Development and analysis of efficient and target-specific antiretroviral recombinases

• Applicant: Professor Dr. Frank Buchholz
• Subject Area: General Genetics and Functional Genome Biology ; Virology ; Cell Biology
• Term: from 2014 to 2018
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 260115349

• Final Report Year: 2018

Final Report Abstract

Based on the here described project work we were able to demonstrate the generation of site-specific recombinases with high therapeutic relevance. In particular, we further developed recombinases Tre and Brec1 to recognize different target sequences in the long-terminal repeats (LTR) of the HIV-1 provirus and herewith, proved a first-in class strategy for eradicating the provirus in infected cells. Remarkable is the positive factor that indel formations and the emergence of resistances, in contrast to other nuclease technologies, such as CRISPR/Cas system, were not observed. Also off-target effects were not detected during the different stages of the experimental processes. Therefore, safety aspects in regard of patient treatment are being considered as very high. Based on these results, a clinical study is going to be initiated in collaboration with the HPI in Hamburg. In addition to the successful development of the HIV-1 recombinases, we were also successful in applying the technology to other therapeutic targets. Thus, the scientific team developed first recombinase variants to inactivate the human-T-cell leukemia virus (HTLV-I), another human pathogenic retrovirus. Moreover, detailed sequence analyzes of specific recombinases as well as structural biology studies on evolved recombinases provided first insights into how DNA specificity of enzymes can be rationally altered.

Publications

• (2016) Antiviral therapy of persistent viral infection using genome editing. Curr Opin Virol. 2016 Oct;20:85-91
  Buchholz F, Hauber J
  
• (2016) Directed evolution of a recombinase that excises the provirus of most HIV-1 primary isolates with high specificity. Nature Biotechnology 34, 401–409
  Karpinski J, Hauber I, Chemnitz J, Schäfer C, Paszkowski-Rogacz M, Chakraborty D, Beschorner N, Hofmann-Sieber H, Lange UC, Grundhoff A, Hackmann K, Schrock E, Abi-Ghanem J, Pisabarro MT, Surendranath V, Schambach A, Lindner C, van Lunzen J, Hauber J & Buchholz F
  
• (2016) Discovery of Nigri/nox and Panto/pox site-specific recombinase systems facilitates advanced genome engineering. Sci Rep. 2016 Jul 22;6:30130
  Karimova M, Splith V, Karpinski J, Pisabarro MT, Buchholz F
  
• (2017) Crystal structure of an engineered, HIV-specific recombinase for removal of integrated proviral DNA. Nucleic Acids Res., 2017 Sep 19;45(16):9726-9740
  Meinke G, Karpinski J, Buchholz F, Bohm A
  
• (2017) Designer-Rekombinasen für präzises Genome Editing. BIOspektrum. 02.17:151-154
  Karpinski J, Schneider M, Lansing F, Hauber J, Buchholz F