the first 10 genomic principal components as independent variables. Participants with either prevalent or incident aortic stenosis were included as cases and all available carriers were compared with 404294 noncarriers (LDLRtv: 98 carriers, 5440 total cases and 398952 controls; APOBtv: 401 carriers, 5433 total cases and 399262 controls; PCSK9tv: 514 carriers, 5434 total cases and 399374 controls). In panel D, results are similarly shown for variants that were predicted to be damaging by AlphaMissense (LDLR-AM: 594 carriers, 5450 total cases and 399438 controls; APOB-AM: 634 carriers, 5434 total cases and 399494 controls; PCSK9-AM: 527 total carriers, 5433 cases and 399388 controls; combined analysis of APOB-AM or PCSK9-AM (highlighted in blue): 1160 carriers, 5437 total cases and 400017 controls). AS, aortic stenosis.

Figure 2.. Associations of protein-disrupting variants in LDLR, APOB and PCSK9 with aortic stenosis in a meta-analysis of UK Biobank and All of Us

Associations of predicted truncating variants (tv), variants predicted to be damaging by AlphaMissense (AM) and the PCSK9 R46L variant with aortic stenosis were examined separately in UK Biobank (n = 421,049 after removing related individuals) and All of Us (n = 195,519 after removing related individuals) using Firth logistic regression with variant carrier status, age, age², sex, genotyping array and the first 10 genomic principal components as independent variables. Participants with either prevalent or incident aortic stenosis were included as cases. The results were combined in an inverse variance weighted meta-analysis based on effect estimates and P-values from the two datasets including a total of 616,568 participants. Wald confidence intervals are shown. CI, confidence interval.

Figure 3.. Association of loss-of-function variants in LDLR, PCSK9 and APOB with peak velocity across the aortic valve in 57,371 UK Biobank participants

The associations of predicted truncating variants (tv) and variants predicted to be damaging by AlphaMissense (AM) in LDLR, APOB or PCSK9 with peak velocity across the aortic valve were examined in 57,371 UK Biobank participants who had undergone cardiac magnetic resonance imaging. Burden testing for variants in APOB, LDLR, and PCSK9 was conducted using REGENIE v3.3 with peak velocity as the outcome, adjusting for the imaging device serial number, age, age², sex, genotyping array, and the first 10 genomic principal components. CI, confidence interval.

Figure 4.. Probability of incident aortic stenosis in carriers of rare protein-disrupting mutations in LDLR, APOB and PCSK9 in UK Biobank

The figure depicts the probability of aortic stenosis during a median of 13.6 [interquartile range 12.8–14.3] years of follow-up in participants who had no history of aortic stenosis at study enrollment and who were carriers of a predicted protein-disrupting variants in LDLR (red), in carriers of predicted protein-disrupting variants in APOB or PCSK9 (green), and in noncarriers (blue). P-values were derived with Cox proportional hazards models, comparing each variant carrier group separately with noncarriers and adjusting for sex, age at enrollment, the first 10 principal components and genotyping array.