The present invention provides a method for restoring immune tolerance in vivo. The invention relates to the use of a recombinant gene encoding auto-antigens or parts thereof for restoring immune tolerance to the auto-antigens in vivo, under transcriptional control of polyomaviral early and late promoters. In a preferred embodiment, the invention relates to the use of recombinant polyomaviral gene delivery vector particles, such as simian virus 40 (SV40) viral vector particles encoding one or multiple auto-antigens or parts thereof under transcriptional control of the SV40 early and late promoter, for restoring immune tolerance to the auto-antigens in vivo. The invention also relates to compositions comprising recombinant genes or polyomaviral vectors and uses thereof as treatment for degenerative or dystrophic diseases.