Fig. 2: Plasma proteomic heterogeneity during RA development.

a Number of individuals in different clinical subgroups. b Dendrogram illustrating hierarchical clustering of proteomic data across samples. c Heatmap displaying unsupervised k-means clustering of proteins across healthy individuals, at-risk individuals, ACPA-positive RA patients and ACPA-negative RA patients (two-sided Student’s t test, p < 0.05 and 1.5-fold change). The top enriched pathways for each cluster are shown (two-sided Fisher’s exact test, p < 0.05). d Volcano plot of differentially expressed proteins (DEPs) between at-risk individuals who converted to RAs (converters) and non-converters (two-sided Student’s t test, p < 0.05 and 1.5-fold change). The red and blue dots represent upregulated and downregulated proteins, respectively. e Bar plot displaying the top enriched pathways of DEPs between converters and non-converters (two-sided Fisher’s exact test). f Schematic (left) of proteomic analysis design for samples collected from three at-risk individuals before and after RA onset (created with BioRender.com. Sun, R. (2025) https://BioRender.com/6iee3nb). Venn diagram (middle) showing overlapped DEPs in two comparisons: red circle includes DEPs between converter and non-converter; blue circle includes DEPs before and after RA onset in three converters. Scatter plot (right) displaying the intensity of the overlapped DEPs before and after RA onset (two-sided Student’s t test). g Violin plot displaying the intensity of antibody segments across four clinical groups (two-sided Student’s t test). Box plots inside showing the median (center line), the 25th and 75th percentiles (bounds of box), and the minimum and maximum values (whiskers). ACPA⁺ indicates ACPA-positive, and ACPA^- indicates ACPA-negative. Significance is indicated as follows: *p < 0.05, **p < 0.01 and ***p < 0.001, ns means p ≥ 0.05. Source data are provided as a Source Data file.