Therapeutic B-cell depletion with obinutuzumab modulates key immunopathological pathways in lupus nephritis: an exploratory whole blood transcriptomic analysis of the phase II NOBILITY trial

This study characterised the impact of obinutuzumab on B-cell and immune pathways in lupus nephritis (LN) using whole blood transcriptomics from the phase II NOBILITY trial (NCT02550652). Adults with LN received obinutuzumab or placebo plus standard therapy. Bulk RNA-seq was performed in blood samples from 88 participants and analysed for differentially expressed genes (DEGs) and gene set enrichment. To provide cell-type context, we mapped the identified DEGs onto a publicly available single-cell RNA-seq (scRNA-seq) dataset from peripheral blood mononuclear cells of 162 patients with systemic lupus erythematosus, using the Scanpy toolkit, enabling identification of specific B-cell subsets and other cell types within the scRNA-seq dataset. Compared with placebo, obinutuzumab induced significant and early differential expression of 289 genes (absolute fold change >1.5, adjusted p < 0.05), downregulating B-cell-related genes, including MS4A1 (CD20), CD19 and FCRL5 [enriched in pathogenic atypical B cells (ABCs)]; these effects persisted through week 52. Cellular deconvolution confirmed transcriptional changes were driven by depletion of the B-cell compartment. Gene set enrichment confirmed greater suppression of B-cell activation/proliferation pathways and the upregulation of innate immune effector mechanisms related to phagocytosis and leucocyte degranulation, leading us to hypothesise potential engagement of antibody-dependent cellular cytotoxicity/phagocytosis mechanisms. Exploratory analyses revealed these transcriptomic changes occurred irrespective of clinical outcome, and that obinutuzumab achieved efficacy independent of historically limiting low-affinity Fc γ receptor polymorphisms. This transcriptomic analysis shows that obinutuzumab downregulates B-cell gene signatures including genes enriched in pathogenic ABCs, and modulates innate immune pathways in LN, providing mechanistic insight into obinutuzumab's pharmacodynamic effects.