Highly efficient in vitro and in vivo delivery of functional RNAs using new versatile MS2-chimeric retrovirus-like particles

RNA delivery is an attractive strategy to achieve transient gene expression in research projects and in cell- or gene-based therapies. Despite significant efforts investigating vector-directed RNA transfer, there is still a requirement for better efficiency of delivery to primary cells and in vivo. Retroviral platforms drive RNA delivery, yet retrovirus RNA-packaging constraints limit gene transfer to two genome-molecules per viral particle. To improve retroviral transfer, we designed a dimerization-independent MS2-driven RNA packaging system using MS2-Coat-retrovirus chimeras. The engineered chimeric particles promoted effective packaging of several types of RNAs and enabled efficient transfer of biologically active RNAs in various cell types, including human CD34+ and iPS cells. Systemic injection of high-titer particles led to gene expression in mouse liver and transferring Cre-recombinase mRNA in muscle permitted widespread editing at the ROSA26 locus. We could further show that the VLPs were able to activate an osteoblast differentiation pathway by delivering RUNX2- or DLX5-mRNA into primary human bone-marrow mesenchymal-stem cells. Thus, the novel chimeric MS2-lentiviral particles are a versatile tool for a wide range of applications including cellular-programming or genome-editing.

[1]  Hyun-Jai Cho,et al.  Induction of pluripotent stem cells from adult somatic cells by protein-based reprogramming without genetic manipulation. , 2010, Blood.

[2]  J. Collins,et al.  Toehold Switches: De-Novo-Designed Regulators of Gene Expression , 2014, Cell.

[3]  D. Curiel,et al.  Stable in vivo gene transduction via a novel adenoviral/retroviral chimeric vector , 1997, Nature Biotechnology.

[4]  J. Darlix,et al.  Properties and functions of the nucleocapsid protein in virus assembly , 2010, RNA biology.

[5]  Ralf Herwig,et al.  ConsensusPathDB: toward a more complete picture of cell biology , 2010, Nucleic Acids Res..

[6]  Ewelina Bolcun-Filas,et al.  A Mouse Geneticist’s Practical Guide to CRISPR Applications , 2014, Genetics.

[7]  J. Tisdale,et al.  Optimal conditions for lentiviral transduction of engrafting human CD34+ cells , 2011, Gene Therapy.

[8]  Rui Zhang,et al.  MS2 VLP-based delivery of microRNA-146a inhibits autoantibody production in lupus-prone mice , 2012, International journal of nanomedicine.

[9]  J. Murray,et al.  Crystal structures of MS2 coat protein mutants in complex with wild-type RNA operator fragments. , 1998, Nucleic acids research.

[10]  C. Dani,et al.  Stathmin-like 2, a developmentally-associated neuronal marker, is expressed and modulated during osteogenesis of human mesenchymal stem cells. , 2008, Biochemical and biophysical research communications.

[11]  J. Pagès,et al.  Mobilization of Full-Length Semliki Forest Virus Replicon by Retrovirus Particles , 2006, Journal of Virology.

[12]  P. Roingeard,et al.  Vesicular stomatitis virus glycoprotein: a transducing coat for SFV‐based RNA vectors , 2004, The journal of gene medicine.

[13]  T. Cordonnier,et al.  3D environment on human mesenchymal stem cells differentiation for bone tissue engineering , 2010, Journal of materials science. Materials in medicine.

[14]  É. Cohen,et al.  Design of a trans protease lentiviral packaging system that produces high titer virus , 2007, Retrovirology.

[15]  M. Summers,et al.  How retroviruses select their genomes , 2005, Nature Reviews Microbiology.

[16]  E. Querido,et al.  Using fluorescent proteins to study mRNA trafficking in living cells. , 2008, Methods in cell biology.

[17]  J. Mallet,et al.  Beta Cells within Single Human Islets Originate from Multiple Progenitors , 2008, PloS one.

[18]  Kuo Zhang,et al.  MS 2 VLP-based delivery of microRNA-146 a inhibits autoantibody production in lupus-prone mice , 2012 .

[19]  A. Schambach,et al.  Retrovirus-based mRNA transfer for transient cell manipulation. , 2013, Methods in molecular biology.

[20]  Myriam Gorospe,et al.  MS2-TRAP (MS2-tagged RNA affinity purification): tagging RNA to identify associated miRNAs. , 2012, Methods.

[21]  Edouard Bertrand,et al.  Retroviral genomic RNAs are transported to the plasma membrane by endosomal vesicles. , 2003, Developmental cell.

[22]  George M. Church,et al.  CRISPR/Cas9‐Directed Genome Editing of Cultured Cells , 2014, Current protocols in molecular biology.

[23]  A. Muotri,et al.  Efficient generation of human iPSCs by a synthetic self-replicative RNA. , 2013, Cell stem cell.

[24]  A. Schambach,et al.  Cellular Restriction of Retrovirus Particle-Mediated mRNA Transfer , 2008, Journal of Virology.

[25]  P. Stockley,et al.  MS2 viruslike particles: a robust, semisynthetic targeted drug delivery platform. , 2013, Molecular pharmaceutics.

[26]  H. Stedman,et al.  Safety and Efficacy of Regional Intravenous (RI) Versus Intramuscular (IM) Delivery of rAAV1 and rAAV8 to Nonhuman Primate Skeletal Muscle. , 2008, Molecular therapy : the journal of the American Society of Gene Therapy.

[27]  H. Stedman,et al.  Safety and efficacy of regional intravenous (r.i.) versus intramuscular (i.m.) delivery of rAAV1 and rAAV8 to nonhuman primate skeletal muscle. , 2008, Molecular therapy : the journal of the American Society of Gene Therapy.

[28]  J. Darlix,et al.  Nucleocapsid mutations turn HIV-1 into a DNA-containing virus , 2008, Nucleic acids research.

[29]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[30]  A. Schambach,et al.  Gene therapy on the move , 2013, EMBO molecular medicine.

[31]  P. Bieniasz,et al.  Imaging the interaction of HIV-1 genomes and Gag during assembly of individual viral particles , 2009, Proceedings of the National Academy of Sciences.

[32]  R. Poot,et al.  RNA folding kinetics regulates translation of phage MS2 maturation gene. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[33]  P. Layrolle,et al.  Pericyte-Like Progenitors Show High Immaturity and Engraftment Potential as Compared with Mesenchymal Stem Cells , 2012, PloS one.

[34]  Lei Chen,et al.  Retroviral pseudotransduction for targeted cell manipulation. , 2004, Molecular cell.

[35]  T. Ichisaka,et al.  Induction of Pluripotent Stem Cells From Adult Human Fibroblasts by Defined Factors , 2008 .

[36]  J. Wozney,et al.  Dlx5 Specifically Regulates Runx2 Type II Expression by Binding to Homeodomain-response Elements in the Runx2 Distal Promoter* , 2005, Journal of Biological Chemistry.

[37]  J. Pagès,et al.  Influence of untranslated regions on retroviral mRNA transfer and expression , 2013, BMC Biotechnology.

[38]  P. Bieniasz,et al.  Global Changes in the RNA Binding Specificity of HIV-1 Gag Regulate Virion Genesis , 2014, Cell.

[39]  D. Heymann,et al.  Mechanisms of bone repair and regeneration. , 2009, Trends in molecular medicine.

[40]  D. Trono,et al.  A Third-Generation Lentivirus Vector with a Conditional Packaging System , 1998, Journal of Virology.

[41]  W. Sessa,et al.  Integrase-deficient lentiviral vectors mediate efficient gene transfer to human vascular smooth muscle cells with minimal genotoxic risk. , 2012, Human gene therapy.

[42]  Yuchen Liu,et al.  Construction of circular miRNA sponges targeting miR-21 or miR-221 and demonstration of their excellent anticancer effects on malignant melanoma cells. , 2013, The international journal of biochemistry & cell biology.

[43]  D. Lindemann,et al.  Efficient transient genetic manipulation in vitro and in vivo by prototype foamy virus-mediated nonviral RNA transfer. , 2014, Molecular therapy : the journal of the American Society of Gene Therapy.

[44]  H. Stedman,et al.  Regional intravascular delivery of AAV-2-F.IX to skeletal muscle achieves long-term correction of hemophilia B in a large animal model. , 2005, Blood.

[45]  T. Schlake,et al.  Protective efficacy of in vitro synthesized, specific mRNA vaccines against influenza A virus infection , 2012, Nature Biotechnology.

[46]  Shankar Srinivas,et al.  Cre reporter strains produced by targeted insertion of EYFP and ECFP into the ROSA26 locus , 2001, BMC Developmental Biology.

[47]  L. Naldini,et al.  Endogenous microRNA regulation suppresses transgene expression in hematopoietic lineages and enables stable gene transfer , 2006, Nature Medicine.

[48]  A. Schambach,et al.  Protein transduction from retroviral Gag precursors , 2010, Proceedings of the National Academy of Sciences.

[49]  M. Yanik,et al.  Innate Immune Suppression Enables Frequent Transfection with RNA Encoding Reprogramming Proteins , 2010, PloS one.

[50]  T. Ichisaka,et al.  Induction of Pluripotent Stem Cells from Adult Human Fibroblasts by Defined Factors , 2007, Cell.

[51]  Howard Y. Chang,et al.  Long noncoding RNAs in cell-fate programming and reprogramming. , 2014, Cell stem cell.

[52]  D. Scherman,et al.  Plasmid electrotransfer of eye ciliary muscle: principles and therapeutic efficacy using hTNF‐α soluble receptor in uveitis , 2006, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[53]  A. Schambach,et al.  Deciphering the impact of parameters influencing transgene expression kinetics after repeated cell transduction with integration‐deficient retroviral vectors , 2015, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[54]  V. Lohmann HCV replicons: overview and basic protocols. , 2009, Methods in molecular biology.

[55]  D. Steinemann,et al.  Modified lentiviral LTRs allow Flp recombinase-mediated cassette exchange and in vivo tracing of "factor-free" induced pluripotent stem cells. , 2014, Molecular therapy : the journal of the American Society of Gene Therapy.

[56]  A I Saeed,et al.  TM4: a free, open-source system for microarray data management and analysis. , 2003, BioTechniques.

[57]  H. Nakauchi,et al.  Stepwise Differentiation of Pluripotent Stem Cells into Osteoblasts Using Four Small Molecules under Serum-free and Feeder-free Conditions , 2014, Stem cell reports.

[58]  G. Sukhikh,et al.  Mesenchymal Stem Cells , 2002, Bulletin of Experimental Biology and Medicine.

[59]  J. Screen,et al.  Further Characterization of Cells Expressing STRO‐1 in Cultures of Adult Human Bone Marrow Stromal Cells , 1999, Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research.

[60]  T. Cathomen,et al.  Novel lentiviral vectors with mutated reverse transcriptase for mRNA delivery of TALE nucleases , 2014, Scientific Reports.

[61]  R. Singer,et al.  Localization of ASH1 mRNA particles in living yeast. , 1998, Molecular cell.

[62]  H. Hassan,et al.  The role of BMP-6, IL-6, and BMP-4 in mesenchymal stem cell-dependent bone development: effects on osteoblastic differentiation induced by parathyroid hormone and vitamin D(3). , 2004, Stem cells and development.