Clinical Utility of Protein Language Models in Resolution of Variants of Uncertain Significance in KCNQ1, KCNH2 , and SCN5A Compared With Patch-Clamp Functional Characterization.

Autor:	Ye D; Department of Molecular Pharmacology and Experimental Therapeutics (Windland Smith Rice Sudden Death Genomics Laboratory). Department of Cardiovascular Medicine, Division of Heart Rhythm Services (Windland Smith Rice Genetic Heart Rhythm Clinic). Department of Pediatric and Adolescent Medicine, Division of Pediatric Cardiology, Mayo Clinic., Garmany R; Department of Molecular Pharmacology and Experimental Therapeutics (Windland Smith Rice Sudden Death Genomics Laboratory). Department of Cardiovascular Medicine, Division of Heart Rhythm Services (Windland Smith Rice Genetic Heart Rhythm Clinic). Department of Pediatric and Adolescent Medicine, Division of Pediatric Cardiology, Mayo Clinic., Martinez-Barrios E; Department of Molecular Pharmacology and Experimental Therapeutics (Windland Smith Rice Sudden Death Genomics Laboratory). Department of Cardiovascular Medicine, Division of Heart Rhythm Services (Windland Smith Rice Genetic Heart Rhythm Clinic). Department of Pediatric and Adolescent Medicine, Division of Pediatric Cardiology, Mayo Clinic., Gao X; Department of Molecular Pharmacology and Experimental Therapeutics (Windland Smith Rice Sudden Death Genomics Laboratory). Department of Cardiovascular Medicine, Division of Heart Rhythm Services (Windland Smith Rice Genetic Heart Rhythm Clinic). Department of Pediatric and Adolescent Medicine, Division of Pediatric Cardiology, Mayo Clinic., Neves RAL; Department of Molecular Pharmacology and Experimental Therapeutics (Windland Smith Rice Sudden Death Genomics Laboratory). Department of Cardiovascular Medicine, Division of Heart Rhythm Services (Windland Smith Rice Genetic Heart Rhythm Clinic). Department of Pediatric and Adolescent Medicine, Division of Pediatric Cardiology, Mayo Clinic., Tester DJ; Department of Molecular Pharmacology and Experimental Therapeutics (Windland Smith Rice Sudden Death Genomics Laboratory). Department of Cardiovascular Medicine, Division of Heart Rhythm Services (Windland Smith Rice Genetic Heart Rhythm Clinic). Department of Pediatric and Adolescent Medicine, Division of Pediatric Cardiology, Mayo Clinic., Bains S; Department of Molecular Pharmacology and Experimental Therapeutics (Windland Smith Rice Sudden Death Genomics Laboratory). Department of Cardiovascular Medicine, Division of Heart Rhythm Services (Windland Smith Rice Genetic Heart Rhythm Clinic). Department of Pediatric and Adolescent Medicine, Division of Pediatric Cardiology, Mayo Clinic., Zhou W; Department of Molecular Pharmacology and Experimental Therapeutics (Windland Smith Rice Sudden Death Genomics Laboratory). Department of Cardiovascular Medicine, Division of Heart Rhythm Services (Windland Smith Rice Genetic Heart Rhythm Clinic). Department of Pediatric and Adolescent Medicine, Division of Pediatric Cardiology, Mayo Clinic., Giudicessi JR; Department of Molecular Pharmacology and Experimental Therapeutics (Windland Smith Rice Sudden Death Genomics Laboratory). Department of Cardiovascular Medicine, Division of Heart Rhythm Services (Windland Smith Rice Genetic Heart Rhythm Clinic). Department of Pediatric and Adolescent Medicine, Division of Pediatric Cardiology, Mayo Clinic., Ackerman MJ; Department of Molecular Pharmacology and Experimental Therapeutics (Windland Smith Rice Sudden Death Genomics Laboratory). Department of Cardiovascular Medicine, Division of Heart Rhythm Services (Windland Smith Rice Genetic Heart Rhythm Clinic). Department of Pediatric and Adolescent Medicine, Division of Pediatric Cardiology, Mayo Clinic.
Jazyk:	angličtina
Zdroj:	Circulation. Genomic and precision medicine [Circ Genom Precis Med] 2024 Oct; Vol. 17 (5), pp. e004584. Date of Electronic Publication: 2024 Aug 09.
DOI:	10.1161/CIRCGEN.124.004584
Abstrakt:	Background: Genetic testing for cardiac channelopathies is the standard of care. However, many rare genetic variants remain classified as variants of uncertain significance (VUS) due to lack of epidemiological and functional data. Whether deep protein language models may aid in VUS resolution remains unknown. Here, we set out to compare how 2 deep protein language models perform at VUS resolution in the 3 most common long-QT syndrome-causative genes compared with the gold-standard patch clamp. Methods: A total of 72 rare nonsynonymous VUS (9 KCNQ1, 19 KCNH2 , and 50 SCN5A ) were engineered by site-directed mutagenesis and expressed in either HEK293 cells or TSA201 cells. Whole-cell patch-clamp technique was used to functionally characterize these variants. The protein language models, evolutionary scale modeling, version 1b and AlphaMissense, were used to predict the variant effect of missense variants and compared with patch clamp. Results: Considering variants in all 3 genes, the evolutionary scale modeling, version 1b model had a receiver operating characteristic curve-area under the curve of 0.75 ( P =0.0003). It had a sensitivity of 88% and a specificity of 50%. AlphaMissense performed well compared with patch-clamp with an receiver operating characteristic curve-area under the curve of 0.85 ( P <0.0001), sensitivity of 80%, and specificity of 76%. Conclusions: Deep protein language models aid in VUS resolution with high sensitivity but lower specificity. Thus, these tools cannot fully replace functional characterization but can aid in reducing the number of variants that may require functional analysis. Competing Interests: Dr Ackerman is a consultant for Abbott, BioMarin Pharmaceutical, Boston Scientific, Bristol Myers Squibb, Daiichi Sankyo, Illumina, Invitae, Medtronic, Solid Biosciences, Tenaya Therapeutics, and UpToDate. Dr Ackerman and Mayo Clinic are involved in an equity/intellectual property/royalty relationship with AliveCor, Anumana, ARMGO Pharma, Pfizer, and Thryv Therapeutics. However, none of these entities have contributed to this study in any manner. The other authors report no conflicts.
Databáze:	MEDLINE
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