Trisomy 21 Promotes an Inflammatory Hyperresponsiveness in the Brain and Modulates Transcriptional Regulation in a Cell Type–Specific Manner

Patients with type I interferonopathies, a collection of disorders leading to elevated levels of type I interferon (IFN), have a neuropathological hallmark of basal ganglia calcification thought to result from persistent IFN-dependent inflammation. Similar calcification patterns have been detected in Down syndrome (DS) individuals as young as one year of age and worsens over time, implying that the underlying mechanism begins early and progresses throughout development. Neuropathological studies have identified many patterns of abnormal development in DS brains, including hypocellularity, defective oligodendrocyte differentiation and function, and, of particular interest to us, elevated astrocyte counts and altered microglial morphological phenotypes. We hypothesize that the type I IFN receptor, encoded by IFNAR1/2, which is triplicated in DS as it is on chromosome 21, creates a pro-inflammatory environment that results in calcification, altered development, and disorganization of the fetal brain. Recently, it has been shown that there is a population of basally IFN-I–responsive microglia that express interferon-stimulated genes (ISGs) in the developing brain of mice; this population can expand in response to developmental trauma, and similar microglia have been implicated in Alzheimer’s pathophysiology in both mice and humans. It is possible that DS brains have an expanded population of these microglia and/or other populations of CNS cells with heightened type I IFN responsiveness, even in the absence of acute stressors. To evaluate causes and effects of inflammation during development in DS, we have generated hiPSCs from patients and typical controls and have used them to generate astrocytes and microglia. We have shown that DS astrocytes are hyperresponsive to stimulation with IFN-α2b and have further conducted bulk RNA sequencing on fibroblasts, astrocytes, and microglia with or without IFN stimulation. We have found that the transcriptional signature in fibroblasts and astrocytes differs greatly between DS and CT as well as between cell types. Microglia depict a less robustly altered transcriptome. Further, IFN-α2b treatment produces a predictable, dose-dependent increase in expression of ISGs that is more pronounced in DS. Overall, our results indicate that IFN-signaling in the DS brain can result in dramatic transcriptional dysregulation in a cell type–specific manner.