Defective B cell tolerance in SLE lymph nodes underpins VH4-34 "clonal damnation" and PD-1+TOX+ autoreactive B cells expansion.

Systemic Lupus Erythematosus (SLE) is a chronic autoimmune disease driven by uncensored B and T cell autoreactivity. Understanding this pathogenic process has been hampered by lack of studies of secondary lymphoid organs in human SLE. Using minimally invasive lymph node fine needle aspirates (LN-FNAs), we profiled tissue-resident immune cells from 59 SLE patients and 34 healthy controls through high-dimensional 43-color flow cytometry, antigen-specific tetramer probing, and sc-RNA sequencing with paired VH/VL repertoire analysis. Our findings reveal hyperactive lymph node immunity in SLE characterized by spontaneous germinal center (GC) activation, plasma cell accumulation enriched in mature CD19- and CD138+ antibody-secreting cells, and increased frequencies of both GC-TFH and PD-1+CXCR5- T extra-follicular helper cells. SLE lymph nodes harbored large oligoclonal B cell families with altered isotype usage, dominated by IgG1 and IgG4. Critically, self-reactive 9G4+ and Ro60+ B cells showed defective tolerance checkpoint control, accumulating in activated naïve, GC, and plasma cell compartments with distinctive PD-1+Tox+ expression absent in viral-specific responses. Single-cell repertoire analysis revealed VH4-34 clones in SLE BGC and BPC, that in contrast to HD, had not experienced clonal redemption. Instead, SLE VH4-34 clones displayed low somatic hypermutation and preserved the AVY hydrophobic patch associated with autoreactivity. Monoclonal antibody testing confirmed that unmutated AVY+ VH4-34 clones retained polyreactivity against naïve B cells, apoptotic cells, and multiple self-antigens. Together, these results define "clonal damnation" as a key mechanism in SLE whereby autoreactive VH4-34 clones of pathogenic potential escape tolerance checkpoints, expand in germinal centers, and differentiate into tissue plasma cells while preserving germline-encoded self-reactivity. Combined, our study defines critical mechanisms of tolerance breakdown in lupus pathogenesis.