An in vivo and in vitro spatiotemporal atlas of human fetal midbrain development

The dopaminergic system has key roles in human physiology and is implicated in a broad range of neurological and neuropsychiatric conditions that are increasingly investigated using induced pluripotent stem cell-derived midbrain models. To determine the similarity of such models to human systems, we undertook single cell and spatial profiling of first and second trimester fetal midbrain and compared it to in vitro midbrain models. Our initial histological analysis of second trimester fetal midbrain revealed structural complexity already similar to that of adult tissue, although this similarity did not fully extend to transcriptional activity. Moreover, we show that in vitro models recapitulate the transcriptional activity of late first trimester fetal midbrain, while 3D models replicate the spatial organization and cellular microenvironments of first and second trimester fetal midbrain. Understanding the extent of human tissue recapitulation in midbrain laboratory models is essential to justify their use as biological proxies. Overall design: For spatial transcriptomics data: Fetal midbrain samples from four timepoints were profiled with spatial transcriptomics. Each sample had three biological replicates. Four spatial transcriptomics capture areas (each containing six organoids) were also profiled. The fetal samples are: PC_AGE_1_REP_1 PC_AGE_1_REP_2 PC_AGE_1_REP_3 PC_AGE_2_REP_1 PC_AGE_2_REP_2 PC_AGE_2_REP_3 PC_AGE_3_REP_1 PC_AGE_3_REP_2 PC_AGE_3_REP_3 PC_AGE_4_REP_1 PC_AGE_4_REP_2 PC_AGE_4_REP_3 The organoid samples are: OCT_BLOCK_1 OCT_BLOCK_2 OCT_BLOCK_3 OCT_BLOCK_4 For single-cell transcriptomics data: In vitro 2D and 3D organoids (both iPSC-derived samples) were profiled throughout neuronal differentiation, along with fetal midbrain from first and second trimester. For 2D models, samples from 2 donors (2 controls) were collected at days 40 and 70 of differentiation. For 3D models, samples from 4 donors (2 controls, 2 patients, one patient-corrected line) were collected at days 40, 70 and 120 of differentiation. Fetal midbrain samples were collected at post-conceptional weeks 10, 12, 16 and 20. To reduce the batch effects between donors, individual donors were pooled at the time of sequencing. The biological samples described below correspond to 10x libraries (samples processes through the same GEM well). The 2D and 3D models are: mid_organoids8644112 mid_organoids8644113 mid_organoids8644114 mid_organoids8643920 mid_organoids8643921 mid_organoids8643922 mid_organoids8644016 mid_organoids8644017 mid_organoids8644018 The fetal samples are: F10121620_A F10121620_B F10121620_C F10121620_D