Distinct inflammatory and immune recovery patterns after CD19-directed CAR T-cell therapy in SLE and B-cell lymphoma

Abstract Introduction: While CD19-directed Chimeric Antigen Receptor (CAR) T-cell therapy is now established as a standard of care in relapsed/refractory B-cell lymphoma, we and others showed its feasibility and effectiveness in adult and adolescent patients with refractory systemic lupus erythematosus (SLE) (Mackensen et al., Nat Med 2022; Müller et al., NEJM 2024; Krickau et al., Lancet 2024). Furthermore, we recently demonstrated that - despite similar CAR T-cell kinetics – patients with SLE experience less severe adverse events than patients with B-cell lymphoma (Müller et al., Blood 2025). While side effects of CAR T-cell therapy are widely studied, resolution of CAR T-cell-induced but also disease-specific inflammation is still poorly understood. Methods: We performed deep serum proteomics in SLE patients (N=18; all patients in CR) and lymphoma patients [DLBCL NOS (N=39), MCL (N=3), other types of NHL (N=6); 50% in lasting CR > 6 months] before and at day +7, +14, +30, +90, and +365 after CAR T-cell therapy. In addition, healthy control samples of age-matched donors (SLE controls: n=18; lymphoma controls: n=30) were also analyzed. Persistence of CAR T-cells within patients and reconstitution of T- and B-cells were measured by flow cytometry and linked to serum proteome profiles. All patients received either commercial CAR T-cell products or the investigational medicinal product MB-CART19.1 (in-house manufactured 2nd generation anti-CD19 CAR T-cells with a 4.1BB co-stimulatory domain) in our center. Results: To characterize inflammatory signatures, we performed serum proteomics using the Olink® Target 96 Immuno-Oncology Panel across the CAR T-cell treatment course. Prior to CAR T-cell therapy, both B-cell lymphoma and SLE patients exhibit an inflammatory serum milieu - characterized by elevated levels of IL-6, IL-1α, IFN-γ, and CXCL10 - compared to age- and sex-matched healthy donors (HDs). One-year after CAR T-cell therapy, lymphoma patients maintained elevated pro-inflammatory cytokine levels compared to HDs, whereas SLE patients demonstrated resolution of IL-6-driven inflammation and reduction of SLE-associated cytokines including IL-8, CXCL13, MCP-1, and MCP-3. Concurrently, SLE patients showed increased expression of cytokines linked to immune cell reconstitution (TGF-b1, TRAIL, CXCL5, CXCL12, IL-7). This immune-restorative shift coincided with the loss of CAR T-cell persistence in SLE patients, suggesting a link between the persistence of CAR T-cells and resolution of inflammation. Principal component analysis (PCA) of serum proteins identified that angiogenic markers ANGPT-1 and VEGF-2 as well as immune-reconstituting cytokines CXCL5 and CXCL12, contributed to distinct clustering of SLE patients one-year post-CAR T-cell therapy, aligning them more closely with HDs. In contrast, no such clustering was observed in B-cell lymphoma patients prior to or post CAR T-cell therapy compared with HDs. Notably, the shift of cytokine expression and the resolution of IL-6–driven inflammation in SLE patients are further supported by the rapid reconstitution of T and B cells after CAR T-cell therapy, with upregulated serum IL-7 and CXCL12 likely contributing to T-cell and B-cell recovery, respectively. This pattern was specific to SLE patients, whereas persistent inflammation and ongoing B-cell aplasia could be observed in patients with B-cell lymphoma. Conclusion: Taken together, our data reveal a resolution of systemic inflammation specific to SLE patients following CAR T-cell therapy, compared to patients with B-cell lymphoma. This resolution might be linked to the shorter persistence of CAR T-cells in SLE patients and thus benefit the reconstitution of the adaptive immune system.