Multiplexed in vivo base editing identifies functional gene-variant-context interactions DOI Creative Commons
Jonuelle Acosta,

Grace A. Johnson,

Samuel I. Gould

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 26, 2025

Human genome sequencing efforts in healthy and diseased individuals continue to identify a broad spectrum of genetic variants associated with predisposition, progression, therapeutic outcomes for diseases like cancer 1-6 . Insights derived from these studies have significant potential guide clinical diagnoses treatment decisions; however, the relative importance functional impact most remain poorly understood. Precision editing technologies base prime can be used systematically engineer interrogate diverse types endogenous their native context 7-9 We others recently developed applied scalable sensor-based screening approaches measure phenotypes produced by thousands mutations vitro 10-12 However, physiological vivo setting, including contextual differences depending on tissue or microenvironment, remains unexplored. Here, we integrate new cross-species sensor libraries syngeneic mouse models develop multiplexed platform systematic analysis primary disseminated malignancies. this screen 13,840 RNAs designed 7,783 human cancer-associated mapping 489 protein-coding genes, allowing us construct rich compendium putative interactions between mutations, contexts. Our findings suggest that environment cellular organotropism are important determinants specific gene-variant phenotypes. also show many effects fail detected standard CRISPR-Cas9 nuclease often produce discordant phenotypes, potentially due site-specific amino acid selection- separation-of-function mechanisms. This versatile could deployed investigate how variation impacts other diseases, as well avenues treat disease.

Language: Английский

Multiplexed in vivo base editing identifies functional gene-variant-context interactions DOI Creative Commons
Jonuelle Acosta,

Grace A. Johnson,

Samuel I. Gould

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 26, 2025

Human genome sequencing efforts in healthy and diseased individuals continue to identify a broad spectrum of genetic variants associated with predisposition, progression, therapeutic outcomes for diseases like cancer 1-6 . Insights derived from these studies have significant potential guide clinical diagnoses treatment decisions; however, the relative importance functional impact most remain poorly understood. Precision editing technologies base prime can be used systematically engineer interrogate diverse types endogenous their native context 7-9 We others recently developed applied scalable sensor-based screening approaches measure phenotypes produced by thousands mutations vitro 10-12 However, physiological vivo setting, including contextual differences depending on tissue or microenvironment, remains unexplored. Here, we integrate new cross-species sensor libraries syngeneic mouse models develop multiplexed platform systematic analysis primary disseminated malignancies. this screen 13,840 RNAs designed 7,783 human cancer-associated mapping 489 protein-coding genes, allowing us construct rich compendium putative interactions between mutations, contexts. Our findings suggest that environment cellular organotropism are important determinants specific gene-variant phenotypes. also show many effects fail detected standard CRISPR-Cas9 nuclease often produce discordant phenotypes, potentially due site-specific amino acid selection- separation-of-function mechanisms. This versatile could deployed investigate how variation impacts other diseases, as well avenues treat disease.

Language: Английский

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