Faculty Bibliography

Background/Purpose: Patients with systemic lupus erythematosus (SLE) are at high risk for severe disease from COVID-19 and decreased vaccine efficacy, due to inherent immune perturbations and frequent immunosuppressant use. The impact of vaccine responses was "pressure" tested in New York City (NYC) from December 2021-February 2022, due to the highly infectious omicron BA.1 variant which resulted in a significant increase in COVID-19 cases and hospitalizations. This study was performed to assess clinical efficacy and seroreactivity in SLE patients with and without an additional vaccination dose after initial vaccine series, particularly during the omicron BA.1 surge in NYC.
Method(s): COVID-19 infections after vaccination were evaluated during patient encounters and chart review in subjects from the NYU Lupus Cohort who received an initial SARS-CoV-2 vaccine series with follow-up for at least 6 months or until breakthrough infection. Clinical follow-up was required after February 4, 2022 (when NYC COVID-19 cases returned to their preomicron BA.1 baseline), with last patient follow-up recorded April 24, 2022. Positive PCR or antigen-based testing was required, performed at the clinical site or self-reported. Fifty-seven patients receiving additional vaccine doses were evaluated longitudinally for recombinant SARS-CoV-2 spike receptor binding domain antibodies (#BT10500; R&D Systems). Low post-vaccine antibody response was defined as <=100 units/ml.
Result(s): Among the 163 subjects evaluated, 125 (76.7%) received an additional COVID-19 vaccination after the initial series. Demographics and medication usage were similar in patients who did and did not receive the additional vaccination dose, with 50% on at least one immunosuppressant and 16% on more than one at the time of the initial vaccine. Twentyeight (63.6%) of the 44 patients with a breakthrough infection had received an additional vaccination compared to 97 (81.5%) of the 119 without breakthrough infection (p=0.022) (Table 1). Of the 44 COVID-19 cases, only 2 occurred prior to the omicron wave, both in patients who did not receive the additional dose. There were no COVID-19 related deaths and two patients were hospitalized. Among the 57 patients with serologic evaluation, the median antibody level after initial vaccination series was 397 u/mL (IQR 57-753), and 1036 (IQR 517-1338.5) after the additional dose. After initial vaccination, 21 (37%) had low ELISA responses, but only 4 (7%) continued to have low responses after the additional dose. There was no association between the level of antibody after the additional dose and COVID-19 breakthrough.
Conclusion(s): SLE patients from a cohort of patients in NYC who received an additional SARS-CoV-2 vaccine dose were significantly less likely to have a subsequent COVID-19 infection compared to those who only completed their initial vaccine series. SLE patients demonstrated an improvement in serologic response after an additional dose of SARS-CoV-2 vaccine. The mild disease in all vaccinated patients is reassuring given the risks inherent and frequent immunosuppressant use in this patient population

Background/Purpose: SLE is characterized by autoantibody production. The most common lupus-specific serology is the anti-dsDNA antibody (anti-DNA). Traditionally, anti-DNA is measured by an enzyme immunoassay or equivalent such as multiplex flow immunoassay (EIA), which is considered sensitive. In contrast, the crithidia luciliae immunofluorescence test (CLIFT) is considered more specific. Serial measurement of anti-DNA is often used to monitor lupus disease activity. With NYU's extensive multi-race/ethnic lupus registry, we studied the relationship between these two methods, their association with lupus nephritis (LN), and their ability to predict subsequent flares.
Method(s): Using the NYU Lupus Registry of patients who meet ACR, SLICC, or EULAR criteria, we identified patients who had one or more simultaneous anti-DNA results by multiplex EIA and CLIFT. We report on their concordance (e.g., always, never, or fluctuating), association with LN, and ability to predict flare within 90 days using the SELENA-SLEDAI Flare Index. To account for degree of positivity, we defined tertiles for EIA and CLIFT as low positive [11-50 and 1:10-1:40], mild positive [51-200 and 1:80-1:320], and high positive [> 200 and > 1:640]. Table 1. 586 total visits with paired EIA and CLIFT. H = high positive M = mild positive L = low positive defined in Methods section Table 2. Relationship between EIA, CLIFT and hypocomplementemia with lupus nephritis. Chi-square test comparing significance between 60/100 v 72/100 (EIA/CLIFT) p = 0.07 Table 3. Relationship between EIA, CLIFT, hypocomplementemia and flare within 90 days Results: 207 patients had one or more paired anti-DNA results generating 586 paired results (Table 1). Cohort demographics: 92% Female, 22% Hispanic ethnicity, 24% Black, 16% Asian, 49% White, 10% Other. Overall, 377 pairs were always concordant, and 209 were never concordant. 236 pairs demonstrated titer concordance and 350 with titer discordance. Of the 207 patients, 64 patients had only one and 143 patients had two or more paired tests. Of the 64 patients, 46 were always concordant: 18 had positive EIA/CLIFT and 28 had negative EIA/CLIFT. The remaining 18 patients were never concordant: 8 had +EIA/-CLIFT and 10 had-EIA/+CLIFT. The concordance of the 143 patients with multiple paired results: 73 always, 23 never, and 47 fluctuating. Whether by one or multiple paired tests, 41/207 patients were never concordant. 100 of the 207 patients had LN associated with +EIA in 60 and +CLIFT in 72 (Table 2). Hypocomplementemia was present in 88% of +EIA and 89% of +CLIFT patients with LN. 51 visits in 42 patients had paired anti-DNA results and a SELENA-SLEDAI Flare Index assessment within 90 days. 7 patients had mild flares with +EIA in 4 and +CLIFT in 3. 4 patients had severe flares with +EIA and +CLIFT in 3 (Table 3). Low C3 and or C4 occurred in 1 of 7 (14%) mild flares and in 4 of 4 (100%) severe flares.
Conclusion(s): Our data demonstrate that discordance of positivity between two assays for anti-DNA occurred in 41/207 (20%) patients, in 207/586 (36%) visits and in 350/586 (60%) visits magnitude of positivity nonconcordant. EIA positivity is associated with LN less often than CLIFT positivity. Flares were infrequent and associated with either EIA or CLIFT positivity, with severe flares more likely if accompanied by hypocomplementemia. We recommend the utility of more than one anti-DNA assay in routine monitoring for lupus disease activity

Background/Purpose: Lupus nephritis (LN) is characterized by considerable variability in its clinical manifestations and histopathological findings. Understanding the cellular and molecular mechanisms underlying this heterogeneity is key for the development of personalized treatments for LN.
Method(s): Droplet-based single-cell RNA-sequencing was applied to the analysis of dissociated kidney samples, collected from 155 LN patients with active kidney disease and 30 living donor controls as part of a large-scale, multi-center study. 73,440 immune cells passing quality control were identified, spanning 134 cell subsets, representing various populations of tissue-resident and infiltrating leukocytes, as well as the activation states these cells assume as part of their diseaserelated activation and differentiation (Fig. 1). Principal component analysis (PCA) was used to characterize the variability in cell subset frequencies across the LN patients. Relationships between the resulting principal components (PCs) and the demographic, clinical and histopathological features of the patients were then assessed. Figure 1. Single-cell RNA-sequencing was used to profile immune cells isolated from the kidneys of LN patients and healthy controls. Five main lineages of cells were identified, as shown in a Uniform Manifold Approximation and Projection (UMAP) plot: myeloid cells, T/NK cells, B cells, plasma cells and dividing cells. The cells of each lineage were further split into finer subsets of cells (color-coded).
Result(s): The first PC (PC1), explaining 33% of the total variability in cell subset frequencies, reflected the balance between lymphocytes and monocytes/macrophages. The second PC (PC2), explaining an additional 21% of the total variability, represented the degree of macrophage differentiation to an alternatively activated phagocytic profile. The third and fourth PCs, bringing the total explained variability to 74%, were related to the balance between cell-mediated and humoral immune responses. PC1 was significantly correlated with the Chronicity index, such that patients with a higher percentage of lymphocytes compared to monocytes/macrophages had a higher Chronicity score (rho =-0.439, p-value < 0.001; Fig. 2A). A high degree of macrophage differentiation, as represented by PC2, was associated with a high Activity score (rho =-0.495, p-value < 0.001; Fig. 2B), and, in addition, with proliferative or mixed histology class, compared to pure membranous nephritis (p-value = 0.001, Kruskal-Wallis test). We further identified a significant correlation of these PCs with age; specifically, older patients had a higher relative frequency of lymphocytes compared to monocytes/macrophages, a lesser degree of macrophage differentiation, and a higher representation of cells putatively involved in a humoral immune response compared to a cell-mediated one.
Conclusion(s): These results identify distinct leukocyte populations active in different LN patients and, possibly, different stages of disease, and suggest potential therapeutic targets, that must be validated in mechanistic studies. This approach may pave the way to personalized treatment of LN

BACKGROUND:Complement activation has been associated with adverse pregnancy outcomes (APO) in SLE. Pregnant women with SLE were studied to evaluate whether complement dysregulation within the first two pregnancy trimesters predicts APO. METHODS:Pregnant women fulfilled classification criteria for SLE. APO included neonatal death, preterm delivery before 36 weeks and small for gestational age newborn. Pre-eclampsia was also evaluated. Erythrocyte complement receptor 1 (ECR1) and erythrocyte-bound C4d (EC4d) were measured by flow cytometry. Complement proteins C3 and C4 were measured by immunoturbidimetry and anti-double-stranded DNA by ELISA in serum. Statistical analysis consisted of t-test, confusion matrix-derived diagnostic analysis, and multivariate logistic regression. RESULTS:Fifty-one women had 57 pregnancies and 169 visits during the study. Baseline visits occurred mainly in the first (n=32) and second trimester (n=21). Fourteen (24.6%) pregnancies resulted in 21 APO with preterm delivery being the most common (n=10). ECR1 <5.5 net mean fluorescence intensity in the first trimester predicted APO with a diagnostic OR (DOR) of 18.33 (95% CI: 2.39 to 140.4; t-test p=0.04). Other individual biomarkers did not reach statistical significance. To estimate the likelihood of APO, we developed an algorithm that included the week of pregnancy, ECR1 and EC4d. From this algorithm, a Pregnancy Adversity Index (PAI) was calculated, and a PAI >0 indicated an elevated likelihood of pregnancy complications (DOR: 20.0 (95% CI: 3.64 to 109.97)). CONCLUSIONS:Low levels of ECR1 in early or mid-pregnancy are predictive of an APO. Incorporating the weeks of gestation and both ECR1 and EC4d generated a PAI, which further predicted serious pregnancy complications.

OBJECTIVES/OBJECTIVE:Current treatments are effective only in 30% of lupus nephritis patients emphasizing the need for novel therapeutic strategies. To develop mechanistic hypotheses and explore novel biomarkers, we analyzed the longitudinal urinary proteomic profiles in patients with lupus nephritis undergoing treatment. METHODS:We quantified 1,000 urinary proteins in 30 patients with lupus nephritis at the time of the diagnostic renal biopsy and after 3, 6, and 12 months. The proteins and molecular pathways detected in the urine proteome were then analyzed with respect to baseline clinical features and longitudinal trajectories. The intrarenal expression of candidate biomarkers was evaluated using single cell transcriptomics of renal biopsies from lupus nephritis patients. RESULTS:Our analysis revealed multiple biological pathways including chemotaxis, neutrophil activation, platelet degranulation, and extracellular matrix organization that could be noninvasively quantified and monitored in the urine. We identified 237 urinary biomarkers associated with lupus nephritis as compared to controls without SLE. IL-16, CD163, and TGF-β mirrored intrarenal nephritis activity. Response to treatment was paralleled by a reduction of urinary IL-16, a CD4 ligand with proinflammatory and chemotactic properties. Single cell RNA sequencing independently demonstrated that IL16 is the second most expressed cytokine by most infiltrating immune cells in lupus nephritis kidneys. IL-16 producing cells were found at key sites of kidney injury. CONCLUSION/CONCLUSIONS:Urine proteomics may profoundly change the diagnosis and management of lupus nephritis by noninvasively monitor active intrarenal biological pathways. These findings implicate IL-16 in lupus nephritis pathogenesis designating it as a potentially treatable target and biomarker.

OBJECTIVE:Previous studies suggest a link between high serum type I interferon (IFN) and lupus nephritis (LN). We determined whether serum IFN activity is associated with subtypes of LN and studied renal tissues and cells to understand the impact of IFN in LN. METHODS:). Podocyte cell line gene expression was measured by real-time PCR. RESULTS:expression was not closely co-localized with pDCs. IFN directly activated podocyte cell lines to induce chemokines and proapoptotic molecules. CONCLUSION/CONCLUSIONS:Systemic high IFN is involved in the pathogenesis of severe LN. We do not find co-localization of pDCs with IFN signature in renal tissue, and instead observe the greatest intensity of IFN signature in glomerular areas, which could suggest a blood source of IFN.

OBJECTIVE:To evaluate seroreactivity and disease flares after COVID-19 vaccination in a multi-ethnic/racial cohort of patients with systemic lupus erythematosus (SLE). METHODS:90 SLE patients and 20 healthy controls receiving a complete COVID-19 vaccine regimen were included. IgG seroreactivity to the SARS-CoV-2 spike receptor-binding domain (RBD) and SARS-CoV-2 microneutralization were used to evaluate B cell responses; IFN-γ production to assess T cell responses was measured by ELISpot. Disease activity was measured by the hybrid SLE disease activity index (SLEDAI) and flares were assigned by the SELENA/SLEDAI flare index. RESULTS:Overall, fully vaccinated SLE patients produced significantly lower IgG antibodies against SARS-CoV-2 spike RBD than controls. Twenty-six SLE patients (28.8%) generated an IgG response below that of the lowest control (<100 units/ml). In logistic regression analyses, the use of any immunosuppressant or prednisone and a normal anti-dsDNA level prior to vaccination associated with decreased vaccine responses. IgG seroreactivity to the SARS-CoV-2 Spike RBD strongly correlated with the SARS-CoV-2 microneutralization titers and antigen-specific IFN-γ production determined by ELISpot. In a subset of patients with poor antibody responses, IFN-γ production was likewise diminished. Pre-/post-vaccination SLEDAI scores were similar. Only 11.4% of patients had a post-vaccination flare; 1.3% were severe. CONCLUSION/CONCLUSIONS:In a multi-ethnic/racial study of SLE patients 29% had a low response to the COVID-19 vaccine which was associated with being on immunosuppression. Reassuringly, disease flares were rare. While minimal protective levels remain unknown, these data suggest protocol development is needed to assess efficacy of booster vaccination.