Mechanisms of gene expression control in the p53 network

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Trisomy 21 (T21) is the most common human chromosomal disorder, leading to the condition known as Down syndrome (DS) (1, 2). A remarkable observation enabled by the significant increase in the life expectancy of people with DS is that T21 protects these individuals from some medical conditions, while strongly predisposing them to others, providing a strong rationale for the NIH INCLUDE project (INvestigation of Co-occurring conditions across the Lifespan to Understand Down syndromE). In particular, and related to the mission of the NCI, epidemiological studies have revealed that people with DS display significantly lower rates of solid malignancies (3, 4), while being highly predisposed to many types of leukemias (5-8). Despite the obvious potential of the population with DS to advance our understanding of tumorigenesis and leukemogenesis, little is known about the molecular and cellular mechanisms by which T21 causes this differential ‘malignancy spectrum’. Clearly, research in this area will benefit not only people with DS, but also the typical population at large. Consistent with a key area of emphasis of the INCLUDE project (immune system dysregulation), we recently discovered that T21 causes constitutive activation of the Interferon (IFN) response across diverse cell types (9), which is likely due to the fact that four of the six IFN receptors (IFNRs) are encoded on chr21 (10). Accordingly, T21 cells are hypersensitive to IFN ligands, display hyperactivation of JAK/STAT signaling, and overexpression of IFN-Stimulated Genes (ISGs) (9-12). Furthermore, in a large plasma proteomics cohort study, we identified dozens of inflammatory cytokines with mechanistic links to IFN signaling that are dysregulated in people with DS (13). Strikingly, the IFN response was recently identified as a core pathway dysregulated in multiple mouse models of DS carrying triplication of the IFNR gene cluster (14). Additionally, several lines of evidence indicate that T21 may increase activity of the tumor suppressor p53 in both IFN-dependent and -independent ways. IFN-independent mechanisms could include aneuploidy itself, which is a known p53-activating stimulus (15), and the overexpression of chr21-encoded proteins, such as ETS2, a transcription factor, and DYRK1A, a kinase, both of which stimulate p53 activity (16, 17). IFN-dependent mechanisms include direct induction of the p53 promoter by Type I IFNs (18), interaction of the IFN-activated transcription factor STAT1 with p53 to enhance p53 activity (19), and three ISGs induced by T21 -ISG15, IFI16 and PYHIN1- that enhance p53 activity by diverse mechanisms (20-23). Altogether, these observations support the hypothesis that T21 can enhance the activity of the p53 network in people with DS, with potentially beneficial and deleterious effects (e.g. enhanced tumor suppression versus accelerated aging, senescence, and neurodegeneration). Therefore, consistent with Component 1 of the INCLUDE project, we hypothesize that hyperactive IFN signaling contributes to the different disease spectrum in people with DS. More specifically, within the scope of the parent NCI R01 award, we propose to investigate the interplay between T21, IFN signaling, and the p53 network. Our Specific Aims for this Supplement are: 1. To define the impact of trisomy 21 and IFN hyperactivity on the p53 transcriptional program. With NIH funding, our team was the first to employ genome-wide measurements of nascent RNA synthesis (i.e. GRO-seq) to identify the direct p53 transcriptional program using a small molecule inhibitor of the p53-MDM2 interaction called Nutlin (24, 25). Related to Aim 1 of the parent R01, we will use our published multi-omics pipeline combining p53 ChIP-seq, GRO-seq, and RNA-seq, to test the hypothesis that T21 enhances the p53 transcriptional program. We will use an available panel of iPSCs with and without T21 as a paradigm to identify quantitative (i.e. global) and/or qualitative (i.e. gene-specific) impacts of T21 on p53 signaling, and to define to what degree these changes are driven by enhanced JAK/STAT signaling. 2. To define the impact of trisomy 21 and IFN hyperactivity on the cellular response to non-genotoxic p53 activation in diverse cell types. With funding provided by the parent award, we completed an exhaustive characterization of the p53 signaling cascade elicited by Nutlin in diverse cancer cell lines (24-29). Now, in response to emphasis in the INCLUDE project on iPSCs and a pan-omics cohort study of people with DS, we will characterize the cellular response to Nutlin treatment in three available panels of matched cell types with and without T21: iPSCs, skin fibroblasts, and PBMCs derived from an ongoing cohort study of people with DS. We will use established cell phenotyping assays to test the hypothesis that T21 alters p53-mediated cellular responses, such as cell cycle arrest and apoptosis, and define to what degree these effects are dependent upon elevated JAK/STAT signaling. Altogether, completion of these experiments will enable future studies to define the interplay between IFN signaling and the p53 network in the differential development of co-morbidities in people with DS. QVR supplement abstract