Science - USA (2022-02-18)

continuous exposure that occurs in vivo
during progenitor expansion ( 26 ); and (ii)
three-dimensional (3D) cortical brain organoids
(henceforth COs in the figures and organoids in
the text) differentiated from induced pluripotent
stem cells (iPSCs), a neurodevelopmental model

that recapitulates salient features of human cor-

ticogenesis, including, as we previously showed

( 27 ), the emergence of outer radial glia cells,

which is a cell population with a central role in

multiple human-specific brain diseases ( 28 Ð 31 ).

Organoids present two key advantages that

warrant their comparison with fetal progenitors.

First, they derive from highly standardized, self-

renewing sources (iPSCs), which overcomes the

inherent limitations, technical and ethical alike,

of fetal progenitor procurement. Second, orga-

noids are a developing system, which allows

Caporaleet al.,Science 375 , eabe8244 (2022) 18 February 2022 5 of 15

AB

C Gene Expression dysregulation of SFARI DEGs in HFPNSC Gene Expression dysregulation of SFARI DEGs in CO

TopGO Enrichment

concordant DEGs

TopGO Enrichment

discordant DEGs

Clusters of DEGs across human cellular systems

CO HFPNSC

Concordant

Clusters

Discordant

Clusters

SRP-dependent cotranslational

protein targeting to membrane

translational initiation

nuclear-transcribed mRNA

catabolic process

viral transcription

cytoplasmic translation

mitochondrial electron transport

NADH to ubiquinone

ribosomal large

subunit assembly

ribosomal small

subunit assembly

establishment of apical/basal cell

polarity

regulation of plasma membrane

organization

post-embryonic animal

morphogenesis

cytoplasmic translation

membrane depolarization during

action potential

positive regulation of autophagy

positive regulation of actin lament

bundle assembly

extracellular matrix organization

D Gene Expression dysregulation of SFARI CO-DEGs in HFPNSC Gene Expression dysregulation of SFARI HFPNSC-DEGs in CO

Fig. 3. Pathophysiological relevance of MIX N effects on human cellular
models.(A) Heatmap showing the relative gene abundance (z-scores of
SVA-corrected values) of the DEGs that are consistently and discordantly
dysregulated upon exposure of HFPNSCs and COs to MIX N. (The rows across
the heatmaps refer to the same genes plotted in the two experimental systems,
with vertical white spaces visually defining gene clusters and experimental
systems.) (B) Results of GO enrichment analysis performed on the DEGs that are
consistently or discordantly dysregulated in HFPNSCs and COs. Bar plots depict

thePvalues for the top eight biological process GO terms. (C) Plots of gene

expression levels (SVA-corrected values) across exposure conditions for the

DEGs that overlap with the list of SFARI genes in HFPNSCs and COs, respectively.

(D) Gene expression levels (SVA-corrected values) across exposure conditions

for the DEGs that overlap with the list of SFARI genes in COs plotted for

HFPNSCs, and vice versa. (Pvalues and FDR are calculated through differential

expression analysis for each experimental model.) In (C) and (D), gray bars

indicate the mean expression value for each gene in each exposure condition.

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