All Publications

  • Peptide nucleic acid-dependent artifact can lead to false-positive triplex gene editing signals. Proceedings of the National Academy of Sciences of the United States of America Ho, P. Y., Zhang, Z., Hayes, M. E., Curd, A., Dib, C., Rayburn, M., Tam, S. N., Srivastava, T., Hriniak, B., Li, X., Leonard, S., Wang, L., Tarighat, S., Sim, D. S., Fiandaca, M., Coull, J. M., Ebens, A., Fordyce, M., Czechowicz, A. 2021; 118 (45)


    Triplex gene editing relies on binding a stable peptide nucleic acid (PNA) sequence to a chromosomal target, which alters the helical structure of DNA to stimulate site-specific recombination with a single-strand DNA (ssDNA) donor template and elicits gene correction. Here, we assessed whether the codelivery of PNA and donor template encapsulated in Poly Lactic-co-Glycolic Acid (PLGA)-based nanoparticles can correct sickle cell disease and x-linked severe combined immunodeficiency. However, through this process we have identified a false-positive PCR artifact due to the intrinsic capability of PNAs to aggregate with ssDNA donor templates. Here, we show that the combination of PNA and donor templates but not either agent alone results in different degrees of aggregation that result in varying but highly reproducible levels of false-positive signal. We have identified this phenomenon in vitro and confirmed that the PNA sequences producing the highest supposed correction in vitro are not active in vivo in both disease models, which highlights the importance of interrogating and eliminating carryover of ssDNA donor templates in assessing various gene editing technologies such as PNA-mediated gene editing.

    View details for DOI 10.1073/pnas.2109175118

    View details for PubMedID 34732575

  • Control of DUX4 Expression in Facioscapulohumeral Muscular Dystrophy and Cancer. Trends in molecular medicine Karpukhina, A., Tiukacheva, E., Dib, C., Vassetzky, Y. S. 2021


    DUX4, a gene encoding a transcription factor involved in early embryogenesis, is located within the D4Z4 subtelomeric repeat on chromosome 4q35. In most healthy somatic tissues, DUX4 is heavily repressed by multiple genetic and epigenetic mechanisms, and its aberrant expression is linked to facioscapulohumeral muscular dystrophy (FSHD) where it has been extensively studied. Recently, DUX4 expression has been implicated in oncogenesis, although this is much less explored. In this review, we discuss multiple levels of control of DUX4 expression, including enhancer-promoter interactions, DNA methylation, histone modifications, noncoding RNAs, and telomere positioning effect. We also connect disparate data on intrachromosomal contacts involving DUX4 and emphasize the feedback loops in DUX4 regulation. Finally, we bridge data on DUX4 in FSHD and cancer and discuss prospective approaches for future FSHD therapies and the potential outcomes of DUX4 inhibition in cancer.

    View details for DOI 10.1016/j.molmed.2021.03.008

    View details for PubMedID 33863674