Programmable RNA editing by recruiting endogenous ADAR using engineered RNAs.

Abstract:

:Current tools for targeted RNA editing rely on the delivery of exogenous proteins or chemically modified guide RNAs, which may lead to aberrant effector activity, delivery barrier or immunogenicity. Here, we present an approach, called leveraging endogenous ADAR for programmable editing of RNA (LEAPER), that employs short engineered ADAR-recruiting RNAs (arRNAs) to recruit native ADAR1 or ADAR2 enzymes to change a specific adenosine to inosine. We show that arRNA, delivered by a plasmid or viral vector or as a synthetic oligonucleotide, achieves editing efficiencies of up to 80%. LEAPER is highly specific, with rare global off-targets and limited editing of non-target adenosines in the target region. It is active in a broad spectrum of cell types, including multiple human primary cell types, and can restore α-L-iduronidase catalytic activity in Hurler syndrome patient-derived primary fibroblasts without evoking innate immune responses. As a single-molecule system, LEAPER enables precise, efficient RNA editing with broad applicability for therapy and basic research.

journal_name

Nat Biotechnol

journal_title

Nature biotechnology

authors

Qu L,Yi Z,Zhu S,Wang C,Cao Z,Zhou Z,Yuan P,Yu Y,Tian F,Liu Z,Bao Y,Zhao Y,Wei W

doi

10.1038/s41587-019-0178-z

subject

Has Abstract

pub_date

2019-09-01 00:00:00

pages

1059-1069

issue

9

eissn

1087-0156

issn

1546-1696

pii

10.1038/s41587-019-0178-z

journal_volume

37

pub_type

杂志文章
  • A human beta-cell line for transplantation therapy to control type 1 diabetes.

    abstract::A human pancreatic beta-cell line that is functionally equivalent to primary beta-cells has not been available. We established a reversibly immortalized human beta-cell clone (NAKT-15) by transfection of primary human beta-cells with a retroviral vector containing simian virus 40 large T-antigen (SV40T) and human telo...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt1145

    authors: Narushima M,Kobayashi N,Okitsu T,Tanaka Y,Li SA,Chen Y,Miki A,Tanaka K,Nakaji S,Takei K,Gutierrez AS,Rivas-Carrillo JD,Navarro-Alvarez N,Jun HS,Westerman KA,Noguchi H,Lakey JR,Leboulch P,Tanaka N,Yoon JW

    更新日期:2005-10-01 00:00:00

  • Efficient epitope mapping by bacteriophage lambda surface display.

    abstract::A bacteriophage lambda surface expression system, lambda foo, was used for epitope mapping of human galectin-3. We constructed random epitope and peptide libraries and compared their efficiencies in the mapping. The galectin-3 cDNA was randomly digested by DNase 1 to make random epitope libraries. The libraries were s...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt0197-74

    authors: Kuwabara I,Maruyama H,Mikawa YG,Zuberi RI,Liu FT,Maruyama IN

    更新日期:1997-01-01 00:00:00

  • Continuous evolution of SpCas9 variants compatible with non-G PAMs.

    abstract::The targeting scope of Streptococcus pyogenes Cas9 (SpCas9) and its engineered variants is largely restricted to protospacer-adjacent motif (PAM) sequences containing G bases. Here we report the evolution of three new SpCas9 variants that collectively recognize NRNH PAMs (where R is A or G and H is A, C or T) using ph...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/s41587-020-0412-8

    authors: Miller SM,Wang T,Randolph PB,Arbab M,Shen MW,Huang TP,Matuszek Z,Newby GA,Rees HA,Liu DR

    更新日期:2020-04-01 00:00:00

  • Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape.

    abstract::We describe protein interaction quantitation (PIQ), a computational method for modeling the magnitude and shape of genome-wide DNase I hypersensitivity profiles to identify transcription factor (TF) binding sites. Through the use of machine-learning techniques, PIQ identified binding sites for >700 TFs from one DNase ...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt.2798

    authors: Sherwood RI,Hashimoto T,O'Donnell CW,Lewis S,Barkal AA,van Hoff JP,Karun V,Jaakkola T,Gifford DK

    更新日期:2014-02-01 00:00:00

  • Reversal of diabetes with insulin-producing cells derived in vitro from human pluripotent stem cells.

    abstract::Transplantation of pancreatic progenitors or insulin-secreting cells derived from human embryonic stem cells (hESCs) has been proposed as a therapy for diabetes. We describe a seven-stage protocol that efficiently converts hESCs into insulin-producing cells. Stage (S) 7 cells expressed key markers of mature pancreatic...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt.3033

    authors: Rezania A,Bruin JE,Arora P,Rubin A,Batushansky I,Asadi A,O'Dwyer S,Quiskamp N,Mojibian M,Albrecht T,Yang YH,Johnson JD,Kieffer TJ

    更新日期:2014-11-01 00:00:00

  • NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice.

    abstract::Nitrogen-use efficiency of indica varieties of rice is superior to that of japonica varieties. We apply 16S ribosomal RNA gene profiling to characterize root microbiota of 68 indica and 27 japonica varieties grown in the field. We find that indica and japonica recruit distinct root microbiota. Notably, indica-enriched...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/s41587-019-0104-4

    authors: Zhang J,Liu YX,Zhang N,Hu B,Jin T,Xu H,Qin Y,Yan P,Zhang X,Guo X,Hui J,Cao S,Wang X,Wang C,Wang H,Qu B,Fan G,Yuan L,Garrido-Oter R,Chu C,Bai Y

    更新日期:2019-06-01 00:00:00

  • Purification of recombinant proteins by fusion with thermally-responsive polypeptides.

    abstract::Elastin-like polypeptides (ELPs) undergo a reversible, inverse phase transition. Below their transition temperature (Tt), ELPs are soluble in water, but when the temperature is raised above Tt, phase transition occurs, leading to aggregation of the polypeptide. We demonstrate a method for purification of soluble fusio...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/15100

    authors: Meyer DE,Chilkoti A

    更新日期:1999-11-01 00:00:00

  • Epigenetic modifications in pluripotent and differentiated cells.

    abstract::Epigenetic modifications constitute a complex regulatory layer on top of the genome sequence. Pluripotent and differentiated cells provide a powerful system for investigating how the epigenetic code influences cellular fate. High-throughput sequencing of these cell types has yielded DNA methylation maps at single-nucl...

    journal_title:Nature biotechnology

    pub_type: 杂志文章,评审

    doi:10.1038/nbt.1684

    authors: Meissner A

    更新日期:2010-10-01 00:00:00

  • Optical tracking and detection of immunomagnetically selected and aligned cells.

    abstract::We have developed a platform for cell analysis based on immunomagnetic selection and magnetic alignment of cells in combination with an epi-illumination tracking and detection system. Whole blood was labeled with ferromagnetic nanoparticles and fluorescent probes, and placed in a magnetic field in a chamber. Cells lab...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/70761

    authors: Tibbe AG,de Grooth BG,Greve J,Liberti PA,Dolan GJ,Terstappen LW

    更新日期:1999-12-01 00:00:00

  • Using virally expressed melanoma cDNA libraries to identify tumor-associated antigens that cure melanoma.

    abstract::Multiple intravenous injections of a cDNA library, derived from human melanoma cell lines and expressed using the highly immunogenic vector vesicular stomatitis virus (VSV), cured mice with established melanoma tumors. Successful tumor eradication was associated with the ability of mouse lymphoid cells to mount a tumo...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt.2157

    authors: Pulido J,Kottke T,Thompson J,Galivo F,Wongthida P,Diaz RM,Rommelfanger D,Ilett E,Pease L,Pandha H,Harrington K,Selby P,Melcher A,Vile R

    更新日期:2012-03-18 00:00:00

  • Analysis of 589,306 genomes identifies individuals resilient to severe Mendelian childhood diseases.

    abstract::Genetic studies of human disease have traditionally focused on the detection of disease-causing mutations in afflicted individuals. Here we describe a complementary approach that seeks to identify healthy individuals resilient to highly penetrant forms of genetic childhood disorders. A comprehensive screen of 874 gene...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt.3514

    authors: Chen R,Shi L,Hakenberg J,Naughton B,Sklar P,Zhang J,Zhou H,Tian L,Prakash O,Lemire M,Sleiman P,Cheng WY,Chen W,Shah H,Shen Y,Fromer M,Omberg L,Deardorff MA,Zackai E,Bobe JR,Levin E,Hudson TJ,Groop L,Wang J,

    更新日期:2016-05-01 00:00:00

  • MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification.

    abstract::Efficient analysis of very large amounts of raw data for peptide identification and protein quantification is a principal challenge in mass spectrometry (MS)-based proteomics. Here we describe MaxQuant, an integrated suite of algorithms specifically developed for high-resolution, quantitative MS data. Using correlatio...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt.1511

    authors: Cox J,Mann M

    更新日期:2008-12-01 00:00:00

  • MicroRNA-mediated species-specific attenuation of influenza A virus.

    abstract::Influenza A virus leads to yearly epidemics and sporadic pandemics. Present prophylactic strategies focus on egg-grown, live, attenuated influenza vaccines (LAIVs), in which attenuation is generated by conferring temperature sensitivity onto the virus. Here we describe an alternative approach to attenuating influenza ...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt.1542

    authors: Perez JT,Pham AM,Lorini MH,Chua MA,Steel J,tenOever BR

    更新日期:2009-06-01 00:00:00

  • BMP4 initiates human embryonic stem cell differentiation to trophoblast.

    abstract::The excitement and controversy surrounding the potential role of human embryonic stem (ES) cells in transplantation therapy have often overshadowed their potentially more important use as a basic research tool for understanding the development and function of human tissues. Human ES cells can proliferate without a kno...

    journal_title:Nature biotechnology

    pub_type:

    doi:10.1038/nbt761

    authors: Xu RH,Chen X,Li DS,Li R,Addicks GC,Glennon C,Zwaka TP,Thomson JA

    更新日期:2002-12-01 00:00:00

  • Plant viral genes in DNA idiotypic vaccines activate linked CD4+ T-cell mediated immunity against B-cell malignancies.

    abstract::DNA delivery of tumor antigens can activate specific immune attack on cancer cells. However, antigens may be weak, and immune capacity can be compromised. Fusion of genes encoding activating sequences to the tumor antigen sequence facilitates promotion and manipulation of effector pathways. Idiotypic determinants of B...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/90816

    authors: Savelyeva N,Munday R,Spellerberg MB,Lomonossoff GP,Stevenson FK

    更新日期:2001-08-01 00:00:00

  • Enrichment and analysis of peptide subsets using fluorous affinity tags and mass spectrometry.

    abstract::Although mass spectrometry has become a powerful tool for the functional analysis of biological systems, complete proteome characterization cannot yet be achieved. Instead, the sheer complexity of living organisms demands fractionation of cellular extracts to enable more targeted analyses. Here, we introduce the conce...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt1076

    authors: Brittain SM,Ficarro SB,Brock A,Peters EC

    更新日期:2005-04-01 00:00:00

  • Detecting and characterizing circular RNAs.

    abstract::Circular RNA transcripts were first identified in the early 1990s but knowledge of these species has remained limited, as their study through traditional methods of RNA analysis has been difficult. Now, novel bioinformatic approaches coupled with biochemical enrichment strategies and deep sequencing have allowed compr...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt.2890

    authors: Jeck WR,Sharpless NE

    更新日期:2014-05-01 00:00:00

  • Therapeutic silencing of miR-10b inhibits metastasis in a mouse mammary tumor model.

    abstract::MicroRNAs (miRNAs) are increasingly implicated in the regulation of metastasis. Despite their potential as targets for anti-metastatic therapy, miRNAs have only been silenced in normal tissues of rodents and nonhuman primates. Therefore, the development of effective approaches for sequence-specific inhibition of miRNA...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt.1618

    authors: Ma L,Reinhardt F,Pan E,Soutschek J,Bhat B,Marcusson EG,Teruya-Feldstein J,Bell GW,Weinberg RA

    更新日期:2010-04-01 00:00:00

  • Visualizing lipid-formulated siRNA release from endosomes and target gene knockdown.

    abstract::A central hurdle in developing small interfering RNAs (siRNAs) as therapeutics is the inefficiency of their delivery across the plasma and endosomal membranes to the cytosol, where they interact with the RNA interference machinery. With the aim of improving endosomal release, a poorly understood and inefficient proces...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt.3298

    authors: Wittrup A,Ai A,Liu X,Hamar P,Trifonova R,Charisse K,Manoharan M,Kirchhausen T,Lieberman J

    更新日期:2015-08-01 00:00:00

  • Glycosylase base editors enable C-to-A and C-to-G base changes.

    abstract::Current base editors (BEs) catalyze only base transitions (C to T and A to G) and cannot produce base transversions. Here we present BEs that cause C-to-A transversions in Escherichia coli and C-to-G transversions in mammalian cells. These glycosylase base editors (GBEs) consist of a Cas9 nickase, a cytidine deaminase...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/s41587-020-0592-2

    authors: Zhao D,Li J,Li S,Xin X,Hu M,Price MA,Rosser SJ,Bi C,Zhang X

    更新日期:2021-01-01 00:00:00

  • Cell penetrating PNA constructs regulate galanin receptor levels and modify pain transmission in vivo.

    abstract::Peptide nucleic acids (PNAs) form stable and tight complexes with complementary DNA and/or RNA and would be promising antisense reagents if their cellular delivery could be improved. We show that a 21-mer PNA, complementary to the human galanin receptor type 1 mRNA, coupled to the cellular transporter peptides, transp...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt0998-857

    authors: Pooga M,Soomets U,Hällbrink M,Valkna A,Saar K,Rezaei K,Kahl U,Hao JX,Xu XJ,Wiesenfeld-Hallin Z,Hökfelt T,Bartfai T,Langel U

    更新日期:1998-09-01 00:00:00

  • Directed evolution of proteins by exon shuffling.

    abstract::Evolution of eukaryotes is mediated by sexual recombination of parental genomes. Crossovers occur in random, but homologous, positions at a frequency that depends on DNA length. As exons occupy only 1% of the human genome and introns about 24%, by far most of the crossovers occur between exons, rather than inside. The...

    journal_title:Nature biotechnology

    pub_type: 杂志文章,评审

    doi:10.1038/88084

    authors: Kolkman JA,Stemmer WP

    更新日期:2001-05-01 00:00:00

  • Resolution of cutaneous inflammation after local elimination of macrophages.

    abstract::We constructed an immunotoxin, composed of an antibody directed against the high-affinity IgG receptor CD64 and Ricin-A, with the aim of resolving chronic inflammation through elimination of activated macrophages. In vitro, this immunotoxin proved very efficient in inducing apoptosis in activated macrophages, leaving ...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/71908

    authors: Thepen T,van Vuuren AJ,Kiekens RC,Damen CA,Vooijs WC,van De Winkel JG

    更新日期:2000-01-01 00:00:00

  • Rapid identification of DNA-binding proteins by mass spectrometry.

    abstract::We report a protocol for the rapid identification of DNA-binding proteins. Immobilized DNA probes harboring a specific sequence motif are incubated with cell or nuclear extract. Proteins are analyzed directly off the solid support by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The det...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/12873

    authors: Nordhoff E,Krogsdam AM,Jorgensen HF,Kallipolitis BH,Clark BF,Roepstorff P,Kristiansen K

    更新日期:1999-09-01 00:00:00

  • Mutation detection by electrocatalysis at DNA-modified electrodes.

    abstract::Detection of mutations and damaged DNA bases is important for the early diagnosis of genetic disease. Here we describe an electrocatalytic method for the detection of single-base mismatches as well as DNA base lesions in fully hybridized duplexes, based on charge transport through DNA films. Gold electrodes modified w...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/80301

    authors: Boon EM,Ceres DM,Drummond TG,Hill MG,Barton JK

    更新日期:2000-10-01 00:00:00

  • Controlled light-exposure microscopy reduces photobleaching and phototoxicity in fluorescence live-cell imaging.

    abstract::Fluorescence microscopy of living cells enables visualization of the dynamics and interactions of intracellular molecules. However, fluorescence live-cell imaging is limited by photobleaching and phototoxicity induced by the excitation light. Here we describe controlled light-exposure microscopy (CLEM), a simple imagi...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt1278

    authors: Hoebe RA,Van Oven CH,Gadella TW Jr,Dhonukshe PB,Van Noorden CJ,Manders EM

    更新日期:2007-02-01 00:00:00

  • Statistical pattern matching facilitates the design of polyvalent inhibitors of anthrax and cholera toxins.

    abstract::Numerous biological processes involve the recognition of a specific pattern of binding sites on a target protein or surface. Although ligands displayed by disordered scaffolds form stochastic rather than specific patterns, theoretical models predict that recognition will occur between patterns that are characterized b...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt1204

    authors: Rai P,Padala C,Poon V,Saraph A,Basha S,Kate S,Tao K,Mogridge J,Kane RS

    更新日期:2006-05-01 00:00:00

  • Microbial synthesis of medium-chain chemicals from renewables.

    abstract::Linear, medium-chain (C8-C12) hydrocarbons are important components of fuels as well as commodity and specialty chemicals. As industrial microbes do not contain pathways to produce medium-chain chemicals, approaches such as overexpression of endogenous enzymes or deletion of competing pathways are not available to the...

    journal_title:Nature biotechnology

    pub_type: 杂志文章,评审

    doi:10.1038/nbt.4022

    authors: Sarria S,Kruyer NS,Peralta-Yahya P

    更新日期:2017-12-01 00:00:00

  • Hematopoietic stem cell gene transfer in a tumor-prone mouse model uncovers low genotoxicity of lentiviral vector integration.

    abstract::Insertional mutagenesis represents a major hurdle to gene therapy and necessitates sensitive preclinical genotoxicity assays. Cdkn2a-/- mice are susceptible to a broad range of cancer-triggering genetic lesions. We exploited hematopoietic stem cells from these tumor-prone mice to assess the oncogenicity of prototypica...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt1216

    authors: Montini E,Cesana D,Schmidt M,Sanvito F,Ponzoni M,Bartholomae C,Sergi Sergi L,Benedicenti F,Ambrosi A,Di Serio C,Doglioni C,von Kalle C,Naldini L

    更新日期:2006-06-01 00:00:00

  • Turnover-based in vitro selection and evolution of biocatalysts from a fully synthetic antibody library.

    abstract::This report describes the selection of highly efficient antibody catalysts by combining chemical selection from a synthetic library with directed in vitro protein evolution. Evolution started from a naive antibody library displayed on phage made from fully synthetic, antibody-encoding genes (the Human Combinatorial An...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt828

    authors: Cesaro-Tadic S,Lagos D,Honegger A,Rickard JH,Partridge LJ,Blackburn GM,Plückthun A

    更新日期:2003-06-01 00:00:00