Transcriptomic effects of hydroxychloroquine in CD4+ T cells from patients with systemic lupus erythematosus: An exploratory pilot study

Objectives Hydroxychloroquine (HCQ) is a cornerstone of systemic lupus erythematosus (SLE) management, yet its precise molecular impact on CD4+ T cells, particularly regarding disease duration, remains to be fully elucidated. This exploratory study aimed to characterize the two-time-point transcriptomic changes induced by HCQ in CD4+ T cells and explore whether these effects differ between early and established disease phases. Methods We performed a pre- and post-treatment RNA sequencing analysis on CD4+ T cells isolated from five SLE patients before and 3 months after initiating HCQ therapy. Patients were stratified into an induction phase (early, treatment-naïve disease) and a maintenance phase (long-standing disease with concomitant treatments). Differentially expressed genes (DEGs) were identified, and key findings were validated at the protein level using an immunoassay. Results Despite significant inter-individual heterogeneity, HCQ induced distinct transcriptomic shifts, which were notably more pronounced in induction-phase patients than in maintenance-phase patients. In the induction phase, 56 genes were upregulated and 193 genes were downregulated (fold change ≥2, nominal raw p < 0.05), including the canonical Th1 cytokine IFNG, chemokine receptors CXCR3 and CCR5, the co-stimulatory molecule CD40, and multiple histone genes. In contrast, the maintenance phase showed 71 upregulated and 46 downregulated DEGs. A chi-square test revealed a statistically significant difference in the direction of gene regulation between the two phases, suggesting a predominant gene downregulation in the early phase. Downstream GO and KEGG pathway analyses evaluated under FDR-adjusted significance (adj. p < 0.05) highlighted alterations in “Cytokine-cytokine receptor interaction” and “SLE” pathways. Validation in an independent cohort ( n = 10) confirmed significant decreases in serum IFN-γ and IL-10 levels following HCQ treatment. Conclusions This exploratory pilot study provides pre- and post-treatment transcriptomic evidence that HCQ exerts multifaceted immunomodulatory effects on CD4+ T cells, suppressing Th1-related, CD40, and histone pathways. These effects appear particularly robust in early-stage SLE, providing a molecular rationale for the clinical benefit of early HCQ introduction.