Efficient Delivery of Genome-Editing Proteins In Vitro and In Vivo

Efficient intracellular delivery of proteins is needed to fully realize the potential of protein therapeutics. Current methods of protein delivery commonly suffer from low tolerance for serum, poor endosomal escape and limited in vivo efficacy. Here we report that common cationic lipid nucleic acid transfection reagents can potently deliver proteins that are fused to negatively supercharged proteins, that contain natural anionic domains or that natively bind to anionic nucleic acids. This approach mediates the potent delivery of nM concentrations of Cre recombinase, TALE- and Cas9-based transcription activators, and Cas9:sgRNA nuclease complexes into cultured human cells in media containing 10% serum. Delivery of unmodified Cas9:sgRNA complexes resulted in up to 80% genome modification with substantially higher specificity compared to DNA transfection. This approach also mediated efficient delivery of Cre recombinase and Cas9:sgRNA complexes into the mouse inner ear in vivo, achieving 90% Cre-mediated recombination and 20% Cas9-mediated genome modification in hair cells.

[1]  V. Patravale,et al.  Endosomal escape: a bottleneck in intracellular delivery. , 2014, Journal of nanoscience and nanotechnology.

[2]  Scott D. Putney,et al.  Improving protein therapeutics with sustained-release formulations , 1998, Nature Biotechnology.

[3]  J. Keith Joung,et al.  Improving CRISPR-Cas nuclease specificity using truncated guide RNAs , 2014, Nature Biotechnology.

[4]  J. T. Corwin,et al.  Post-translational protein modification as the substrate for long-lasting memory , 2005 .

[5]  K. Arnos Hereditary Hearing Loss , 1994 .

[6]  A. Schepartz,et al.  Intrinsically cell-permeable miniature proteins based on a minimal cationic PPII motif. , 2007, Journal of the American Chemical Society.

[7]  David E. Golan,et al.  Protein therapeutics: a summary and pharmacological classification , 2008, Nature Reviews Drug Discovery.

[8]  David R. Liu,et al.  Potent Delivery of Functional Proteins into Mammalian Cells in Vitro and in Vivo Using a Supercharged Protein , 2010, ACS chemical biology.

[9]  David R. Liu,et al.  Mammalian cell penetration, siRNA transfection, and DNA transfection by supercharged proteins , 2009, Proceedings of the National Academy of Sciences.

[10]  David R. Liu,et al.  Engineering and identifying supercharged proteins for macromolecule delivery into mammalian cells. , 2012, Methods in enzymology.

[11]  Bradley E. Bernstein,et al.  In silico abstraction of zinc finger nuclease cleavage profiles reveals an expanded landscape of off-target sites , 2013, Nucleic acids research.

[12]  L. Tessarollo,et al.  Targeted mutation in the neurotrophin-3 gene results in loss of muscle sensory neurons. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[13]  Mathias Winterhalter,et al.  Protein encapsulation in liposomes: efficiency depends on interactions between protein and phospholipid bilayer. , 2002, BMC biotechnology.

[14]  Rudolf Jaenisch,et al.  One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering , 2013, Cell.

[15]  David R. Liu,et al.  High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity , 2013, Nature Biotechnology.

[16]  J. Keith Joung,et al.  Robust, synergistic regulation of human gene expression using TALE activators , 2013, Nature Methods.

[17]  Anne R. Pariser,et al.  Neutralizing antibodies to therapeutic enzymes: considerations for testing, prevention and treatment , 2008, Nature Biotechnology.

[18]  J. R. Holt,et al.  Differentiation of neurons from neural precursors generated in floating spheres from embryonic stem cells , 2009, BMC Neuroscience.

[19]  G. Yarrington Molecular Cell Biology , 1987, The Yale Journal of Biology and Medicine.

[20]  Shubiao Zhang,et al.  Toxicity of cationic lipids and cationic polymers in gene delivery. , 2006, Journal of controlled release : official journal of the Controlled Release Society.

[21]  David R. Liu,et al.  Supercharging proteins can impart unusual resilience. , 2007, Journal of the American Chemical Society.

[22]  Ronald A. Li,et al.  Modified mRNA directs the fate of heart progenitor cells and induces vascular regeneration after myocardial infarction , 2013, Nature Biotechnology.

[23]  Luigi Naldini,et al.  Viral vectors for gene therapy: the art of turning infectious agents into vehicles of therapeutics , 2001, Nature Medicine.

[24]  Hao Yin,et al.  Genome editing with Cas9 in adult mice corrects a disease mutation and phenotype , 2014, Nature Biotechnology.

[25]  Suresh Ramakrishna,et al.  Gene disruption by cell-penetrating peptide-mediated delivery of Cas9 protein and guide RNA , 2014, Genome research.

[26]  W. Low,et al.  Correction of metabolic, craniofacial, and neurologic abnormalities in MPS I mice treated at birth with adeno-associated virus vector transducing the human alpha-L-iduronidase gene. , 2004, Molecular therapy : the journal of the American Society of Gene Therapy.

[27]  David R. Liu,et al.  Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification , 2014, Nature Biotechnology.

[28]  Steven F Dowdy,et al.  Transducible TAT-HA fusogenic peptide enhances escape of TAT-fusion proteins after lipid raft macropinocytosis , 2004, Nature Medicine.

[29]  Sarah Seifert,et al.  Image-based analysis of lipid nanoparticle–mediated siRNA delivery, intracellular trafficking and endosomal escape , 2013, Nature Biotechnology.

[30]  Thomas Gaj,et al.  Cell-Penetrating Peptide-Mediated Delivery of TALEN Proteins via Bioconjugation for Genome Engineering , 2014, PloS one.

[31]  P. Cullis,et al.  Liposomal drug delivery systems: from concept to clinical applications. , 2013, Advanced drug delivery reviews.

[32]  Judy Lieberman,et al.  Antibody mediated in vivo delivery of small interfering RNAs via cell-surface receptors , 2005, Nature Biotechnology.

[33]  Morgan L. Maeder,et al.  CRISPR RNA-guided activation of endogenous human genes , 2013, Nature Methods.

[34]  James E. DiCarlo,et al.  RNA-Guided Human Genome Engineering via Cas9 , 2013, Science.

[35]  J. Kamps,et al.  Targeted SAINT-O-Somes for improved intracellular delivery of siRNA and cytotoxic drugs into endothelial cells. , 2010, Journal of controlled release : official journal of the Controlled Release Society.

[36]  Boris Klebanov,et al.  Influence of Cationic Lipid Composition on Gene Silencing Properties of Lipid Nanoparticle Formulations of siRNA in Antigen-Presenting Cells , 2011, Molecular therapy : the journal of the American Society of Gene Therapy.

[37]  Chantal Pichon,et al.  Chemical vectors for gene delivery: a current review on polymers, peptides and lipids containing histidine or imidazole as nucleic acids carriers , 2009, British journal of pharmacology.

[38]  B. Bettencourt,et al.  Safety and efficacy of RNAi therapy for transthyretin amyloidosis. , 2013, The New England journal of medicine.

[39]  Jeffry D. Sander,et al.  CRISPR-Cas systems for editing, regulating and targeting genomes , 2014, Nature Biotechnology.

[40]  A. Annenkov,et al.  Latent cytokines for targeted therapy of inflammatory disorders , 2014, Expert opinion on drug delivery.

[41]  David A. Scott,et al.  Double Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing Specificity , 2013, Cell.

[42]  N. Segil,et al.  Math1-driven GFP expression in the developing nervous system of transgenic mice. , 2003, Gene expression patterns : GEP.

[43]  John Calvin Reed,et al.  Intracellular Delivery of Proteins with a New Lipid-mediated Delivery System* , 2001, The Journal of Biological Chemistry.

[44]  Luke A. Gilbert,et al.  Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression , 2013, Cell.

[45]  Jeffrey C. Miller,et al.  A rapid and general assay for monitoring endogenous gene modification. , 2010, Methods in molecular biology.

[46]  David R. Liu,et al.  Cellular uptake mechanisms and endosomal trafficking of supercharged proteins. , 2012, Chemistry & biology.

[47]  E. Rebar,et al.  Genome editing with engineered zinc finger nucleases , 2010, Nature Reviews Genetics.

[48]  M. Morris,et al.  A peptide carrier for the delivery of biologically active proteins into mammalian cells , 2001, Nature Biotechnology.

[49]  A. Lee,et al.  Design of noninflammatory synthetic siRNA mediating potent gene silencing in vivo. , 2006, Molecular therapy : the journal of the American Society of Gene Therapy.

[50]  Daesik Kim,et al.  Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins , 2014, Genome research.

[51]  Roger Y Tsien,et al.  Systemic in vivo distribution of activatable cell penetrating peptides is superior to that of cell penetrating peptides. , 2009, Integrative biology : quantitative biosciences from nano to macro.

[52]  Kevin W Eliceiri,et al.  NIH Image to ImageJ: 25 years of image analysis , 2012, Nature Methods.

[53]  Leaf Huang,et al.  Structure and function of lipid-DNA complexes for gene delivery. , 2000, Annual review of biophysics and biomolecular structure.

[54]  Richard Heller,et al.  Electroporation for the delivery of DNA-based vaccines and immunotherapeutics: current clinical developments. , 2009, Molecular therapy : the journal of the American Society of Gene Therapy.