Human dorsal forebrain organoids show differentiation-state-specific protein secretion

The human brain microenvironment undergoes dynamic changes during development, which have been incompletely characterized in <i>in vitro</i> models including neural organoids. Here, we used liquid chromatography-mass spectrometry to investigate proteome and secretome changes in human dorsal forebrain organoids derived from three hiPSC lines at days 20, 35, and 50 of differentiation. Proteome and immunohistochemical analysis revealed reduced proliferation and increased differentiation of progenitor cells gradually over time. In contrast, secretome analysis showed distinct characteristics at each timepoint - notably, at day 35, the numbers of cell adhesion molecules, synaptic proteins, and proteases were increased. Taken together, we present a resource describing the dynamic features of a neural organoid proteome and secretome across different genetic backgrounds. We describe the unique niche composition of neural organoids during the period of neurogenesis and suggest that synaptic proteins may play a role in guiding neurogenesis.