AbstractDown syndrome (DS) is the most common genetic form of intellectual disability caused by the presence of an additional copy of human chromosome 21 (Hsa21). To provide novel insights into genotype–phenotype correlations, we screened the in vivo DS mouse library with standardized behavioural tests, magnetic resonance imaging (MRI) and digged into hippocampal gene expression. Altogether this approach brings novel insights into the field. First, we unravelled genetic interactions between different regions of the chromosome 21 and how they importantly contribute in altering the outcome of the phenotypes. Then, in depth analysis of misregulated expressed genes involved in synaptic dysfunction highlitghed 6 biological cascades centered around DYRK1A, GSK3β, NPY, SNARE, RHOA and NPAS4. Finally, we provide a novel vision of the existing altered gene-gene crosstalk and molecular mechanisms targeting specific hubs in DS models that should become central to advance in our understanding of DS and therapies development.Author SummaryDown syndrome (DS) is the most frequent cause of intellectual disability and is caused by increase in gene dosage and multiple genetic interaction but not so many have been described so far. Taking advantage of DS mouse models, we investigated behavior and cognition, brain morphology and hippocampal gene expression in a controlled environment and we unraveled how multiple genetic interactions between different regions of the chromosome 21 contribute in altering the outcome of the behavioural, morphological and molecular/pathways phenotypes. Nonetheless we found multiple deregulated genes in the hippocampus, where overlapping DS models show convergence in the biological cascades altered, observed via building protein-protein interaction and regulatory networks, and centered in 6 main hubs: DYRK1A, GSK3β, NPY, SNARE, RHOA and NPAS4. Although four of them were already described to be altered in some DS models, we validated two additional ones, RHOA and NPAS4, and we have built a novel vision of the existing altered gene-gene crosstalk and molecular mechanisms, targeting 6 specific highly interconnected hubs in DS models, that should become central to advance in our understanding of DS physiopathology and therapy development.