Fig. 2: Transcriptional gene expression analyses show significant and opposite changes in the neuronal development and differentiation in the DA neurons with 16p11.2 CNVs. | Nature Communications

Fig. 2: Transcriptional gene expression analyses show significant and opposite changes in the neuronal development and differentiation in the DA neurons with 16p11.2 CNVs.

From: 16p11.2 deletion is associated with hyperactivation of human iPSC-derived dopaminergic neuron networks and is rescued by RHOA inhibition in vitro

Fig. 2

a Expression of TH in the control, 16pdup, and 16pdel DA neurons at day 50 of differentiation, analyzed with the next-generation sequencing method (Illumina). b Expression of selected genes from 16p11.2 gene region in the control, 16pdup, and 16pdel DA neurons. SPN (p = 0.0005 16pdup, p < 0.0001 16pdel), KIF22 (p = 0.0166 16pdup, p < 0.0001 16pdel), MAZ (p < 0.0001 16pdel), ASPHD1 (p < 0.0001 16pdel), TMEM219 (p = 0.0005 16pdup, p < 0.0001 16pdel), TAOK2 (p = 0.0482 16pdup, p < 0.0001 16pdel), INO80E (p = 0.0034 16pdup, p < 0.0001 16pdel), AC093512.2 (p < 0.0001 16pdup, p < 0.0001 16pdel), PPP4C (p = 0.0029 16pdup, p < 0.0001 16pdel), CORO1A (p < 0.0001 16pdel), CDIPT (p = 0.0027 16pdup, p < 0.0001 16pdel), SEZ6L2 (p < 0.0001 16pdel), KCTD13 (p < 0.0001 16pdel), HIRIP3 (p = 0.0004 16pdup, p < 0.0001 16pdel), DOC2A (p < 0.0001 16pdel), FAM57B (p < 0.0001 16pdel), and MAPK3 (p = 0.0155 16pdup, p < 0.0001 16pdel). Data are presented as mean ± SD, and the number of biologically independent samples are n = 4 control, n = 6 16pdup, and n = 7 16pdel in (a, b). Gene expression differences were analyzed with two-way ANOVA with Dunnett’s multiple comparisons test, *p < 0.05, **p < 0.01, ***p < 0.001, and ****p < 0.0001 in (b). c Gene co-expression module M19 and first-principal component of gene expressions relative to the genes in 16p11.2 region in the three genotypes studied. d Gene co-expression module M25 and first-principal component of gene expressions relative to the genes in 16p11.2 region in the three genotypes studied. e Gene ontology categories of the module M19 genes that were expressed at lower levels in the 16pdel cells compared to control cells or 16pdup cells. f Gene ontology categories of the module M25 genes that were expressed at lower levels in the 16pdup cells compared to control cells or cells with 16p deletion. The number of biologically independent samples in the co-expression analyses are n = 4 control, n = 6 16pdup, and n = 7 16pdel in (c–f). g–j Quantitative RT-PCR analyses of selected genes associated to DA neuron function in neuropsychiatric disorders and in drug addiction that were detected in the gene co-expression modules and gene ontology categories of RNAseq data. g Selected genes that were expressed at higher levels in the 16pdup cells compared to control cells: LRRC4C (p = 0.0233 16pdup), G0S2 (p = 0.0057 16pdup), and TFRC (p = 0.0081 16pdup). h Selected genes that were expressed at lower levels in the DA neurons with 16.11.2 CNVs compared to control cells: GRIK3 (p = 0.0066 16pdup), EPHA7 (p = 0.027 16pdup, p = 0.0227 16pdel), WNT3 (p = 0.0295 16pdel), SH3GL2 (p = 0.0237 16pdup), and DRD2 (p = 0.0074 16pdup). i Selected genes expressed at higher levels in the 16pdel cells compared to control cells SLC6A2 (p = 0.0119 16pdel), PCDHB5 (p = 0.0217 16pdel), and GRIA4. j Selected genes expressed in opposite direction in the 16pdel and 16pdup cells; DSCAM (p = 0.0301 16pdel), SYN3 (p = 0.0036 16pdup), KCND2 (p = 0.0157 16pdup), GSG1L (p = 0.0120 16pdup), OPRM1 (p = 0.0011 16pdup). g–j Log 2 fold changes are presented as mean ± SEM compared to gene expression levels of control cells (adjusted to 0), one-sample t test and Wilcoxon’s test, p values: *p < 0.05, **p < 0.01, ***p < 0.001. The number of biologically independent samples are n = 3 control, n = 5 16pdup, and n = 3 16pdel in (g–j). Source data are provided as a Source Data file.

Back to article page