Evidence map›Paper›PMID 38942756›Full record

ArticleNature communications2024

PAM-flexible Engineered FnCas9 variants for robust and ultra-precise genome editing and diagnostics.

Sundaram Acharya, Asgar Hussain Ansari, Prosad Kumar Das, Seiichi Hirano, Meghali Aich, Riya Rauthan, Sudipta Mahato, Savitri Maddileti, Sajal Sarkar, Manoj Kumar and 14 more

Abstract read
In one paragraph

Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.

0numbers the graph read from it
0cells of the map it votes in
16citing 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

16 citing papers in PubMed.

  1. Article
  2. Review
  3. How Genomic and Structural Context Could Shape JAK-STAT Variant Pathogenicity.Twin research and human genetics : the official journal of the International Society for Twin Studies · 2026
    Article
  4. Review
  5. Structure-Guided Engineering of a Cas12i Nuclease Unlocks Near-PAMless Genome Editing.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026
    Article
  6. Article
  7. Review
  8. Prime editing in mammals: From promise to practicalities.Molecular therapy. Nucleic acids · 2025
    Review
  9. Review
  10. Article
  11. Try before you buy: Empirical comparison of base editing approaches.Molecular therapy : the journal of the American Society of Gene Therapy · 2025
    Article
  12. Article
  13. Review
  14. Review
  15. Article
  16. Review
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

24 authors.

Sundaram AcharyaCSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India. acharyasundaram.ac@gmail.com.ORCID 0000-0001-5164-6328
Asgar Hussain AnsariCSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.ORCID 0000-0002-1172-9521
Prosad Kumar DasCSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.ORCID 0009-0008-6821-807X
Seiichi HiranoDepartment of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
Meghali AichCSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.
Riya RauthanCSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.
Sudipta MahatoCenter for Ocular Regeneration, Prof. Brien Holden Eye Research Centre, Hyderabad Eye Research Foundation, LV Prasad Eye Institute, Hyderabad, 500034, Telangana, India.
Savitri MaddiletiCenter for Ocular Regeneration, Prof. Brien Holden Eye Research Centre, Hyderabad Eye Research Foundation, LV Prasad Eye Institute, Hyderabad, 500034, Telangana, India.
Sajal SarkarCSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.
Manoj KumarCSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.
Rhythm PhutelaCSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.
Sneha GulatiCSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.
Abdul RahmanCSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.
Arushi GoelCSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.
C AfzalCSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.
Deepanjan PaulCSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.
Trupti AgrawalCenter for Ocular Regeneration, Prof. Brien Holden Eye Research Centre, Hyderabad Eye Research Foundation, LV Prasad Eye Institute, Hyderabad, 500034, Telangana, India.ORCID 0000-0002-2346-9958
Vinay Kumar PulimamidiCenter for Ocular Regeneration, Prof. Brien Holden Eye Research Centre, Hyderabad Eye Research Foundation, LV Prasad Eye Institute, Hyderabad, 500034, Telangana, India.
Subhadra JalaliSrimati Kannuri Santhamma Centre for vitreoretinal diseases, Anant Bajaj Retina Institute, Kallam Anji Reddy Campus, L V Prasad Eye Institute, Hyderabad, Telangana, India.
Hiroshi NishimasuDepartment of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.ORCID 0000-0002-2505-1416
Indumathi MariappanCenter for Ocular Regeneration, Prof. Brien Holden Eye Research Centre, Hyderabad Eye Research Foundation, LV Prasad Eye Institute, Hyderabad, 500034, Telangana, India.ORCID 0000-0001-7059-3030
Osamu NurekiDepartment of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.ORCID 0000-0003-1813-7008
Souvik MaitiCSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.
Debojyoti ChakrabortyCSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India. debojyoti.chakraborty@igib.in.ORCID 0000-0002-2300-4333

Funding

Lady Tata Memorial Trust GAP198
6 · The paper itself

Abstract

The clinical success of CRISPR therapies hinges on the safety and efficacy of Cas proteins. The Cas9 from Francisella novicida (FnCas9) is highly precise, with a negligible affinity for mismatched substrates, but its low cellular targeting efficiency limits therapeutic use. Here, we rationally engineer the protein to develop enhanced FnCas9 (enFnCas9) variants and broaden their accessibility across human genomic sites by ~3.5-fold. The enFnCas9 proteins with single mismatch specificity expanded the target range of FnCas9-based CRISPR diagnostics to detect the pathogenic DNA signatures. They outperform Streptococcus pyogenes Cas9 (SpCas9) and its engineered derivatives in on-target editing efficiency, knock-in rates, and off-target specificity. enFnCas9 can be combined with extended gRNAs for robust base editing at sites which are inaccessible to PAM-constrained canonical base editors. Finally, we demonstrate an RPE65 mutation correction in a Leber congenital amaurosis 2 (LCA2) patient-specific iPSC line using enFnCas9 adenine base editor, highlighting its therapeutic utility.

Indexed as

CRISPR-Associated Protein 9CRISPR-Cas SystemsFrancisellaGene EditingBacterial ProteinsGenome, HumanHEK293 CellsHumansLeber Congenital AmaurosisMutationProtein EngineeringRNA, Guide, CRISPR-Cas SystemsStreptococcus pyogenesBacterial ProteinsCas9 protein, Francisella novicidaCRISPR-Associated Protein 9RNA, Guide, CRISPR-Cas Systems

Identifiers

PMID38942756
PMCPMC11213958

What OpenQuestion holds

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LicenceCC BY
Read underepoch 390

Registered trials

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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.