Faculty Bibliography

Background 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. Methods 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 the Accelerating Medicines Partnership (AMP) in SLE consortium -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 (figure 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. Results The main source of variability in immune cell subset frequencies, as represented by the first PC (PC1), reflected the balance between lymphocytes and monocytes/macrophages. Subsequent PCs represented the balance between B cells and T cells (PC2); the levels of cytotoxic T lymphocytes and NK cells, as compared to plasma cells (PC3); and the degree of macrophage differentiation to an alternatively activated phagocytic profile (PC4). 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 = -0.422, p-value < 0.001; figure 2A). A high degree of macrophage differentiation, as represented by PC4, was associated with a high Activity score (rho = 0.387, p-value < 0.001; figure 2B), and, in addition, with proliferative or mixed histology class, compared to pure membranous nephritis (p-value = 0.001, Kruskal-Wallis test). The ratio of B cells to T cells, as represented by PC2, demonstrated a positive correlation with the Activity index (rho = 0.311, p-value < 0.001). We further identified a significant correlation of PC1 with age; specifically, older patients had a higher relative frequency of lymphocytes compared to monocytes/macrophages (rho = -0.239, p-value = 0.003). Our analysis indicated that these relations are not driven by demographic, clinical and technical sources of variation in our data, including race, ethnicity, the mixture of different nephritic classes, and the inclusion of both first and later biopsies. Conclusion Our work identifies distinct leukocyte populations active in different LN patients and, possibly, different stages of disease, and points to potential therapeutic targets, that must be validated in mechanistic studies. This approach may pave the way to personalized treatment of LN

OBJECTIVE:To estimate the annual incidence rate of SLE in the USA. METHODS:A meta-analysis used sex/race/ethnicity-specific data spanning 2002-2009 from the Centers for Disease Control and Prevention network of four population-based state registries to estimate the incidence rates. SLE was defined as fulfilling the 1997 revised American College of Rheumatology classification criteria. Given heterogeneity across sites, a random effects model was employed. Applying sex/race/ethnicity-stratified rates, including data from the Indian Health Service registry, to the 2018 US Census population generated estimates of newly diagnosed SLE cases. RESULTS:The pooled incidence rate per 100 000 person-years was 5.1 (95% CI 4.6 to 5.6), higher in females than in males (8.7 vs 1.2), and highest among black females (15.9), followed by Asian/Pacific Islander (7.6), Hispanic (6.8) and white (5.7) females. Male incidence was highest in black males (2.4), followed by Hispanic (0.9), white (0.8) and Asian/Pacific Islander (0.4) males. The American Indian/Alaska Native population had the second highest race-specific SLE estimates for females (10.4 per 100 000) and highest for males (3.8 per 100 000). In 2018, an estimated 14 263 persons (95% CI 11 563 to 17 735) were newly diagnosed with SLE in the USA. CONCLUSIONS:A network of population-based SLE registries provided estimates of SLE incidence rates and numbers diagnosed in the USA.

High levels of autoimmune antibodies are observed in COVID-19 patients but their specific contribution to disease severity and clinical manifestations remains poorly understood. We performed a retrospective study of 115 COVID-19 hospitalized patients with different degrees of severity to analyze the generation of autoimmune antibodies to common antigens: a lysate of erythrocytes, the lipid phosphatidylserine (PS) and DNA. High levels of IgG autoantibodies against erythrocyte lysates were observed in a large percentage (up to 36%) of patients. Anti-DNA and anti-PS antibodies determined upon hospital admission correlated strongly with later development of severe disease, showing a positive predictive value of 85.7% and 92.8%, respectively. Patients with positive values for at least one of the two autoantibodies accounted for 24% of total severe cases. Statistical analysis identified strong correlations between anti-DNA antibodies and markers of cell injury, coagulation, neutrophil levels and erythrocyte size. Anti-DNA and anti-PS autoantibodies may play an important role in the pathogenesis of COVID-19 and could be developed as predictive biomarkers for disease severity and specific clinical manifestations.

Background/Purpose: Patients with immune mediated inflammatory disorders (IMIDs) have an inherently heightened susceptibility to infection and may be considered high risk for developing COVID-19. While data regarding the COVID-19 vaccine's immunogenicity in an immunocompetent adult population is rapidly emerging, the ability of IMID patients to adequately respond to these vaccines is not known. Here, we investigate the humoral and cellular immune response to mRNA COVID-19 vaccines in patients with IMIDs on immunomodulatory treatment Methods: Patients with immune mediated inflammatory disorders (IMIDs) have an inherently heightened susceptibility to infection and may be considered high risk for developing COVID-19. While data regarding the COVID-19 vaccine's immunogenicity in an immunocompetent adult population is rapidly emerging, the ability of IMID patients to adequately respond to these vaccines is not known. Here, we investigate the humoral and cellular immune response to mRNA COVID-19 vaccines in patients with IMIDs on immunomodulatory treatment.
Result(s): The NY cohort baseline characteristics are found in Table 1. The Erlangen cohort consisted of 182 healthy subjects, 11 subjects with IMID receiving TNFi monotherapy, and 20 subjects with IMID on MTX monotherapy. In both cohorts, healthy individuals and those with IMID not on MTX were similar in age, while those IMID patients receiving MTX were generally older. In the NY cohort, of the healthy participants, 96.3% demonstrated adequate humoral immune response. Patients with IMID not on MTX achieved a similar rate of high antibody response rate (91.8%), while those on MTX had a lower rate of adequate humoral response (75.0%) (Figure 1A). This remains true even after the exclusion of patients who had evidence of prior COVID-19 infection (P= 0.014). Of note, 3 out of the 4 IMID patients receiving rituximab did not produce an adequate response. Similarly, in the Erlangen validation cohort, 98.3% of healthy controls, 90.9% of patients with IMID receiving TNFi monotherapy, and 50.0% receiving MTX monotherapy achieved adequate immunogenicity (Figure 1B). These differences remain significant when combining the cohorts, using a stricter definition of adequate response, and in a subgroup analysis by age. Cellular response was also analyzed in a subgroup of the NY cohort before and after second vaccination. Activated CD8+ T cells (CD8+ T cells expressing Ki67 and CD38) and the granzyme B-producing subset of these activated CD8+ T cells, were induced in immunocompetent adults and those with IMID not on MTX, but not induced in patients receiving MTX (Figure 2).
Conclusion(s): In two independent cohorts of IMID patients, MTX, a widely used immunomodulator for the treatment of several IMIDs, adversely affected humoral and cellular immune response to COVID-19 mRNA vaccines. Although precise cut offs for immunogenicity that correlate with vaccine efficacy are yet to be established, our findings suggest that different strategies may need to be explored in patients with IMID taking MTX to increase the chances of immunization efficacy against SARS-CoV-2, as has been demonstrated for other viral vaccines

Background/Purpose: Anti-Ro autoantibody production often precedes the development of Systemic Lupus Erythematosus (SLE) or Sjogren's syndrome (SS) by years. For anti-Ro+ mothers enrolled in the Research Registry for Neonatal Lupus (RRNL), progression to SS or SLE occurs in about a quarter, while most remain asymptomatic or develop only minor rheumatic symptoms (Asym/UAS). Thus, RRNL mothers uniquely offer a promise to identify genotype-phenotype relationships that are important to preclinical autoimmunity. Since multiple SLE risk alleles from Class II HLA genes are present in anti-Ro+ mothers, we examined interactions of specific microbiome taxa with Class II HLA by independent analytic paths with the goal to identify HLA-related microbiome associations in Anti-Ro+ Mothers of Children with Neonatal Lupus.
Method(s): Subjects included 125 RRNL mothers and 23 healthy controls. Stool microbiomes of anti-Ro+ women in RRNL (Asym/UAS, SS/SLE), and healthy controls (HC) were processed using 16S ribosomal RNA sequencing. Sera/ plasma were evaluated for cytokines and autoantibody levels. Alleles from HLA Class II genes were genotyped using NextGen sequencing of HLA region or imputed (HIBAG) from GWAS data. Independent analytic paths sought to explore associations of specific taxa and class II HLA included: 1) use of a cumulative logit model to test interactions between FDR significant genera and HLA alleles and 2) assignment of SLE, SS, UAS patients and HC to molecular phenotype clusters by Random Forest (RF), an unsupervised machine learning tool using Z-score transformed cytokine soluble mediators and autoantibody values with settings and the gap statistic that were used to estimate the optimal number of patients and HC within clusters. The overlapping distribution of SS/SLE, HLA alleles and taxa at clusters were then examined.
Result(s): Findings related to DRB1*15:01 and an interaction with genera of the Ruminococcaceae family were tested. Oscillibacter, with FDR-adjusted significance was shown to exhibit evidence of an interaction (P=0.033 (OR=0.60 (0.37-0.96)). In order to authenticate that SLE HLA risk alleles modify the strength of the association, we examined the molecular phenotype clusters from RF clustering. Radar plots were used to visualize the distribution HLA alleles and the enrichment of microbiome taxa within these clinically relevant phenotypic clusters (Figure 1). DRB1*1501 shows enrichment at cluster 4. Interestingly, the distribution of Oscillibacter, but not Coprococcus 3 was nearly superimposable with the Class II HLA allele with enrichment at cluster 4. However, the distribution of DRB1*1501 was not enriched at cluster profiles representing evaluations of DRB1*0301 and SS/SLE disease classification (Figure 2) demonstrating a limitation of DRB1*1501 to predict risk for transition from benign to pathologic autoimmunity in anti-Ro+ mothers of children with neonatal lupus.
Conclusion(s): These data support the use of molecular phenotypes that are linked to genetic-environmental interactions to identify HLA-related microbiome associations

Background/Purpose: The clinical heterogeneity of SLE with its complex pathogenesis remains challenging as we strive to provide optimal management. The contribution of platelets to endovascular homeostasis, inflammation and immune regulation highlights their potential importance in SLE. Prior work from our group showed that the Fcgamma receptor type IIa (FcgammaRIIa)-R/H131 biallelic polymorphism is associated with increased platelet activity and cardiovascular risk in SLE. The study was initiated to investigate the platelet transcriptome in patients with SLE and evaluate its association across FcgammaRIIa genotypes and distinct clinical features.
Method(s): RNA-sequencing was done on platelets isolated from 51 patients fulfilling criteria for the classification of SLE based on recent EULAR/ACR definitions, and 18 healthy controls matched on age, sex, and race. Unsupervised clustering, differential gene expression, and gene set enrichment analysis (GSEA) were used to analyze differences between SLE patients and controls, and SLE subpopulations, based on SELENA SLEDAI Hybrid disease activity, specific organ manifestations, and FcgammaRIIa genotype. Weighted Gene Correlation Network Analysis (WGCNA) was performed to create a modular transcriptomic framework.
Result(s): Our cross-sectional SLE cohort (N=51, age = 41.1+/-12.3, 100% female, 45% Hispanic, 24% black, 22% Asian, 51% white, SLEDAI = 4.4+/-4.2) was comprised of patients consecutively enrolled excluding those on aspirin or anticoagulants. Compared to the 18 controls, there were 2290 (p.adj < 0.05) differentially expressed genes. ( Figure 1 A, B) GSEA revealed positive enrichment for pathways related to interferon response, TNFa signaling, and coagulation in SLE. ( Figure 1C) WGCNA was used to create a modular transcriptomic framework. ( Figure 2A ) Modules enriched for platelet activity, immune response, and WNT signaling were significantly increased in SLE versus controls. Moreover, modules enriched for interferon response and WNT signaling paralleled increases in disease activity. ( Figure 2B) When analyzing patients with proteinuria, modules associated with oxidative phosphorylation and platelet activity were unexpectedly decreased. (Figure 2C) Analyzing the ratio of fold changes between SLE/Control vs SLE Proteinuria/SLE No Proteinuria, genes increased in SLE and those with proteinuria were enriched for immune effector processes, while genes increased in SLE but decreased in proteinuria were enriched for coagulation and cell adhesion. (Figure 2D) The module enriched for FCR activation was decreased in SLE and was affected by the FcgammaRIIa genotype. (Figure 3A) FcgammaRIIa R131 and H131 patients showed significantly different platelet transcriptomes. (Figure 3B) The combination of SLE with an FcgammaRIIa R131 variant leads to a significant increase in the platelet activity module not seen in controls. (Figure 3C)
Conclusion(s): These analyses reveal that SLE patients have a significantly different platelet transcriptome from controls, different phenotypic presentations of SLE patients associate with distinct platelet transcriptomic signatures, and FCGR2a variants may differentially influence the role of platelets in the contribution to SLE disease activity