Background/Purpose: Systemic lupus erythematosus (SLE) is characterized by aberrant B cell activation and autoantibody production. CD19-targeted chimeric antigen receptor (CAR) T-cell therapy induces a short, deep B cell depletion and showed promising clinical efficacy in patients with refractory SLE. However, it is poorly understood how the B cell system evolves after reconstitution and whether pathogenic immune phenotypes reemerge.

Methods: 18 patients with active, refractory SLE (15 with lupus nephritis) received autologous CD19-CAR T-cell therapy. Longitudinal, high dimensional phenotyping of blood B cells was performed using spectral flow cytometry. B cells were analyzed before therapy (N = 18), at first reappearance (N = 14) and at early (3-6 months, N = 10), late (12+ months, N = 10) and long-term (median 24 months) reconstitution. B cells from 10 healthy donors were included as control. scRNA-Seq was performed at baseline and early reconstitution.

Results: Patients with active SLE showed aberrant B cell subsets and frequencies, including an increase in circulating plasmablasts and IgD− CD27− double negative (DN) memory B cells. CAR T cell therapy led to transient depletion of CD19+ B cells in all patients. After a median follow up of 17 (range: 3 – 36) months, B cells had reconstituted in 14/18 (78%) of patients. B cells recovered between 28 to 420 (mean: 169) days after CAR T, with a transient increase in immature B cells during reconstitution. At reconstitution and 6 months thereafter, the new B cell compartment consisted predominantly of CD20+ IgD+ CD27− naïve B cells. Accordingly, all other subsets, including switched and unswitched memory B cells and circulating plasmablasts were reduced. HLA-DR expression was decreased after reconstitution, indicating reduced stimulation. Surprisingly, IgD− CD27− double negative (DN) and Tbet+ age associated B cells (ABCs), reappeared one year after CAR-T cell therapy. However, fresh DN cells consisted almost exclusively of CXCR5+ CD11c− Tbet− DN1 cells, whereas disease associated CD11c+ CXCR5− Tbet+ DN2 cells stayed reduced, constituting less than 5% of peripheral CD19+ B cells. This was confirmed by identification of DN2 cells in scRNA-Seq showing reduced frequencies after therapy.Concordantly, new switched memory B cells, which slowly reappeared after a mean of 12 months after therapy, were mostly CXCR5+, while CXCR5− switched memory B cells were not accumulated. New plasmablasts were rarely detected (< 1% of CD19+ cells) and displayed substantially reduced activation (CD95low HLA-DRlow). Frequencies of atypical B cell subsets remained low and indistinguishable from healthy individuals even at late follow-up.

Conclusion: Deep B cell depletion, as mediated via CD19-CAR T cell therapy, profoundly remodels the B cell compartment. New B cells appear to predominantly repopulate from CXCR5+ cells, suggesting less utilization of extrafollicular B cell maturation pathways. Accordingly, new B cells display overall reduced activation levels, while disease-associated DN2 cells, atypical B cell subsets and activated plasmablasts remained cleared long after reconstitution. These changes indicate a deep and durable reset of adaptive immunity even long after B cell reconstitution.

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ACR Meeting Abstracts - https://acrabstracts.org/abstract/reduction-in-extrafollicular-b-cell-responses-in-sle-patients-after-car-t-cell-therapy/