{ "abstract": "BACKGROUND:: An estimated 1 in 500 people lives with hypertrophic cardiomyopathy (HCM), a disease for which genetic diagnosis can identify family members at risk and increasingly guide therapy. Variants in the MYBPC3 gene, which encodes cardiac myosin-binding protein C (cMyBP-C), account for a significant proportion of HCM cases. However, many of these are classified as variants of uncertain significance, complicating clinical decision-making. Scalable methods for variant interpretation in disease-specific cell types are crucial for understanding variant impact and uncovering disease mechanisms.\n\nMETHODS:: We developed a scaled multidimensional mapping strategy to evaluate the functional impact of variants across a critical domain of cMyBP-C. We incorporate saturation base editing at the native MYBPC3 locus, a long-read RNA sequencing-enabled assay of variant splice effects, and measurements of HCM-relevant phenotypes, including cMyBP-C abundance, hypertrophic signaling, and ubiquitin-proteasome function in human induced pluripotent stem cell–derived cardiomyocytes.\n\nRESULTS:: Our multidimensional mapping strategy enabled high-resolution functional analysis of MYBPC3 variants in induced pluripotent stem cell–derived cardiomyocytes. Our massively parallel splicing assay identified novel splice-disrupting variants. Targeted transient base editing generated a comprehensive variant library at the native locus, capturing diverse variant effects on cellular HCM-relevant phenotypes. Integration of functional assays revealed that decreased cMyBP-C abundance is a key driver of HCM-related phenotypes. In parallel, downregulation of protein degradation was observed to correlate with MYBPC3 loss of function, and novel potential disease mechanisms were identified for missense variants near a critical binding domain. Bayesian estimates of variant effects enable the reclassification of clinical variants.\n\nCONCLUSIONS:: This work provides a platform for extending genome engineering in induced pluripotent stem cells to multiplexed assays of variant effects across diverse disease-relevant cellular phenotypes, enhancing our understanding of variant pathogenicity and uncovering novel biological mechanisms that could inform therapeutic strategies.", "abstract_shown": true, "affiliations": [ "Stanford Center for Inherited Cardiovascular Disease, Department of Medicine, Division of Cardiovascular Medicine, (Y.Y., K.C., D.S., A.F., B.J.F., C.C., L.W., Q.W., J.E.G., Y.H., F.B., R.H.W., A.S., A.T., R.A., M.T.W., M.M., E.A.A., V.N.P.), Stanford School of Medicine, Palo Alto, CA.", "Department of Pediatrics (D.S., B.J.F.), Stanford School of Medicine, Palo Alto, CA.", "Medical Scientist Training Program, University of Pittsburgh, PA (A.K.).", "Department of Genetics (H.N.D.J., J.E.G.), Stanford School of Medicine, Palo Alto, CA.", "ETH Zurich, Switzerland (C.C.).", "School of Biomedical Engineering, Shanghai Jiao Tong University, China (Q.W.).", "Brigham and Women’s Hospital, HMS, Boston, MA (M.J.O., C.A.M.).", "Donnelly Centre and Department of Molecular Genetics, University of Toronto, ON, Canada (D.T., F.P.R.).", "University of Vermont, Larner College of Medicine, Burlington (A.T.).", "Department of Medicine, Department of Chemical and Systems Biology, and Cardiovascular Institute, Stanford University, Palo Alto, CA (M.M.).", "Department of Medicine, Division of Genomic Medicine and Clinical Pharmacology (D.M.R., A.M.G.), Vanderbilt University Medical Center, Nashville, TN.", "Department of Pharmacology (D.M.R.), Vanderbilt University Medical Center, Nashville, TN.", "Department of Biomedical Informatics (D.M.R.), Vanderbilt University Medical Center, Nashville, TN.", "Department of Computational and Systems Biology, University of Pittsburgh School of Medicine ; PA (F.P.R.)." ], "article_type": "research article", "arxiv": null, "author_total": 27, "authors": [ { "affs": [ 0 ], "name": "Yuta Yamamoto", "orcid": "0000-0001-6129-9745" }, { "affs": [ 0 ], "name": "Kaiser Chua", "orcid": "0009-0009-1730-6149" }, { "affs": [ 0, 1 ], "name": "David Staudt", "orcid": "0000-0002-3399-9311" }, { "affs": [ 0 ], "name": "Alexis Ferrasse" }, { "affs": [ 2 ], "name": "Anna Kirillova", "orcid": "0000-0003-2113-5257" }, { "affs": [ 3 ], "name": "Hannah N. De Jong", "orcid": "0000-0002-8699-9702" }, { "affs": [ 0, 1 ], "name": "Brendan J. Floyd", "orcid": "0000-0003-3185-0174" }, { "affs": [ 0, 4 ], "name": "Christian Cadisch", "orcid": "0009-0008-4822-312X" }, { "affs": [ 0 ], "name": "Laurens Wiel", "orcid": "0000-0003-3410-760X" }, { "affs": [ 0, 5 ], "name": "Qianru Wang", "orcid": "0000-0002-7219-7522" }, { "affs": [ 6 ], "name": "Matthew J. O’Neill" }, { "affs": [ 7 ], "name": "Daniel Tabet", "orcid": "0009-0006-5480-7733" }, { "affs": [ 0, 3 ], "name": "John E. Goryznski" }, { "affs": [ 0 ], "name": "Yong Huang", "orcid": "0009-0000-6727-4960" }, { "affs": [ 0 ], "name": "Fang Bai", "orcid": "0000-0003-0639-8104" }, { "affs": [ 0 ], "name": "Rachel H. Wilson", "orcid": "0000-0003-3114-7040" }, { "affs": [ 0 ], "name": "Arman Sharma" }, { "affs": [ 0, 8 ], "name": "Althea Tapales" }, { "affs": [ 0 ], "name": "Rani Agrawal" }, { "affs": [ 0 ], "name": "Matthew T. Wheeler", "orcid": "0000-0001-8721-3022" }, { "affs": [ 0, 9 ], "name": "Mark Mercola", "orcid": "0000-0002-1430-2013" }, { "affs": [ 6 ], "name": "Calum A. MacRae", "orcid": "0000-0001-5181-2664" }, { "affs": [ 10, 11, 12 ], "name": "Dan M. Roden", "orcid": "0000-0002-6302-0389" }, { "affs": [ 7, 13 ], "name": "Frederick P. Roth", "orcid": "0000-0002-6628-649X" }, { "affs": [ 10 ], "name": "Andrew M. Glazer", "orcid": "0000-0002-3938-4713" }, { "affs": [ 0 ], "name": "Euan A. Ashley", "orcid": "0000-0001-9418-9577" }, { "affs": [ 0 ], "name": "Victoria N. Parikh", "orcid": "0000-0002-5138-5559" } ], "bibtex": "https://research.draconitic.com/paper/0ecnnbm39efzk.bib", "cited_by": 4, "doi": "10.1161/circulationaha.125.075535", "fulltext_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13506205/", "id": "0ecnnbm39efzk", "issns": [ "0009-7322", "1524-4539" ], "landing_url": "https://doi.org/10.1161/circulationaha.125.075535", "language": "en", "licence": "CC-BY-NC-ND-4.0", "licence_label": "CC BY-NC-ND 4.0", "licence_source": "article", "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/", "metadata_licence": null, "native_subjects": [ [ "heading", "10014" ], [ "heading", "10035" ], [ "heading", "10052" ], [ "heading", "Original Research" ], [ "openalex", "2705|Cardiomyopathy and Myosin Studies" ] ], "openalex": "W4410768182", "pdf_url": null, "pmcid": "PMC13506205", "pmid": "42437345", "published": "2026-07-12", "publisher": null, "ris": "https://research.draconitic.com/paper/0ecnnbm39efzk.ris", "sources": [ { "first_seen": "2026-11-04T12:22:50Z", "native_id": "PMC13506205", "source": "pmc", "url": "https://doi.org/10.1161/circulationaha.125.075535" } ], "subjects": [ { "field": "medicine", "origin": "openalex:2705|Cardiomyopathy and Myosin Studies", "subfield": "cardiovascular" } ], "title": "Scaled Multidimensional Assays of Variant Effect Identify Sequence-Function Relationships in Hypertrophic Cardiomyopathy", "title_text": "Scaled Multidimensional Assays of Variant Effect Identify Sequence-Function Relationships in Hypertrophic Cardiomyopathy", "type": "peer-reviewed", "updated_at": "2026-11-06T12:20:46Z", "url": "https://research.draconitic.com/paper/0ecnnbm39efzk", "venue": "Circulation", "versions": [] }