Fig 2: Characterization of human DDX53-3TC iPSCs. Blue droplets are FAM-positive droplets (WT), brown are double-positive droplets, gray are negative droplets, and green are VIC-positive droplets (mutant). (Progress of mutant allele frequency from the highest signal wells following clonal selection for 19-2-DDX53-3TC. A) and 50B-DDX53-3TC. B) Expression levels of DDX53 gene in control lines, and testis (positive control) as a fraction of that from an internal control, TBP (N = 4/8 for 19-2 DDX53; N = 3/6 for 50B DDX53; N = 1/3 for testis). Numbers with each bar indicate the number of biological replicates/number of technical replicates. The y-axis shows the ratio of DDX53 transcript to TBP transcript in different samples. C) ***p < 0.001, one way ANOVA with Tukey multiple comparisons test

Fig 3: Representative western blots of DDX53 protein detection in isogenic control (Cntrl 19-2 and Cntrl 50B) and KO (19-2-DDX53-3TC, 50B-DDX53-3TC) in 4-weeks old neurons. A) and B), chemiluminescent or near-infrared detection methods, respectively. Recombinant DDX53 protein (panel A) and testis lysates known to express DDX53 (panel B) were used as positive controls. Note the appearance of an unspecific protein of approximately 60 KDa consistently detected by the anti-DDX53 antibody in both panels that does not match the molecular size of DDX53 indicated in the positive control lanes. β-actin (ACTb) was used as a loading control.

Fig 4: A) Characterization of the neurons to validate their excitatory nature: Mean firing rate of control (19-2) neurons were recorded using MEA during four consecutive readings. Recordings were done after treatment with neurotoxins. Untreated; PTX: Picrotoxin; CNQX: 6-Cyano-7-nitroquinoxaline-2, 3-dione; TTX: Tetrodotoxin (N = 8; mean ± SEM; one-way ANOVA, Sidak's multiple comparisons test). B) and C) Representative Raster plots of neuronal network activity of representative wells of control vs DDX53-3TC. Each row represents an individual microelectrode of the MEA device. Each black bar represents one spike and each row of black bars (spike train) represents spiking activity of a neuron, over a period of 100 s, blue bars represents the burst. Multi-electrode array analysis of DDX53-3TC neurons and respective isogenic controls. D) Weighted mean firing rate of control neurons, and DDX53 mutant neurons (19-2-DDX53-3TC) from 3 to 6 weeks (N: controls for week 3 = 8; week 4 = 16; week 5 = 8; week 6 = 16. N: 19-2-DDX53-3TC for week 3 = 11; week 4 = 15; week 5 = 8; week 6 = 15; mean ± SEM, two-way ANOVA, Sidak's multiple comparisons test). E) Burst frequency of control neurons, and DDX53 mutant neurons (19-2-DDX53-3TC) from 4 to 6 weeks (N: controls for week 4 = 8; week 5 = 8; week 6 = 16. N: 19-2-DDX53-3TC for week 4 = 8; week 5 = 8; week 6 = 15; mean ± SEM, two-way ANOVA, Sidak's multiple comparisons test). F) Network burst frequency of control neurons, and DDX53 mutant neurons (19-2-DDX53-3TC) from 5 & 6 weeks (N: controls for week 5 = 8; week 6 = 16. N: 19-2-DDX53-3TC for week 5 = 8; week 6 = 16; mean ± SEM, two-way ANOVA, Sidak's multiple comparisons test). G) Weighted mean firing rate of control neurons, and DDX53 mutant neurons (50B-DDX53-3TC) from 3–6 weeks (N: controls for week 3 = 18; week 4 = 29; week 5 = 24; week 6 = 26. N: 50B-DDX53-3TC for week 3 = 16; week 4 = 25; week 5 = 24; week 6 = 23; mean ± SEM, two-way ANOVA, Sidak's multiple comparisons test). H) Burst frequency of control neurons, and DDX53 mutant neurons (50B-DDX53-3TC) from 4–6 weeks (N: controls for week 4 = 25; week 5 = 24; week 6 = 23. N: 50B-DDX53-3TC for week 4 = 24; week 5 = 23; week 6 = 21 mean ± SEM, two-way ANOVA, Sidak's multiple comparisons test). I) Network burst frequency of control neurons, and DDX53 mutant neurons (50B-DDX53-3TC) from 4 to 6 weeks (N: controls for week 4 = 8; week 5 = 24; week 6 = 17. N: 50B-DDX53-3TC for week 4 = 6; week 5 = 23; week 6 = 21 mean ± SEM, two-way ANOVA, Sidak's multiple comparisons test)

Fig 5: Heat map of detected RNA-Seq transcripts from DDX53-3TC neurons to their respective isogenic controls. Transcript levels in reads per kilo base per million (RPKM) are shown for different markers of cortical layer, neurons, neural progenitor cells (NPCs), GABAergic and glutamatergic functions. A) Biological replicates for isogenic controls 19-2 (n = 4) and 19-2-DDX53-3TC (n = 3). B) Biological replicates for control 50B (n = 3) and 50B-DDX53-3TC neurons (n = 3). (1-4) indicate the batch number