Oligonucleotide therapies for RNA and DNA : modulation of natural splice-variants, DNA structure & characterization of new synthetic nucleotides and reporter cell lines

Abstract: Oligonucleotide therapy is an evolving field having shown fast and important developments in the last years. From genetics to metabolic, inflammatory, immunodeficiency diseases, cancer and viral infections the medical applications for this type of therapy are becoming broader every day. However, the major challenge for these therapies is still the delivery; thus new chemistries, as well as improved delivery vectors are needed. Equally, the lack of relevant reporter systems hampers the characterization and progress of these emergent “drugs.” This thesis work was aimed to address some of the gaps presented above. Thus, the introduction section starts with a brief overview of the gene therapy. It continues with an explanation of the oligonucleotide therapy strategies and technologies used for RNA and DNA targeting and ends with a clinical case for each approach. The methodology section explains the theoretical and practical aspects of the most relevant techniques in this study and the results section explain the rational and gives a brief presentation of the main results and conclusions for each paper. Paper I presents a new splice-switching approach for treating diseases by regulating proteins at the splicing level. The new principle was to convert the normal splice form to a natural, but less abundant and inactive, splice variant to treat hypercholesterolemia. Paper II shows the development and characterization of a new collection of reporter cell lines for splice- switching. These reporter cell lines can serve as models for cell-type-specific screenings of different ON chemistries and delivery vectors. Paper III and IV demonstrate the development and characterization of a new nucleic acid chemical modification providing an oligomer with cell penetrating properties. Finally, in paper V a new mechanism for gene expression regulation at the genome level is presented.