Fig. 1: FN-f induces alternative splicing events in human chondrocytes.
a Heatmap of differential splicing events between PBS and FN-f treated chondrocytes (n = 101 biologically independent non-OA donors), with each donor providing one chondrocyte culture split for PBS and FN-f treatment. Rows show PSI values for 621 intron junctions from LeafCutter clusters (|∆PSI| > 0.15, adjusted p < 0.05), derived from 590 genes. Significance determined using two-sided Dirichlet-multinomial regression with FDR correction by LeafCutter. Ancestry: AMR (Ad-mixed American), AFR (African), EUR (European), SAS (South Asian). b Pie chart illustrates the distribution of differential alternative splicing intron junction (n = 974) types. c Protein-protein interaction network of 590 differentially spliced genes using high-confidence interactions from STRING database v12.0 (interaction score > 0.900). Network shows genes with protein-protein interactions above the confidence threshold. Colors highlight pathway groups, bold circles indicate genes also differentially spliced in OA tissue, text indicates genes differentially spliced in both FN-f and OA conditions. d Venn diagram showing overlap between FN-f-induced splicing changes (n = 101 donors) and OA-associated splicing changes (n = 16 OA donors versus n = 101 non-OA controls). Statistical significance determined using two-sided Dirichlet-multinomial regression with FDR correction by LeafCutter default method. e Box plots showing ∆PSI in FN-f response for introns differentially spliced in OA. Each dot represents an individual splice junction (n = 237 for increased PSI in OA, n = 221 for decreased PSI in OA). The analysis compares OA vs PBS splicing changes (from 16 OA and 101 non-OA biological donors) with FN-f vs PBS changes (from the same 101 non-OA donors). Box plots show median (center line), 25th and 75th percentiles (box bounds), minimum and maximum values within 1.5Ă— interquartile range (whiskers), with outliers as individual points. Statistical test: one-sided Wilcoxon signed-rank test against theoretical median of zero (p = 2.23 × 10−8 for increased PSI group; p = 1.23 × 10−6 for decreased PSI group). No adjustments were made for multiple comparisons.
