Does transient Type I Interferon exposure shape long-term neurodevelopmental states?

Neurodevelopmental conditions are a heterogeneous and highly prevalent group of disorders with lifelong consequences. Maternal infection and inflammatory cytokines have emerged as important risk factors, but the underlying mechanisms and potential new targets for prevention and therapy are still poorly defined. Our laboratory showed, using human brain organoids, that viral infection of neural stem cells causes organoid defects. Viral infection also triggers IFN-I responses, particularly IFNβ, which can be neuroprotective in a short-term window. However, chronic activation has been implicated in neurodevelopmental toxicity in interferonopathies, raising the question of whether long-term alterations are driven by initial stimulation or by persistent post-stimulation signalling. Preliminary reporter experiments revealed that IFN dose and subtype are key determinants of response heterogeneity, and that high doses can elicit signals persisting for many days. These findings indicate that IFN responses in brain organoids are highly heterogeneous, both across cell populations and over time. This highlights the need for approaches able to capture single-cell diversity and to follow the dynamics of the response beyond the initial stimulation. This project aims to characterize the long-term effects of IFN-I exposure during early brain development and to dissect the contribution of distinct signalling phases. Human brain organoids, including ISRE:tdTomato reporter lines, will be analysed at multiple time points after IFN washout, to track responder populations and to assess phenotypic and molecular changes, through immunofluorescence, single-cell RNA sequencing, ATAC-seq, bulk transcriptomics, to resolve cell-type–specific responses and chromatin accessibility at interferon target loci. In addition, perturbation strategies will be applied using pharmacological inhibitors or genetic approaches to selectively interfere with initial versus post-stimulation. By integrating brain organoid models with single-cell and spatial omics, this work seeks to link acute and persistent IFN-I responses to long-term developmental outcomes, with the goal of identifying therapeutic windows and informing strategies for IFN-related neurodevelopmental disorders.