Integrating bulk and single-cell RNA sequencing to identify mitochondrial quality control-related key genes in rheumatoid arthritis

Mitochondrial quality control (MQC) dysfunction contributes to rheumatoid arthritis (RA), but MQC-related genes in RA remain incompletely characterized. We integrated two bulk blood transcriptomic datasets and one peripheral blood mononuclear cell (PBMC) single-cell RNA-sequencing dataset (248 RA and 88 control bulk samples; 11,719 cells from 3 RA and 3 healthy donors). Weighted gene co-expression network and differential expression analyses, combined with three machine-learning algorithms, identified candidate genes. Functional enrichment, immune infiltration, regulatory network, single-cell, cell–cell communication, pseudotime, metabolic, and reverse transcription quantitative polymerase chain reaction (RT-qPCR) analyses were performed. Nine MQC-related candidate genes were identified; CDC42 and RBBP7 emerged as key genes, with CDC42 upregulated and RBBP7 downregulated in RA. Gene set enrichment analysis (GSEA) linked CDC42 to JAK–STAT signaling, while translation initiation showed opposite enrichment patterns. After multiple-testing correction, 15 immune-cell subsets differed between RA and controls; monocytes positively correlated with CDC42 and negatively with RBBP7. Single-cell analysis showed relatively high RBBP7 expression in B cells, motivating exploratory analyses of B-cell trajectories, metabolism, and predicted CCL5–CCR1 communication with monocytes. RT-qPCR confirmed the mRNA expression patterns. These findings identify CDC42 and RBBP7 as MQC-related key genes associated with distinct immune and metabolic features in blood-derived samples from patients with RA.