Dataset Information

Rapid in vivo multiplexed editing (RIME) of the adult mouse liver.

ABSTRACT:

Background and aims

Assessing mammalian gene function in vivo has traditionally relied on manipulation of the mouse genome in embryonic stem cells or perizygotic embryos. These approaches are time-consuming and require extensive breeding when simultaneous mutations in multiple genes is desired. The aim of this study is to introduce a rapid in vivo multiplexed editing (RIME) method and provide proof of concept of this system.

Approach and results

RIME, a system wherein CRISPR/caspase 9 technology, paired with adeno-associated viruses (AAVs), permits the inactivation of one or more genes in the adult mouse liver. The method is quick, requiring as little as 1 month from conceptualization to knockout, and highly efficient, enabling editing in >95% of target cells. To highlight its use, we used this system to inactivate, alone or in combination, genes with functions spanning metabolism, mitosis, mitochondrial maintenance, and cell proliferation.

Conclusions

RIME enables the rapid, efficient, and inexpensive analysis of multiple genes in the mouse liver in vivo .

SUBMITTER: Katsuda T

PROVIDER: S-EPMC11088813 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature

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Publications

Rapid in vivo multiplexed editing (RIME) of the adult mouse liver.

Katsuda Takeshi T Katsuda Takeshi T Cure Hector H Sussman Jonathan J Simeonov Kamen P KP Krapp Christopher C Arany Zoltan Z Grompe Markus M Stanger Ben Z BZ

Hepatology (Baltimore, Md.) 20221013 2

<h4>Background and aims</h4>Assessing mammalian gene function in vivo has traditionally relied on manipulation of the mouse genome in embryonic stem cells or perizygotic embryos. These approaches are time-consuming and require extensive breeding when simultaneous mutations in multiple genes is desired. The aim of this study is to introduce a rapid in vivo multiplexed editing (RIME) method and provide proof of concept of this system.<h4>Approach and results</h4>RIME, a system wherein CRISPR/caspa ...[more]

PMID: 36037289

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Project description:Human genome sequencing efforts in healthy and diseased individuals continue to identify a broad spectrum of genetic variants associated with predisposition, progression, and therapeutic outcomes for diseases like cancer1-6. Insights derived from these studies have significant potential to guide clinical diagnoses and treatment decisions; however, the relative importance and functional impact of most genetic variants remain poorly understood. Precision genome editing technologies like base and prime editing can be used to systematically engineer and interrogate diverse types of endogenous genetic variants in their native context7-9. We and others have recently developed and applied scalable sensor-based screening approaches to engineer and measure the phenotypes produced by thousands of endogenous mutations in vitro 10-12. However, the impact of most genetic variants in the physiological in vivo setting, including contextual differences depending on the tissue or microenvironment, remains unexplored. Here, we integrate new cross-species base editing sensor libraries with syngeneic cancer mouse models to develop a multiplexed in vivo platform for systematic functional analysis of endogenous genetic variants in primary and disseminated malignancies. We used this platform to screen 13,840 guide RNAs designed to engineer 7,783 human cancer-associated mutations mapping to 489 endogenous protein-coding genes, allowing us to construct a rich compendium of putative functional interactions between genes, mutations, and physiological contexts. Our findings suggest that the physiological in vivo environment and cellular organotropism are important contextual determinants of specific gene-variant phenotypes. We also show that many mutations and their in vivo effects fail to be detected with standard CRISPR-Cas9 nuclease approaches and often produce discordant phenotypes, potentially due to site-specific amino acid selection- or separation-of-function mechanisms. This versatile platform could be deployed to investigate how genetic variation impacts diverse in vivo phenotypes associated with cancer and other genetic diseases, as well as identify new potential therapeutic avenues to treat human disease.

Dataset Information

Rapid in vivo multiplexed editing (RIME) of the adult mouse liver.

Background and aims

Approach and results

Conclusions

Publications

Rapid in vivo multiplexed editing (RIME) of the adult mouse liver.

Similar Datasets

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