Fig. 2: Astrocyte LF2 is associated with increased expression of neuronal synaptic programs.

a, PCA of normalized read counts in neurons shows clustering of samples by time (colored, 0.5 h - day 8) and culture condition (fill, CC = co-culture, MC = mono-culture) across PC1 and PC2, explaining 51.93% and 7.79% of variation, respectively. b, A qq-plot of p-values from linear regression of neuronal gene expression values with LF2 sample weights. Astrocytic LF2 is associated with upregulation of 1,435 neuronal genes that have significant, positive association of expression changes in co-culture with the astrocytic LF2 gene programs. c, Heatmap of standardized expression (z-score logCPM) of the 1,435 upregulated genes associating with LF2 in co-culture. The genes cluster into two groups by hierarchical clustering. Colored annotations on the right of the heatmap indicate genes that were differentially expressed genes (p < 2.8991e-06 [Bonferroni]: red, FDR < 5%: pink) between: 1) neurons at day 2 and day 1 in CC, 2)neurons at day 1 to 6 hours in CC, and 3) neurons in CC and MC at day 2. d, SynGO sunburst plot showing enrichment of synaptic GO terms in the 842 genes with increased expression only in co-culture (Fig. 2c, heatmap cluster 1). The 842 genes were enriched in synaptic gene programs in synaptic vesicle cycle and synapse organization. e, A qq-plot of p-values from permutation analysis (n = 1,000 permutations) of variant burden in the SCHEMA consortium² data for genes associating with LF2 (n = 698). The p-values were calculated using Fisher’s exact test. The pink data point highlights enrichment of the gene set in question, the grey points demonstrate the permutation results. f, The neuronal genes upregulated exclusively in co-culture (Fig. 2c, heatmap cluster 1) included 3 SNAP-n genes: DCC, EPHA3 and DNM3; the genes upregulated also in mono-culture (Fig. 2c, heatmap cluster 2) included 2 SNAP-n genes: GAP-43 and SVB2. Scatter plots show neuronal normalized expression (logCPM) (y-axis) in the function of LF2 sample weights (x-axis). The black line is a fitted linear regression line with a 5% confidence interval.