In vertebrates, the first line of defense against viral infections involves the immediate sensing of viruses, by pattern recognition receptors, and the production of type-I and –III interferons (IFN-I and IFN-III). After being secreted into the extracellular milieu, IFN leads to the rapid induction of a potent antiviral response characterized by the expression of hundreds of IFN-stimulated genes (ISGs) in infected and neighboring cells (Schneider, et al. 2014). These ISGs contribute to the establishment of an antiviral state by directly antagonizing the virus, driving the expression of secondary antiviral products and regulating the antiviral response. IFN signaling also contributes to inflammatory processes through the regulation of immune cell recruitment and activation. Besides their potent antiviral role, IFNs are also involved in cancer immunosurveillance and autoimmunity. Given their broad activity, IFN production and its signaling are tightly regulated in order to allow for viral clearance while limiting tissue damage and cell death.
The Blanco-Melo lab seeks to understand the diverse regulatory processes that control the IFN response, in order to enable the selective manipulation of this potent antiviral pathway for therapeutic purposes.
Current research lines in the lab are:
1. Mechanisms regulating IFN expression during development: Pluripotent stem cells are known to lack a canonical IFN-I/III response upon viral infection, and our previous work actually suggest that the IFN-I system and pluripotency may be incompatible with each other (Eggenberger, et al. 2019). In the lab, we are interested in understanding the mechanisms responsible for the blockade of IFN production and signaling during early development. In collaboration with the tenOever lab at NYU, we are characterizing the transcriptional and epigenetic changes that occur upon viral infection in individual cells at different developmental stages.
2. IFN-induced gene splicing and its impact in the establishment of an antiviral response: It is estimated that >95% of human pre-mRNAs are processed to yield multiple transcripts by alternative splicing, greatly expanding the genetic repertoire of eukaryotic genomes (Nilsen & Graveley, 2010). However, despite its impact on diverse molecular functions and pathways, the effects of alternative splicing on the IFN response have not been fully explored. We are currently characterizing a novel IFN-induced splicing program, the mechanisms controlling this program, and the impact that it has on the cell's ability to mount an efficient antiviral response.
3. Genetic circuits controlling the cellular response to viral infections: We are interested in elucidating the complete gene regulatory network controlled by IFN and their ISGs, their temporal and cell-type specific dynamics, as well as its robustness and evolvability in the face of different viral infections. Currently, we are performing pooled single-cell CRISPR screens, which allow for the systematic characterization of entire biological circuits by evaluating the impact of individual gene perturbations to the cellular transcriptome in a high-throughput fashion (Datlinger, et al. 2017).
Schneider, W.M., Chevillotte, M.D., and Rice, C.M. (2014). Interferon-stimulated genes: a complex web of host defenses. Annu Rev Immunol 32, 513-545. DOI: 10.1146/annurev-immunol-032713-120231
Eggenberger, J., Blanco-Melo, D., Panis, M., Brennand, K.J., and tenOever, B.R. (2019). Type I interferon response impairs differentiation potential of pluripotent stem cells. Proc Natl Acad Sci U S A 116, 1384-1393. DOI: 10.1073/pnas.1812449116
Nilsen, T.W., and Graveley, B.R. (2010). Expansion of the eukaryotic proteome by alternative splicing. Nature 463, 457-463. DOI: 10.1038/nature08909
Datlinger, P., Rendeiro, A.F., Schmidl, C., Krausgruber, T., Traxler, P., Klughammer, J., Schuster, L.C., Kuchler, A., Alpar, D., and Bock, C. (2017). Pooled CRISPR screening with single-cell transcriptome readout. Nat Methods 14, 297-301. DOI: 10.1038/nmeth.4177