PROJECT SUMMARY The fundamental question for the field of Down Syndrome (DS) basic research is how an extra copy of human chromosome 21 (HSA21) translates into the organ-specific pathologies that are observed in the DS population. Structural pathologies in DS, such as brain size and heart malformation, are present at birth, and are generally associated with smaller organs or reduced growth. Therefore, they must be causally related to structural organogenesis defects, reflecting embryologic origins. A mechanistic understanding of DS-specific organogenesis defects is lacking in most cases, although a rich descriptive literature sets the stage for concerted mechanistic studies. Specifically, how Trisomy 21 (T21) causes heart or brain morphogenesis defects, causing CHD or intellectual disability, respectively, is poorly understood. The molecular networks identified by the proposed work, implicated in DS organ-specific cardiac and neuronal progenitors, will serve as a template for understanding the molecular ontogeny of heart and brain defects, as well as other organ defects, in DS. We have defined Hedgehog (Hh) signaling as an explicit development timer during mammalian development, required for maintaining organ-specific progenitor cells and dictating their differentiation in time and space, independent from developmental patterning or proliferation. The controlled balance between organ-specific progenitors and their differentiated counterparts is fundamental to complex organogenesis. The Moskowitz lab found that when Hh signaling is abrogated in cardiac progenitors, they underwent precocious differentiation, resulting in morphogenesis failure. Similarly, the Bhattacharyya lab has recently identified deficits in the Hh pathway in neuronal progenitors that controls their differentiation. We propose the transformative hypothesis that a unifying cause of birth defects in DS is failure of heterochronic timing control of organ-specific progenitor differentiation, resulting in precocious differentiation, a reduction of organ-specific progenitors, morphogenesis failure and birth defects in multiple organs.