Site-saturation mutagenesis of 500 human protein domains

Nature, Год журнала: 2025, Номер unknown

Опубликована: Янв. 8, 2025

Abstract Missense variants that change the amino acid sequences of proteins cause one-third human genetic diseases 1 . Tens millions missense exist in current population, and vast majority these have unknown functional consequences. Here we present a large-scale experimental analysis across many different proteins. Using DNA synthesis cellular selection experiments quantify effect more than 500,000 on abundance 500 protein domains. This dataset reveals 60% pathogenic reduce stability. The contribution stability to fitness varies is particularly important recessive disorders. We combine measurements with language models annotate sites Mutational effects are largely conserved homologous domains, enabling accurate prediction entire families using energy models. Our data demonstrate feasibility assaying at scale provides large consistent reference for clinical variant interpretation training benchmarking computational methods.

Язык: Английский

---

Variant effect predictor correlation with functional assays is reflective of clinical classification performance

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Май 14, 2024

Abstract Understanding the relationship between protein sequence and function is crucial for accurate genetic variant classification. Variant effect predictors (VEPs) play a vital role in deciphering this complex relationship, yet evaluating their performance remains challenging due to data circularity, where same or related used training assessment. High-throughput experimental strategies like deep mutational scanning (DMS) offer promising solution. In study, we extend upon our previous benchmarking approach, assessing of 84 different VEPs DMS experiments from 36 human proteins. addition, new pairwise, VEP-centric ranking method reduces impact VEP score availability on overall ranking. We observe remarkably high correspondence DMS-based benchmarks clinical classification, especially that have not been directly trained variants. Our results suggest comparing against diverse functional assays represents reliable strategy relative However, major challenges interpretation scores persist, highlighting need further research fully leverage computational diagnosis. also address practical considerations end users terms choice methodology.

Язык: Английский

---

Site saturation mutagenesis of 500 human protein domains reveals the contribution of protein destabilization to genetic disease

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Апрель 29, 2024

Abstract Missense variants that change the amino acid sequences of proteins cause one third human genetic diseases 1 . Tens millions missense exist in current population, with vast majority having unknown functional consequences. Here we present first large-scale experimental analysis across many different proteins. Using DNA synthesis and cellular selection experiments quantify impact >500,000 on abundance >500 protein domains. This dataset, Human Domainome 1, reveals >60% pathogenic reduce stability. The contribution stability to fitness varies diseases, is particularly important recessive disorders. Combining measurements language models annotates sites Mutational effects are largely conserved homologous domains, allowing accurate prediction entire families using energy models. demonstrates feasibility assaying at scale provides a large consistent reference dataset for clinical variant interpretation training benchmarking computational methods.

Язык: Английский

---

Pervasive ancestry bias in variant effect predictors

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Май 22, 2024

ABSTRACT Computational variant effect predictors (VEPs) are playing increasingly important roles in the interpretation of human genetic variants. We observe striking differences ways that many VEPs score variants from European compared to non-European populations. advocate for adoption population-free VEPs, i.e. those not trained on population or clinical variants, improve health equity and enhance accuracy diagnoses across diverse

Язык: Английский

---

High resolution deep mutational scanning of the melanocortin-4 receptor enables target characterization for drug discovery

Опубликована: Фев. 18, 2025

Deep Mutational Scanning (DMS) is an emerging method to systematically test the functional consequences of thousands sequence changes a protein target in single experiment. Because its utility interpreting both human variant effects and structure-function relationships, it holds substantial promise improve drug discovery clinical development. However, applications this domain require improved experimental analytical methods. To address need, we report novel DMS methods precisely quantitatively interrogate disease-relevant mechanisms, protein-ligand interactions, assess predicted response treatment. Using these methods, performed melanocortin-4 receptor (MC4R), G protein-coupled (GPCR) implicated obesity active development efforts. We assessed >6,600 amino acid substitutions on MC4R’s function across 18 distinct conditions, resulting >20 million unique measurements. From this, identified variants that have MC4R-mediated Gα s - q -signaling pathways, which could be used design drugs selectively bias activity. also pathogenic are likely amenable corrector therapy. Finally, functionally characterized structural relationships distinguish binding peptide versus small molecule ligands, guide compound optimization. Collectively, results demonstrate powerful empower

Язык: Английский

---

High-resolution deep mutational scanning of the melanocortin-4 receptor enables target characterization for drug discovery

eLife, Год журнала: 2025, Номер 13

Опубликована: Апрель 9, 2025

Deep Mutational Scanning (DMS) is an emerging method to systematically test the functional consequences of thousands sequence changes a protein target in single experiment. Because its utility interpreting both human variant effects and structure-function relationships, it holds substantial promise improve drug discovery clinical development. However, applications this domain require improved experimental analytical methods. To address need, we report novel DMS methods precisely quantitatively interrogate disease-relevant mechanisms, protein-ligand interactions, assess predicted response treatment. Using these methods, performed melanocortin-4 receptor (MC4R), G-protein-coupled (GPCR) implicated obesity active development efforts. We assessed >6600 amino acid substitutions on MC4R’s function across 18 distinct conditions, resulting >20 million unique measurements. From this, identified variants that have MC4R-mediated Gα s - q -signaling pathways, which could be used design drugs selectively bias activity. also pathogenic are likely amenable corrector therapy. Finally, functionally characterized structural relationships distinguish binding peptide versus small molecule ligands, guide compound optimization. Collectively, results demonstrate powerful empower

Язык: Английский

---

High resolution deep mutational scanning of the melanocortin-4 receptor enables target characterization for drug discovery

Опубликована: Дек. 19, 2024

Deep Mutational Scanning (DMS) is an emerging method to systematically test the functional consequences of thousands sequence changes a protein target in single experiment. Because its utility interpreting both human variant effects and structure-function relationships, it holds substantial promise improve drug discovery clinical development. However, applications this domain require improved experimental analytical methods. To address need, we report novel DMS methods precisely quantitatively interrogate disease-relevant mechanisms, protein-ligand interactions, assess predicted response treatment. Using these methods, performed melanocortin-4 receptor (MC4R), G protein-coupled (GPCR) implicated obesity active development efforts. We assessed >6,600 amino acid substitutions on MC4R’s function across 18 distinct conditions, resulting >20 million unique measurements. From this, identified variants that have MC4R-mediated Gα s - q -signaling pathways, which could be used design drugs selectively bias activity. also pathogenic are likely amenable corrector therapy. Finally, functionally characterized structural relationships distinguish binding peptide versus small molecule ligands, guide compound optimization. Collectively, results demonstrate powerful empower

Язык: Английский

---

High resolution deep mutational scanning of the melanocortin-4 receptor enables target characterization for drug discovery

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Окт. 12, 2024

Abstract Deep Mutational Scanning (DMS) is an emerging method to systematically test the functional consequences of thousands sequence changes a protein target in single experiment. Because its utility interpreting both human variant effects and structure-function relationships, it holds substantial promise improve drug discovery clinical development. However, applications this domain require improved experimental analytical methods. To address need, we report novel DMS methods precisely quantitatively interrogate disease-relevant mechanisms, protein-ligand interactions, assess predicted response treatment. Using these methods, performed melanocortin-4 receptor (MC4R), G protein-coupled (GPCR) implicated obesity active development efforts. We assessed >6,600 amino acid substitutions on MC4R’s function across 18 distinct conditions, resulting >20 million unique measurements. From this, identified variants that have MC4R-mediated Gα s - q -signaling pathways, which could be used design drugs selectively bias activity. also pathogenic are likely amenable corrector therapy. Finally, functionally characterized structural relationships distinguish binding peptide versus small molecule ligands, guide compound optimization. Collectively, results demonstrate powerful empower

Язык: Английский

---

LOL-EVE: Predicting Promoter Variant Effects from Evolutionary Sequences

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Ноя. 12, 2024

Abstract Genetic studies reveal extensive disease-associated variation across the human genome, predominantly in noncoding regions, such as promoters. Quantifying impact of these variants on disease risk is crucial to our understanding underlying mechanisms and advancing personalized medicine. However, current computational methods struggle capture variant effects, particularly those insertions deletions (indels), which can significantly disrupt gene expression. To address this challenge, we present LOL-EVE (Language Of Life EVolutionary Effects), a conditional autoregressive transformer model trained 14.6 million diverse mammalian promoter sequences. Leveraging evolutionary information proximal genetic context, predicts indel effects regions. We introduce three new benchmarks for effect prediction comprising identification causal eQTLs, prioritization rare population, disruptions transcription factor binding sites. find that achieves state-of-the-art performance tasks, demonstrating potential region-specific large genomic language models offering powerful tool prioritizing potentially non-coding studies.

Язык: Английский

---

Toward trustable use of machine learning models of variant effects in the clinic

The American Journal of Human Genetics, Год журнала: 2024, Номер unknown

Опубликована: Ноя. 1, 2024

Язык: Английский

---