The gene expression profile of preclinical autoimmune arthritis and its modulation by a tolerogenic disease-protective antigenic challenge

Table 2 Summary of differentially expressed genes in the lymph node cells of different groups of Lewis rats tested ex vivo and in vitro^a

	DEGs, n (%)
Characteristics	Upregulation	Downregulation	Total
Ex vivo
Inc/Nv	322 (100%)	0 (0%)	322
Pk/Nv	31 (53.4%)	27 (46.6%)	58
Rec/Nv	28 (80%)	7 (20%)	35
In vitro
Preclinical arthritis rats	41 (67.2%)	20 (32.8%)	61
Preclinical Bhsp65-tolerized rats	579 (98%)	12 (2%)	591

^aDEG: differentially expressed gene. "Ex vivo" group shows DEGs in lymph node cells (LNCs) at incubation (Inc), peak (Pk) or recovery (Rec) phase compared to naïve (Nv) state; "in vitro" group shows DEGs induced by mycobacterial heat shock protein 65 (Bhsp65) compared to baseline control (LNCs cultured in medium alone). In Bhsp65-tolerized group, only 76 (12.86%) of the 579 DEGs were related to immune activity (innate immunity, cell-mediated immunity and humoral immunity). The major groups comprised genes relating to cellular proliferation 127 (21.5%) and metabolism 137 (23.2%).

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