Computational prediction of protein subdomain stability in MYBPC3 enables clinical risk stratification in hypertrophic cardiomyopathy and enhances variant interpretation

Abstract

Purpose Variants in MYBPC3 causing loss of function are the most common cause of hypertrophic cardiomyopathy (HCM). However, a substantial number of patients carry missense variants of uncertain significance (VUS) in MYBPC3. We hypothesize that a structural-based algorithm, STRUM, which estimates the effect of missense variants on protein folding, will identify a subgroup of HCM patients with a MYBPC3 VUS associated with increased clinical risk. Methods Among 7,963 patients in the multicenter Sarcomeric Human Cardiomyopathy Registry (SHaRe), 120 unique missense VUS in MYBPC3 were identified. Variants were evaluated for their effect on subdomain folding and a stratified time-to-event analysis for an overall composite endpoint (first occurrence of ventricular arrhythmia, heart failure, all-cause mortality, atrial fibrillation, and stroke) was performed for patients with HCM and a MYBPC3 missense VUS. Results We demonstrated that patients carrying a MYBPC3 VUS predicted to cause subdomain misfolding (STRUM+, ΔΔG ≤ −1.2 kcal/mol) exhibited a higher rate of adverse events compared with those with a STRUM- VUS (hazard ratio = 2.29, P = 0.0282). In silico saturation mutagenesis of MYBPC3 identified 4,943/23,427 (21%) missense variants that were predicted to cause subdomain misfolding. Conclusion STRUM identifies patients with HCM and a MYBPC3 VUS who may be at higher clinical risk and provides supportive evidence for pathogenicity.

Amino acid substitutions hydrophilizing the core of titin domains cause dilated cardiomyopathy

“…We anticipate this approach can contribute to reduce the number of DCM patients with unexplained genetic etiology and to inform development of tailored, mechanismbased preventive and therapeutic strategies 3 . Specifically, we envision that emerging high-throughput in silico [46][47][48][49] and in vitro 50 methods will be able to capture pathogenicity potential related to domain destabilization of all possible titin missense variants. Identification of these pathogenic variants is a prerequisite for the development of therapies able to counterbalance domain destabilization, including strategies based on exon skipping 51 or pharmacological chaperones 52 .…”

Basic science methods for the characterization of variants of uncertain significance in hypertrophic cardiomyopathy

“…Other tools utilize high-resolution structural data of proteins and the effect that mutations have on protein folding and stability to predict their pathogenicity ( 37 ). A study of people with MYBPC3 VUS using the STRUM tool (evaluating the change in free energy of domain folding upon introduction of a mutation) showed that mutations that produced misfolding were associated with lower event-free survival ( 38 ).…”

Bringing into focus the central domains C3-C6 of myosin binding protein C

“…Most HCM-causing mutations within MYBPC3 are missense mutations that are expected to incorporate into the sarcomere, suggesting that these domains have a direct effect on regulatory function ( Flashman et al, 2004 ; Helms et al, 2020 ; Thompson et al, 2021 ). Surprisingly, the central domains C3, C5, and C6 are among the most highly mutated regions in MYBPC3 and are hotspots for pathogenic HCM variants ( Desai et al, 2022 ).…”