Evidence map›Paper›PMID 39437714›Full record

ArticleCell reports methods2024

Computationally guided high-throughput engineering of an anti-CRISPR protein for precise genome editing in human cells.

Julia Marsiglia, Kia Vaalavirta, Estefany Knight, Muneaki Nakamura, Le Cong, Nicholas W Hughes

Abstract read
In one paragraph

Article in Cell reports methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

5 citing papers in PubMed.

  1. Review
  2. Review
  3. Protective antigen-mediated delivery of an anti-CRISPR protein for precision genome editing.Proceedings of the National Academy of Sciences of the United States of America · 2025
    Article
  4. Recommendations for robust and reproducible research on ferroptosis.Nature reviews. Molecular cell biology · 2025
    Review
  5. Mechanism of Cas9 inhibition by AcrIIA11.Nucleic acids research · 2025
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors.

Julia MarsigliaAcrobat Genomics, Inc., San Carlos, CA 94070, USA.
Kia VaalavirtaAcrobat Genomics, Inc., San Carlos, CA 94070, USA.
Estefany KnightAcrobat Genomics, Inc., San Carlos, CA 94070, USA.
Muneaki NakamuraAcrobat Genomics, Inc., San Carlos, CA 94070, USA.
Le CongDepartment of Pathology, Stanford University School of Medicine, Stanford, CA 94035, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94035, USA.
Nicholas W HughesAcrobat Genomics, Inc., San Carlos, CA 94070, USA. Electronic address: nick.hughes@acrobatgenomics.com.

Funding

High-throughput optimization of gene editing systems for treating Amyotrophic lateral sclerosisR43AG088777 · NIA · ACROBAT GENOMICS, INC. · PI HUGHES, NICHOLAS · 2024 to 2025
$500k
NIA NIH HHS R43 AG088777
6 · The paper itself

Abstract

The application of CRISPR-Cas systems to genome editing has revolutionized experimental biology and is an emerging gene and cell therapy modality. CRISPR-Cas systems target off-target regions within the human genome, which is a challenge that must be addressed. Phages have evolved anti-CRISPR proteins (Acrs) to evade CRISPR-Cas-based immunity. Here, we engineer an Acr (AcrIIA4) to increase the precision of CRISPR-Cas-based genome targeting. We developed an approach that leveraged (1) computational guidance, (2) deep mutational scanning, and (3) highly parallel DNA repair measurements within human cells. In a single experiment, ∼10,000 Acr variants were tested. Variants that improved editing precision were tested in additional validation experiments that revealed robust enhancement of gene editing precision and synergy with a high-fidelity version of Cas9. This scalable high-throughput screening framework is a promising methodology to engineer Acrs to increase gene editing precision, which could be used to improve the safety of gene editing-based therapeutics.

Indexed as

CRISPR-Cas SystemsGene EditingCRISPR-Associated Protein 9DNA RepairGenome, HumanHEK293 CellsHumansCRISPR-Associated Protein 9anti-CRISPRCP: biotechnologydeep mutational scangene editinghigh-throughput screeningprotein language model

Identifiers

PMID39437714
PMCPMC11574282

What OpenQuestion holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.