PROJECTS

antiviral immunity of embryonic stem cells

Interferons (IFN) are a group of cytokines released by cells in response to infection with viruses and other pathogens. Specifically, type-I interferons can be produced by virtually any cell type in a mammalian organism in response to viral infections, except for embryonic stem cells and oocytes. In clinical settings, the deregulation of the IFN response is associated to autoimmune diseases, such as lupus, or Singleton-Merten syndrome, amongst others.

We are interested in deciphering the mechanisms that control the activation of the type-I interferon response in the differentiated and pluripotent context. We are also interested in understanding how pluripotent cells defend from viruses.

Kases KJ et al (2026) Identification of cellular double-stranded RNAs in mammalian embryonic stem cells. BioRxiv

Witteveldt J et al (2025) Double-stranded RNA sensing drives interferon silencing in early development. Nature Communications 10.1038/s41467-025-66352-0

Witteveldt J, Knol L, Macias S (2019) MiRNA-deficient mouse embryonic stem cells acquire a functional Interferon response. eLife pii: e44171. doi: 10.7554/eLife.44171

Mueller F, Witteveldt J, Macias S (2024) Antiviral defence mechanisms during early mammalian development. Viruses 16(2), 173

mRNA translation control during the antiviral response

One highly effective cellular response to viral infections is the global shutdown of translation known as host shut-off. This response aims at delaying viral replication through preventing viral mRNAs from creating new infectious particles. This effect is mediated by phosphorylation of Eukaryotic initiation factor 2 alpha (eIF2α) by the double stranded RNA binding kinase PKR. The underlying mechanisms of this process are poorly understood, since this effect on translation is not global and ISGs can still be translated during this response. Certain ISGs are known to escape host shut-off through internal ribosome entry site (IRES) dependent translation, however, not all ISGs contain IRES sites.

We are currently investigating host cellular factors that are necessary to efficiently translate type-I interferon mRNAs and other ISGs. We are also investigating the role of IFITs in the translational control during the antiviral response.

Watson S, Bellora N, Macias S (2019) ILF3 is essential to establish the antiviral type I interferon gene expression program. Nucleic Acids Research pii: gkz1060. doi: 10.1093/nar/gkz1060

Avila-Bonilla RG, Macias S (2024) The molecular language of RNA 5'ends; guardians of RNA identity and immunity. RNA 30(4): 327-336

RNA processing factors in human disease

Many human diseases, including cancer, correlate with mutations in RNA processing enzymes, but it is still unclear if defective RNA processing is causative of the disease.

Using genome-wide approaches and CRISPR, we are modelling some of these mutations in human cellular models to characterize the molecular consequences of these mutations in cell physiology but also gene expression. In this manner, we are hoping to provide a molecular landscape of the main pathways or molecules malfunctioning in the disease with the aim of identifying novel therapeutic targets.

Colomer-Boronat et al (2025) DGCR8 haploinsufficiency leads to primate-specific RNA dysregulation and pluripotency defects. Nucleic Acids Research 53(6), gkaf197

Gázquez-Gutiérrez A et al (2026) Control of retrotransposon-driven activation of the interferon response by the double-stranded RNA binding protein DGCR8. Nucleic Acids Research

https://doi.org/10.1093/nar/gkag190

Gordon K et al (2026) DICER1-related tumour predisposition mutations increase 3p-miRNA function and HERVH activity. Nature Communications