Self-organizing models of human trunk organogenesis recapitulate spinal cord and spine co-morphogenesis [scRNA-seq]

Integrated in vitro models of human organogenesis are needed to elucidate the multi-systemic events underlying development and disease. We report the generation of human trunk-like structures that model the co-morphogenesis, patterning, and differentiation of the human spine and spinal cord. We identified differentiation conditions for human pluripotent stem cells favoring the formation of an embryo-like extending antero-posterior (AP) axis. Single cell and spatial transcriptomics show that somitic and spinal cord differentiation trajectories organize along this axis and can self-assemble into neural tubes surrounded by somites upon extracellular matrix addition. Morphogenesis is coupled with AP patterning mechanisms which results, at later stages of organogenesis, in in vivo-like arrays of neural subtypes along a neural tube surrounded by spine and muscle progenitors contacted by neuronal projections. This integrated system of trunk development indicates that in vivo-like multi-tissue morphogenesis and topographic organization of terminal cell types can be achieved in human organoids, opening windows for the development of more complex models of organogenesis. Single-cell RNA-sequencing analyses were performed on 26 pooled trunk organoids at day 7 of differentiation. Libraries were prepared following 10X Chromium Next GEM Single cell 3' v.3.1 manufacturer protocol. For the spatial transcriptomic study (Tomo-sequecing), two human trunk organoids at day 7, were freshly frozen and then sectioned. Each section was sequenced by bulk RNA sequencing. Libraries were prepared using Cel-Seq2 protocol and Illumina TruSeq small RNA adapters (RPI series).