Collection | 10 November 2017

Genome engineering

The ever-improving knowledge of the organization and composition of the genome and the epigenome, together with the expanding technological toolbox for the manipulation of DNA with increasing precision, are propelling the exploration of how genome-engineering approaches can be translated to tackle diseases that escape conventional therapies. [Editorial]

This Collection is updated when relevant new content is published. Content appears in reverse chronological order. See all Collections from Nature Biomedical Engineering.

Research

Restoration of visual function in adult mice with an inherited retinal disease via adenine base editing

Subretinal viral delivery, in mice, of an adenine base editor and a single-guide RNA targeting a nonsense mutation in the Rpe65 gene restores near-normal levels of retinal and visual functions.

Susie Suh,
Elliot H. Choi ⋯
Krzysztof Palczewski

Article | 19 Oct 2020 | Nature Biomedical Engineering

A web tool for the design of prime-editing guide RNAs

A web tool enables the rapid design of prime-editing guide RNAs from reference and edited DNA sequences, for diverse prime-editing applications.

Ryan D. Chow,
Jennifer S. Chen ⋯
Sidi Chen

Article | 28 Sep 2020 | Nature Biomedical Engineering

Extensive germline genome engineering in pigs

Pigs can be genetically modified to inactivate endogenous retroviruses and to display enhanced compatibility with the human immune system using a combination of CRISPR–Cas9 and transposon technologies.

Yanan Yue,
Weihong Xu ⋯
Luhan Yang

Article | 21 Sep 2020 | Nature Biomedical Engineering

High-throughput analysis of the activities of xCas9, SpCas9-NG and SpCas9 at matched and mismatched target sequences in human cells

A comparison of compatibilities in protospacer adjacent motifs and of on-target and off-target activities of Streptococcus pyogenes Cas9 variants at endogenous sites in human cells enables the editing of new genomic sites associated with genetic diseases.

Hui Kwon Kim,
Sungtae Lee ⋯
Hyongbum Henry Kim

Article | 14 Jan 2020 | Nature Biomedical Engineering

Cytosine and adenine base editing of the brain, liver, retina, heart and skeletal muscle of mice via adeno-associated viruses

Optimized adeno-associated viruses delivering split cytosine base editors and adenine base editors with trans-splicing inteins can edit brain, liver, retina, heart and skeletal-muscle tissues at therapeutically relevant efficiencies.

Jonathan M. Levy,
Wei-Hsi Yeh ⋯
David R. Liu

Article | 14 Jan 2020 | Nature Biomedical Engineering

Immune-orthogonal orthologues of AAV capsids and of Cas9 circumvent the immune response to the administration of gene therapy

Orthologous therapeutic proteins can elude the adaptive immune system and allow for effective repeated dosing, as shown for CRISPR gene editing with orthologues of adeno-associated viral capsids and of the Cas9 protein.

Ana M. Moreno,
Nathan Palmer ⋯
Prashant Mali

Article | 22 Jul 2019 | Nature Biomedical Engineering

Adenine base editing in an adult mouse model of tyrosinaemia

Intravenous delivery of an adenine base editor and a single-guide RNA for the Fah gene can correct an A>G splice-site mutation in an adult mouse model of tyrosinaemia.

Chun-Qing Song,
Tingting Jiang ⋯
Wen Xue

Article | 25 Feb 2019 | Nature Biomedical Engineering

Combinatorial interactions of genetic variants in human cardiomyopathy

Genome-edited human pluripotent stem cells and genome-edited mouse models reveal that combinatorial genetic interactions contribute to the complex genetic heritability of human cardiomyopathy.

Dekker C. Deacon,
Cassandra L. Happe ⋯
Neil C. Chi

Article | 7 Feb 2019 | Nature Biomedical Engineering

Spatial control of in vivo CRISPR–Cas9 genome editing via nanomagnets

CRISPR–Cas9-mediated genome editing can be activated locally in vivo via an applied magnetic field, after complexation of magnetic nanoparticles with recombinant baculoviral vectors packaging the CRISPR–Cas9 machinery.

Haibao Zhu,
Linlin Zhang ⋯
Gang Bao

Article | 12 Nov 2018 | Nature Biomedical Engineering

Genome-edited skin epidermal stem cells protect mice from cocaine-seeking behaviour and cocaine overdose

The transplantation of skin cells genetically modified to express an enzyme that hydrolyses cocaine into mice leads to long-lasting levels of the enzyme in the circulation and protects the mice from cocaine-seeking behaviour and cocaine overdose.

Yuanyuan Li,
Qingyao Kong ⋯
Xiaoyang Wu

Article | 17 Sep 2018 | Nature Biomedical Engineering

Nanoparticle delivery of CRISPR into the brain rescues a mouse model of fragile X syndrome from exaggerated repetitive behaviours

Gene editing of a single gene in the brain of an adult mouse model of fragile X syndrome, achieved via the intracranial injection of a nonviral Cas9 delivery vehicle, rescues mice from the exaggerated repetitive behaviours caused by the disease.

Bumwhee Lee,
Kunwoo Lee ⋯
Hye Young Lee

Article | 25 Jun 2018 | Nature Biomedical Engineering

Prediction of off-target activities for the end-to-end design of CRISPR guide RNAs

A cloud-based machine-learning software that scores individual guide–target pairs and provides an overall summary score for a given guide that outperforms competing algorithms for the prediction of CRISPR–Cas9 off-target effects.

Jennifer Listgarten,
Michael Weinstein ⋯
Nicolo Fusi

Article | 10 Jan 2018 | Nature Biomedical Engineering

Macrogenomic engineering via modulation of the scaling of chromatin packing density

A model accounting for the properties of the local chromatin environment predicts the modulation of patterns in gene expression and helps screen for chemotherapeutic adjuvants that lead to an enhanced therapeutic response in cancer cells.

Luay M. Almassalha,
Greta M. Bauer ⋯
Vadim Backman

Article | 6 Nov 2017 | Nature Biomedical Engineering

Ectopic expression of RAD52 and dn53BP1 improves homology-directed repair during CRISPR–Cas9 genome editing

The expression of two specific DNA-repair factors promotes homology-directed repair and enhances the precision of CRISPR–Cas9 gene editing at multiple loci in human cells, including patient-derived induced pluripotent stem cells.

Bruna S. Paulsen,
Pankaj K. Mandal ⋯
Derrick J. Rossi

Article | 9 Oct 2017 | Nature Biomedical Engineering

Nanoparticle delivery of Cas9 ribonucleoprotein and donor DNA in vivo induces homology-directed DNA repair

Gold nanoparticles carrying Cas9 ribonucleoprotein and donor DNA, and complexed with endosomal disruptive polymers, correct the DNA mutation that causes Duchenne muscular dystrophy in mice, with minimal off-target effects.

Kunwoo Lee,
Michael Conboy ⋯
Niren Murthy

Article | 2 Oct 2017 | Nature Biomedical Engineering

Engineering CRISPR–Cpf1 crRNAs and mRNAs to maximize genome editing efficiency

An array of chemically engineered CRISPR RNAs and AsCpf1 messenger RNAs leads to improvements in gene-cutting efficiency up to about 300% with respect to unmodified CRISPR RNA and plasmid-encoding AsCpf1.

Bin Li,
Weiyu Zhao ⋯
Yizhou Dong

Article | 1 May 2017 | Nature Biomedical Engineering

News & Comment

Henceforth CRISPR

In less than a decade, the genome-editing technology now recognized by the Nobel Prize in Chemistry has impacted the biological and biomedical sciences widely. What’s next for CRISPR in biomedicine?

Editorial | 15 Oct 2020 | Nature Biomedical Engineering

Towards better base editing

The editing of single DNA bases in the genome is being optimized for higher editing precision and versatility.

Editorial | 14 Jan 2020 | Nature Biomedical Engineering

Correcting tyrosinaemia via a point mutation

In an adult mouse model of tyrosinaemia, a base editor correcting an A-to-G splice-site mutation in the Fah gene restores the translation of the functional enzyme, promoting the repopulation of the liver with the corrected cells.

Kiran Musunuru

News & Views | 14 Jan 2020 | Nature Biomedical Engineering

Weakly immunogenic CRISPR therapies

Orthologues of CRISPR-associated proteins and of viral vectors evade immune recognition in mice, enabling repeated gene therapy.

Eric A. Wilson &
Karen S. Anderson

News & Views | 7 Oct 2019 | Nature Biomedical Engineering

Momentous CRISPR-enabled developments

The simplicity and powerful capabilities of CRISPR have led to an explosion of genome-editing applications. Their continued development should be nurtured by scientific and legal environments that discourage and penalize irresponsible uses of the technology.

Editorial | 7 Feb 2019 | Nature Biomedical Engineering

Cocaine-metabolizing skin grafts

Graftable skin expressing an enzyme that metabolizes cocaine may offer a new strategy to treat cocaine addiction.

Xin-an Liu &
Paul J. Kenny

News & Views | 7 Feb 2019 | Nature Biomedical Engineering

Local magnetic activation of CRISPR

Magnetic nanoparticles complexed with recombinant baculoviral vectors containing the CRISPR–Cas9 machinery enable the local magnetic activation of genome editing.

Mu-Nung Hsu &
Yu-Chen Hu

News & Views | 7 Feb 2019 | Nature Biomedical Engineering

Complex heritability in cardiomyopathy

Human cardiomyocytes and mice edited to harbour gene variants found in patients with dilated cardiomyopathy reveal combinatorial genetic interactions that contribute to the complex genetic heritability of the disease.

Ning Ma,
Sophia L. Zhang &
Joseph C. Wu

News & Views | 7 Feb 2019 | Nature Biomedical Engineering

CRISPR alleviates muscular dystrophy in dogs

Widespread editing of the mutated DMD gene by CRISPR–Cas9, systemically delivered via an adeno-associated virus, restores dystrophin expression in a canine model of Duchenne muscular dystrophy.

Dongsheng Duan

News & Views | 8 Nov 2018 | Nature Biomedical Engineering

The expanding toolbox for genome engineering

The optimization and diversification of methods for manipulating the genome will enable new therapeutic solutions.

Editorial | 10 Nov 2017 | Nature Biomedical Engineering

Repacking chromatin for therapy

A theoretical model of chromatin packing heterogeneity predicts patterns in gene expression and can be used to screen for effective chemotherapeutic adjuvants.

Alexandra Zidovska

News & Views | 10 Nov 2017 | Nature Biomedical Engineering

Enhanced precision and efficiency

The expression of two DNA repair factors improves the recombination of single-stranded oligodeoxynucleotides with Cas9-induced double-strand breaks, facilitating precise and efficient gene editing.

Sanum Bashir &
Ralf Kühn

News & Views | 10 Nov 2017 | Nature Biomedical Engineering

Nanoparticles for CRISPR–Cas9 delivery

The DNA mutation that causes Duchenne muscular dystrophy in mice can be corrected, with minimal off-target effects, by gold nanoparticles carrying the CRISPR components.

Zachary Glass,
Yamin Li &
Qiaobing Xu

News & Views | 10 Nov 2017 | Nature Biomedical Engineering

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