Health research in the era of artificial intelligence: Advances in gene-editing study DOI Creative Commons
Mengyao Dai, Xiangyang Li, Qí Zhāng

et al.

Medicine Plus, Journal Year: 2024, Volume and Issue: 1(2), P. 100027 - 100027

Published: May 2, 2024

In recent years, gene editing technology, represented by clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) has made a revolutionary breakthrough. Base techniques developed from CRISPR/Cas9 technologies have demonstrated the ability to efficiently achieve single base substitutions at specific genomic sites without double-strand breaks. systems evolved rapidly over past few efficient single-base high-throughput screening, and in vitro vivo applications. particular, screening facilitated functional studies single-nucleotide resolution, offering unprecedented insights into genetic function. Meanwhile, rapid advancement of artificial intelligence (AI) is playing pivotal role assisting genome streamlining data analysis within systems. This review encompasses progress research, focusing on development technologies, exploring editing-based level, underscoring potential synergies between AI studies.

Language: Английский

Machine learning prediction of prime editing efficiency across diverse chromatin contexts DOI
Nicolas Mathis, Ahmed Allam, András Tálas

et al.

Nature Biotechnology, Journal Year: 2024, Volume and Issue: unknown

Published: June 21, 2024

Language: Английский

Citations

15
Recent advances in CRISPR-based functional genomics for the study of disease-associated genetic variants DOI Creative Commons
Heon Seok Kim, Jiyeon Kweon, Yongsub Kim

et al.

Experimental & Molecular Medicine, Journal Year: 2024, Volume and Issue: 56(4), P. 861 - 869

Published: April 1, 2024

Abstract Advances in sequencing technology have greatly increased our ability to gather genomic data, yet understanding the impact of genetic mutations, particularly variants uncertain significance (VUSs), remains a challenge precision medicine. The CRISPR‒Cas system has emerged as pivotal tool for genome engineering, enabling precise incorporation specific variations, including VUSs, into DNA facilitate their functional characterization. Additionally, integration with tools allows high-throughput evaluation transforming data actionable insights. This researchers comprehensively study consequences point paving way enhanced and increasing application review summarizes current editing utilizing systems combination genomics, focus on mutations.

Language: Английский

Citations

13
BacPE: a versatile prime-editing platform in bacteria by inhibiting DNA exonucleases DOI Creative Commons
Hongyuan Zhang, Jiacheng Ma, Zhaowei Wu

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Jan. 27, 2024

Abstract Prime editing allows precise installation of any single base substitution and small insertions deletions without requiring homologous recombination or double-strand DNA breaks in eukaryotic cells. However, the applications bacteria are hindered underlying mechanisms that impede efficient prime remain enigmatic. Here, we report determination vital cellular factors affect bacteria. Genetic screening 129 Escherichia coli transposon mutants identified sbcB , a 3ʹ→5ʹ exonuclease, as key genetic determinant impeding E. combinational which with two additional exonucleases, xseA exoX drastically enhanced efficiency by up to 100-fold. Efficient wild-type can be achieved simultaneously inhibiting exonucleases via CRISPRi. Our results pave way for versatile bacterial genome engineering.

Language: Английский

Citations

12
Revolutionizing in vivo therapy with CRISPR/Cas genome editing: breakthroughs, opportunities and challenges DOI Creative Commons

Arturo Macarrón Palacios,

Patrick Korus,

Bodo G. C. Wilkens

et al.

Frontiers in Genome Editing, Journal Year: 2024, Volume and Issue: 6

Published: Feb. 1, 2024

Genome editing using the CRISPR/Cas system has revolutionized field of genetic engineering, offering unprecedented opportunities for therapeutic applications in vivo . Despite numerous ongoing clinical trials focusing on ex genome editing, recent studies emphasize promise gene technology. However, it is worth noting that complete attainment inherent capabilities therapy humans yet to be accomplished. Before full realization potential, crucial achieve enhanced specificity selectively targeting defective cells while minimizing harm healthy cells. This review examines emerging studies, CRISPR/Cas-based pre-clinical and innovative approaches a wide range diseases. Furthermore, we cancer-specific sequences target genes associated with tumors, shedding light diverse strategies employed cancer treatment. We highlight various challenges explore their prospective translatability overcome these obstacles.

Language: Английский

Citations

11
Prime editing in plants: prospects and challenges DOI
Sanskriti Vats, Jitesh Kumar, Humira Sonah

et al.

Journal of Experimental Botany, Journal Year: 2024, Volume and Issue: 75(17), P. 5344 - 5356

Published: Feb. 16, 2024

Abstract Prime editors are reverse transcriptase (RT)-based genome-editing tools that utilize double-strand break (DSB)-free mechanisms to decrease off-target editing in genomes and enhance the efficiency of targeted insertions. The multiple prime have been developed within a short span time testament potential this technique for This is mainly because possibility generation all types mutations including deletions, insertions, transitions, transversions. reverses several bottlenecks gene technologies limit biotechnological applicability produce designer crops. review evaluates status evolution terms available up editor 5 twin editors, considers developments plants systematic manner. various factors affecting discussed detail, effects temperature, guide (peg)RNA, RT template amongst others. We discuss current obstructions, key challenges, resolutions associated with technique, consider future directions further improvements feasible elevate plants.

Language: Английский

Citations

9
High-throughput screening of human genetic variants by pooled prime editing DOI Creative Commons
Michael Herger, Christina M. Kajba, Megan Buckley

et al.

Cell Genomics, Journal Year: 2025, Volume and Issue: unknown, P. 100814 - 100814

Published: March 1, 2025

Language: Английский

Citations

1
Efficient prime editing in two-cell mouse embryos using PEmbryo DOI Creative Commons
Rebecca Kim, Ryan McNulty, Bradley Joyce

et al.

Nature Biotechnology, Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 6, 2024

Using transient inhibition of DNA mismatch repair during a permissive stage development, we demonstrate highly efficient prime editing mouse embryos with few unwanted, local byproducts (average 58% precise edit frequency, 0.5% on-target error frequency across 13 substitution edits at 8 sites), enabling same-generation phenotyping founders. Whole-genome sequencing reveals that increases off-target indels low-complexity regions in the genome without any obvious phenotype mice.

Language: Английский

Citations

8
Multimodal scanning of genetic variants with base and prime editing DOI Creative Commons
Olivier Belli, Kyriaki Karava, Rick Farouni

et al.

Nature Biotechnology, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 12, 2024

Mutational scanning connects genetic variants to phenotype, enabling the interrogation of protein functions, interactions and variant pathogenicity. However, current methodologies cannot efficiently engineer customizable sets diverse in endogenous loci across cellular contexts high throughput. Here, we combine cytosine adenine base editors a prime editor assess pathogenicity broad spectrum epithelial growth factor receptor gene (EGFR). Using pooled editing guide RNA libraries, install tens thousands spanning full coding sequence EGFR multiple cell lines role these tumorigenesis resistance tyrosine kinase inhibitors. Our scan identifies important hits, supporting robustness approach revealing underappreciated routes activation drug response. We anticipate that multimodal precision mutational can be applied broadly characterize variation any element interest at single-nucleotide resolution.

Language: Английский

Citations

8
Randomizing the human genome by engineering recombination between repeat elements DOI Creative Commons
Jonas Koeppel, Raphaël Ferreira,

Thomas Vanderstichele

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 23, 2024

Abstract While protein-coding genes are characterized increasingly well, 99% of the human genome is non-coding and poorly understood. This gap due to a lack tools for engineering variants that affect sequence necessary extent. To bridge this gap, we have developed toolbox create deletions, inversions, translocations, extrachromosomal circular DNA at scale by highly multiplexed insertion recombinase recognition sites into repetitive sequences with CRISPR prime editing. Using strategy, derived stable cell lines several thousand clonal insertions, highest number novel inserted single genomes. Subsequent induction generated an average more than one hundred megabase-sized rearrangements per cell, thousands across whole population. The ability detect as they track their abundance over time allowed us measure selection pressures acting on different types structural changes. We observed consolidation towards shorter preferentially delete growth-inhibiting depletion translocations. isolated 21 clones multiple recombinase-induced rearrangements. These included viable haploid deletions span hundreds kilobases well triploid HEK293T aneuploidies fold back chromosomes. mapped impact these genetic changes gene expression decipher how regulation. scrambling strategy here makes it possible megabases sequence, move between within chromosomes, implant regulatory elements new contexts which will shed light organization principles humans other species.

Language: Английский

Citations

7
A benchmarked, high-efficiency prime editing platform for multiplexed dropout screening DOI Creative Commons
Ann Cirincione, Danny Simpson, Weihao Yan

et al.

Nature Methods, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 19, 2024

Prime editing installs precise edits into the genome with minimal unwanted byproducts, but low and variable efficiencies have complicated application of approach to high-throughput functional genomics. Here we assembled a prime platform capable high-efficiency substitution suitable for interrogation small genetic variants. We benchmarked this pooled, loss-of-function screening using library ~240,000 engineered guide RNAs (epegRNAs) targeting ~17,000 codons 1–3 bp substitutions. Comparing abundance these epegRNAs across screen samples identified negative selection phenotypes 7,996 nonsense mutations targeted 1,149 essential genes synonymous that disrupted splice site motifs at 3′ exon boundaries. Rigorous evaluation codon-matched controls demonstrated were highly specific intended edit. Altogether, established multiplexed, characterization variants simple readouts. This work establishes (up tens thousands) phenotypes.

Language: Английский

Citations

6