Benchmarking brain organoid recapitulation of fetal corticogenesis

Abstract

Brain organoids are becoming increasingly relevant to dissect the molecular mechanisms underlying psychiatric and neurological conditions. The in vitro recapitulation of key features of human brain development affords the unique opportunity of investigating the developmental antecedents of neuropsychiatric conditions in the context of the actual patients’ genetic backgrounds. Specifically, multiple strategies of brain organoid (BO) differentiation have enabled the investigation of human cerebral corticogenesis in vitro with increasing accuracy. However, the field lacks a systematic investigation of how closely the gene co-expression patterns seen in cultured BO from different protocols match those observed in fetal cortex, a paramount information for ensuring the sensitivity and accuracy of modeling disease trajectories. Here we benchmark BO against fetal corticogenesis by integrating transcriptomes from in-house differentiated cortical BO (CBO), other BO systems, human fetal brain samples processed in-house, and prenatal cortices from the BrainSpan Atlas. We identified co-expression patterns and prioritized hubs of human corticogenesis and CBO differentiation, highlighting both well-preserved and discordant trends across BO protocols, including different degrees of heterochronicity in differentiation across BO models compared to fetal cortex. Our approach provides a framework to directly compare the extent of in vivo/in vitro alignment of neurodevelopmentally relevant processes and their attending temporalities, structured as an accessible resource to query for modelling human corticogenesis and the neuropsychiatric outcomes of its alterations.

GTF2I dosage regulates neuronal differentiation and social behavior in 7q11.23 neurodevelopmental disorders

“…Other genes consistently upregulated in 7Dup in more than one stage were a group of poorly characterized zinc finger transcription factors (e.g., ZNF229, ZNF300, ZNF560, ZNF578). Focusing at each differentiation stage separately, the most outstanding observations included: i) at day 18, a modulation of cell adhesion and ECM components, mostly up-regulated in WBS COs. Of note, several of these genes (e.g., COL12A, PCOLCE, BGN, NID2, EMILI1) belong to a fetal cortex gene co-expression module characterized by non-monotonic expression pattern during cortex development and functionally associated to ECM (Cheroni et al, 2022); ii) at day 50, an upregulation in WBS COs of histone protein genes as well as RG marker Nestin, consistent with the observed increase in proliferative cells in WBSs COs. This was accompanied at the same stage with the up-regulation in 7Dup COs of dorsal forebrain commitment drivers, including FOXG1, LHX2, NEUROD6 and TBR1, whose trend of modulation was conserved in foldchange also at day 100 (Figure S4A); and, iii) the upregulation at day 100 of genes involved in synaptic transmission in WBS COs (e.g., GRIK1, GRIA4, GRIN3A).…”

“…We generated patient-derived COs that recapitulate early to mid-fetal corticogenesis (Cheroni et al, 2022; Paşca et al, 2015; Yoon et al, 2019) from 13 iPSC lines reprogrammed from 8 affected individuals and 5 healthy controls (4-WBS, 4-7Dup and 5 CTL, Figure 1A ), including, respectively, 1 clone per individual following the design that we previously benchmarked (Germain and Testa, 2017), in order to avoid artificial inflation of spurious differential expression due to donors‘ genetic backgrounds. Array comparative genomic hybridization (aCGH) confirmed that the 7q11.23 CNV is preserved upon reprogramming ( Figure S1A ).…”

Forebrain Organoids to Model the Cell Biology of Basal Radial Glia in Neurodevelopmental Disorders and Brain Evolution

“…This revealed similar lineage relationships between aRG and bRG in both systems ( Camp et al, 2015 ; Pollen et al, 2015 ). Subsequent studies readily confirmed the existence of a cell population with a transcriptomic signature of bRG ( Bershteyn et al, 2017 ; Giandomenico et al, 2019 ; Pollen et al, 2019 ; Velasco et al, 2019 ; Cheroni et al, 2022 ). A recent work aimed to understand the reproducibility of organoids, identified consistent generation of diverse cell types, including bRG, in multiple forebrain organoids ( Velasco et al, 2019 ).…”