Evidence map›Paper›PMID 39369271›Full record

ArticleMolecular therapy : the journal of the American Society of Gene Therapy2024

AAV-mediated genome editing is influenced by the formation of R-loops.

Francesco Puzzo, Magdalena P Crossley, Aranyak Goswami, Feijie Zhang, Katja Pekrun, Jada L Garzon, Karlene A Cimprich, Mark A Kay

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Molecular therapy : the journal of the American Society of Gene Therapy, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. Article
  2. Article
  3. Review
  4. R-loops facilitate AAV-mediated nuclease-free gene targeting.Molecular therapy : the journal of the American Society of Gene Therapy · 2024
    Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

8 authors.

Francesco PuzzoDepartment of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.
Magdalena P CrossleyDepartment of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA.
Aranyak GoswamiDepartment of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.
Feijie ZhangDepartment of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.
Katja PekrunDepartment of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.
Jada L GarzonDepartment of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA.
Karlene A CimprichDepartment of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA.
Mark A KayDepartment of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA. Electronic address: markay@stanford.edu.

Funding

HEPATIC GENE TRANSFER FOR TREATMENT OF HEMOPHILIAS A &BR01HL064274 · NHLBI · STANFORD UNIVERSITY · PI Mark A Kay · 2000 to 2026
$13.6M
Transcription-Associated Genome InstabilityR01GM119334 · NIGMS · STANFORD UNIVERSITY · PI Karlene A Cimprich · 2016 to 2026
$4.0M
Molecular Pharmacology Training ProgramT32GM136631 · NIGMS · STANFORD UNIVERSITY · PI BOGYO, MATTHEW, CHEN, JAMES K · 2021 to 2025
$2.0M
BINDING OF MTP TO APOB DURING LIPOPROTEIN ASSEMBLYR01HL064272 · NHLBI · SUNY DOWNSTATE MEDICAL CENTER · PI HUSSAIN, M MAHMOOD · 1999 to 2006
$1.8M
High Throughput DNA Sequencer UpgradeS10OD018220 · OD · STANFORD UNIVERSITY · PI COLLER, JOHN · 2014 to 2014
$596k
Computer ClusterS10OD021763 · OD · STANFORD UNIVERSITY · PI JI, HANLEE P · 2016 to 2016
$481k
NHLBI NIH HHS R01 HL064272NHLBI NIH HHS R01 HL064274NIGMS NIH HHS R01 GM119334NIGMS NIH HHS T32 GM136631NIH HHS S10 OD018220NIH HHS S10 OD021763
6 · The paper itself

Abstract

Recombinant adeno-associated viral vectors (rAAV) hold an intrinsic ability to stimulate homologous recombination (AAV-HR) and are the most used in clinical settings for in vivo gene therapy. However, rAAVs also integrate throughout the genome. Here, we describe DNA-RNA immunoprecipitation sequencing (DRIP-seq) in murine HEPA1-6 hepatoma cells and whole murine liver to establish the similarities and differences in genomic R-loop formation in a transformed cell line and intact tissue. We show enhanced AAV-HR in mice upon genetic and pharmacological upregulation of R-loops. Selecting the highly expressed Albumin gene as a model locus for genome editing in both in vitro and in vivo experiments showed that the R-loop prone 3' end of Albumin was efficiently edited by AAV-HR, whereas the upstream R-loop-deficient region did not result in detectable vector integration. In addition, we found a positive correlation between previously reported off-target rAAV integration sites and R-loop enriched genomic regions. Thus, we conclude that high levels of R-loops, present in highly transcribed genes, may promote rAAV vector genome integration. These findings may shed light on potential mechanisms for improving the safety and efficacy of genome editing by modulating R-loops and may enhance our ability to predict regions most susceptible to off-target insertional mutagenesis by rAAV vectors.

Indexed as

DependovirusGene EditingGenetic VectorsR-Loop StructuresAnimalsCell Line, TumorGenetic TherapyHomologous RecombinationHumansMiceAAVgene editinghomologous recombinationin vivo DRIP-seqliver gene therapyR-loopsvector integration

Identifiers

PMID39369271
PMCPMC11638834

What OpenQuestion holds

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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.