Evidence map›Paper›PMID 39747875›Full record

ArticleNature communications2025

Rational engineering of minimally immunogenic nucleases for gene therapy.

Rumya Raghavan, Mirco J Friedrich, Indigo King, Samuel Chau-Duy-Tam Vo, Daniel Strebinger, Blake Lash, Michael Kilian, Michael Platten, Rhiannon K Macrae, Yifan Song and 2 more

Abstract read
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.

0numbers the graph read from it
0cells of the map it votes in
25citing 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

25 citing papers in PubMed.

  1. Review
  2. Article
  3. Review
  4. Article
  5. A primer on prime: A prime editing update from advances to first-in-human trial.Molecular therapy : the journal of the American Society of Gene Therapy · 2026
    Review
  6. Review
  7. Review
  8. Article
  9. Review
  10. Review
  11. Epigenome editing based treatment: Progresses and challenges.Molecular therapy : the journal of the American Society of Gene Therapy · 2026
    Review
  12. Review
  13. Review
  14. Enhanced cleavage of genomicRNA biology · 2025
    Article
  15. Treating Hearing Loss: From Cochlear Implantation to Gene Therapy.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025
    Review
  16. Review
  17. Peeling back the layers of immunogenicity in Cas9-based genomic medicine.Molecular therapy : the journal of the American Society of Gene Therapy · 2025
    Review
  18. Review
  19. AAV2 delivery of theMolecular therapy. Methods & clinical development · 2025
    Article
  20. 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

12 authors.

Rumya Raghavan *Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
Mirco J Friedrich *Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
Indigo KingCyrus Biotechnology, Seattle, WA, 98121, USA.ORCID 0009-0003-3048-4763
Samuel Chau-Duy-Tam VoBroad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.ORCID 0000-0001-6020-4716
Daniel StrebingerBroad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.ORCID 0000-0001-8732-6414
Blake LashBroad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.ORCID 0000-0003-2445-7948
Michael KilianClinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, DKFZ, Heidelberg, Germany.ORCID 0000-0002-1946-3174
Michael PlattenClinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, DKFZ, Heidelberg, Germany.ORCID 0000-0002-4746-887X
Rhiannon K MacraeBroad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.ORCID 0000-0002-7850-9056
Yifan SongCyrus Biotechnology, Seattle, WA, 98121, USA.
Lucas NivonCyrus Biotechnology, Seattle, WA, 98121, USA.
Feng ZhangBroad Institute of MIT and Harvard, Cambridge, MA, 02142, USA. zhang@broadinstitute.org.ORCID 0000-0003-0178-7995

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Genome editing using CRISPR-Cas systems is a promising avenue for the treatment of genetic diseases. However, cellular and humoral immunogenicity of genome editing tools, which originate from bacteria, complicates their clinical use. Here we report reduced immunogenicity (Red)(i)-variants of two clinically relevant nucleases, SaCas9 and AsCas12a. Through MHC-associated peptide proteomics (MAPPs) analysis, we identify putative immunogenic epitopes on each nuclease. Using computational modeling, we rationally design these proteins to evade the immune response. SaCas9 and AsCas12a Redi variants are substantially less recognized by adaptive immune components, including reduced binding affinity to MHC molecules and attenuated generation of cytotoxic T cell responses, yet maintain wild-type levels of activity and specificity. In vivo editing of PCSK9 with SaCas9.Redi.1 is comparable in efficiency to wild-type SaCas9, but significantly reduces undesired immune responses. This demonstrates the utility of this approach in engineering proteins to evade immune detection.

Indexed as

CRISPR-Cas SystemsGene EditingGenetic TherapyAnimalsCRISPR-Associated Protein 9EndonucleasesEpitopesFemaleHEK293 CellsHumansMiceProprotein Convertase 9Protein EngineeringT-Lymphocytes, CytotoxicCRISPR-Associated Protein 9EndonucleasesEpitopesPCSK9 protein, humanProprotein Convertase 9

Identifiers

PMID39747875
PMCPMC11696374

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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.