From naïve pluripotency to human neural organoids through a three-dimensional morphogenetic continuum

Human central nervous system (CNS) development involves complex transitions from pluripotency to regionalised neural tissues. The early phases of this process are inaccessible in humans but can potentially be modelled in vitro using brain organoids, including to study neurodevelopmental disorders. However, current methods are based on post-implantation-like human pluripotent stem cells (hPSCs), which exhibit a hypermethylated state and show epigenetic memory retention. Here we developed a 3D model of human CNS development, starting from naive human induced PSCs (hiPSCs), which exhibit a hypomethylated pre-implantation-like state of pluripotency and develop into 3D neuroepithelial cysts in a timely morphogenetic continuum. Upon treatment with appropriate signalling cues, naive-derived neuroepithelial cysts can be specified toward different axial identities. Extended culture of anterior-specified organoids results in forebrain-like structures containing both dorsal and ventral neural precursors as well as mature neurons, exhibiting appropriate cellular diversity and functional properties. We applied this system to model Fragile X Syndrome (FXS), an epigenetically regulated neurodevelopmental disorder. We found that FXS patient-derived naive hiPSCs, initially demethylated at the Fmr1 locus, gradually underwent remethylation during organoid development. In addition, Fmr1 silencing started much earlier than can be detected by pre-natal analysis, and is concomitant with the development of mosaicisms. Our approach provides a new platform for studying human CNS development, including early epigenetic events and regional patterning, demonstrating the potential of naive hiPSC-derived organoids for modelling neurodevelopmental disorders with complex epigenetic regulation. Highlights- single naive hiPSCs differentiate into 3D neuroepithelial cysts in a timely morphogenetic continuum - signalling cues at appropriate developmental transitions can direct naive hiPSC- derived organoids to different regional identities of the human CNS - naive hiPSC-derived forebrain organoids display cellular complexity representing both dorsal and ventral identities - forebrain organoids from Fragile X Syndrome patients recapitulate the genetic instability and epigenetic dysregulation of Fmr1 locus.