Faculty Bibliography

Background/Purpose : Compared to Caucasian, African-American ethnicity is associated with a higher risk of developing systemic lupus erythematosus, lupus nephritis, high-risk histological features, resistance to treatment, and mortality. In phase 1 of the Accelerating Medicines Partnership (AMP), we used single-cell genomics to identify ethnicity associated features. Methods : Single cell RNA sequencing was performed on renal biopsies obtained for clinical purpose; one pipeline applying CEL-Seq2 in a leukocyte enriched sample and the other Fluidigm C1 800 in an agnostic approach to dissociated renal cells. Differential abundance of cell populations was determined using a logistic mixed model. Then, the differential expression profile was determined for each cell cluster and interpreted using pathway enrichment analysis. Results : Samples from 19 African-American and 20 Caucasian patients were obtained. We identified 30 cell clusters. Type I and II interferon inducible genes were upregulated in most cell populations. A cluster of T cells with exceptionally high interferon signature was found to be increased in African-Americans (OR 4.8). Macrophages and DC4-like dendritic cells were instead less abundant (OR 0.3). In African-Americans, type I and II interferon response pathways were enriched in several cell types including T cells, B cells, plasma cells, and activated monocytes. The majority of the differentially expressed genes was specifically inducible by type II interferon. In addition, while there was no local expression of type I interferons, interferon gamma was abundantly expressed by infiltrating NK and CD8 T cells. Conclusion : African-American patients with lupus nephritis have a stronger interferon response pathway activation, especially type II. Our findings suggest an intrinsic biological factor underlying the outcome gap and highlight the role of interferon gamma in lupus nephritis, implicating this pathway as a potential therapeutic target in SLE. Further work in Phase 2 of AMP is being pursued to validate and extend these findings

Background/Purpose : SLE diagnostic criteria are important for reliable epidemiologic data. The prevalence of SLE in West Africa is falsely low due to barriers including limited access to both resource and labor-intensive diagnostic testing. Recently, the ACR and EULAR have proposed a weighted classification tool which is thought to improve diagnostic sensitivity and specificity compared to the established ACR and SLICC criteria. Here we aim to investigate the performance of each classification criteria in two West African cohorts--Korle bu Teaching Hospital, Accra Ghana (GH); and Lagos University Teaching Hospital, Lagos, Nigeria (N)--compared to an NYU Langone-African American (AA) cohort. Methods : We collected data on a total of 355 SLE patients: AA: n=151, GH: n=110, and N: n=94, diagnosed by expert clinicians. Clinical information including demographics, SLE criteria, SLEDAI scores, SLICC damage indexes, vital signs, and laboratory values as available was obtained at the initial patient encounter. Longitudinal data was collected over the course of at least 1 year at 6 month intervals during routine clinical visits. Where necessary, clinical charts were retrospectively reviewed, and the proportion of patients in each cohort meeting ACR, SLICC and the ACR/EULAR classification criteria was calculated. Results : The demographics per cohort were as follows: Age (in yrs): AA=43.1, GH=32.4yrs, N=35.5; percent female: AA=90, GH=100, N=97; Mean SLE disease duration (yrs): AA=14.3, GH=2.2, N=4.4. In each cohort, the percentage of patients meeting ACR, SLICC, and ACR/EULAR criteria were AA=96%, 96%, and 95%; GH=85%, 84%, 62%; N=90%, 87%, 61%. This discrepancy was largely due to missing laboratory data particularly with regard to immunologic and hematologic studies. ANA was missing in 0% of the AA cohort, 26% of the GH cohort, and 33% of the N cohort respectively. Compared to the GH and N cohorts, the reference AA cohort was more likely to meet ACR, SLICC, and ACR/EULAR criteria with likelihood ratios (LR) of GH=10.2 p< 0.001 and N=3.0 p=0.08; GH=11.5, p< 0.001 and N=6.3, p=0.01; and GH=46.1 P< 0.001 and N=44.9, p< 0.001 respectively. On average, the mean number of ACR/EULAR points by cohort was AA: 26.1+/-11.8, GH: 21.3+/-8.1, and N: 19.0+/-6.2. While the ANA entry criteria greatly diminished the new ACR/EULAR diagnostic utility in the GH and N cohorts, the weighted point system performed better than either of the ACR or SLICC criteria with 96% of the AA cohort, 92%of the GH, and 95% of the N cohort meeting criteria (LR: AA vs GH=1.9, p=0.2; AA vs N=0.23, p=0.6). Conclusion : Due to a relative lack of resources, supportive laboratory assays including an ANA may be more difficult to attain in developing nations. SLE is a clinical syndrome that may be efficiently diagnosed using the new weighted ACR/EULAR criteria. The entry criteria of ANA 1:80 greatly diminished the diagnostic utility of this classification system in the Ghanaian and Nigerian cohorts compared to the African American cohort. Clinical trials should consider offering wide ANA testing to cohorts in the developing world

Background/Purpose: Both plasmacytoid dendritic cells (pDCs) and switched memory B cells (SMBCs) are considered to be key effector cells in systemic lupus erythematosus. It seems likely that within these classical cell lineages, additional diversity of function will exist that will contribute to disease pathogenesis. To explore this question, we performed single-cell RNA sequencing in pDCs and SMBCs from SLE patients and controls to assess gene expression patterns and cellular sub-groupings within these lineages. Methods : pDCs and SMBCs from SLE patients (n=10) and Healthy controls (n=5) were purified by magnetic separation. For deep sequencing, we used the Fluidigm C1 HT system with 800 capture site chips to capture single cells. Single cell capture was verified by direct visualization using the Array Scan system, allowing us to remove empty wells and wells with multiple cells. After quality control and adaptor trimming, the data was analyzed using SeqGeq software. pDCs and SMBCs were clustered using UMAP and pseudo-time analysis was performed using the Monocle program. Type I IFN activity in SLE plasma was measured using reporter cell assay. Results : A total of 2774 pDCs and 2578 SMBCs from SLE and healthy controls passed the quality control and were used for further analysis. In pDCs, we observed unique clusters for patients with high interferon, low interferon, and controls, indicating that the IFN response is a major determinant of overall gene expression patterns in SLE patient pDCs. IFN signature in pDCs correlated with circulating type I IFN activity in the SLE patients measured at the same time. Other genes upregulated in pDCs included the type I interferon regulator AXL and MACC1. The SMBCs were heterogeneous in patients and controls, and in contrast to the pDCs, the overall clustering pattern was independent of the IFN score. SMBC clusters were predominantly defined by genes indicating cellular activation or proliferation such as HLA-DRs and CREB1, or genes associated with nucleic acid processing such as DNASE1 and SNORD3B-1. Conclusion : We find distinct clusters of cells defined transcriptionally within the pDC and SMBC lineages, and the transcripts which define these subgroups differ between cell lineages. Type I IFN induced transcripts are important to pDC diversity, while in SMBCs transcripts related to cellular activation and nucleic acid processing are critical markers of transcriptional heterogeneity

Objective/UNASSIGNED:Epidemiological data for primary discoid lupus erythematosus (pDLE) remain limited, particularly for racial/ethnic populations in the USA. The Manhattan Lupus Surveillance Program (MLSP) is a population-based retrospective registry of cases with SLE and related diseases including pDLE in Manhattan and was used to provide estimates of the prevalence and incidence of pDLE across major racial/ethnic populations. Methods/UNASSIGNED:MLSP cases were identified from rheumatologists, hospitals and population databases. Two case definitions were used for pDLE: the primary case definition which was any physician diagnosis found in the chart and a secondary case definition which was limited to cases diagnosed by a rheumatologist and/or dermatologist. Rates among Manhattan residents were age-adjusted, and capture-recapture analyses were conducted to assess case under-ascertainment. Results/UNASSIGNED:Based on the primary definition, age-adjusted overall prevalence and incidence rates of pDLE among Manhattan residents were 6.5 and 0.8 per 100 000 person-years, which increased to 9.0 and 1.3 after capture-recapture adjustment. Prevalence and incidence rates were approximately two and six times higher, respectively, among women compared with men (p<0.0001). Higher prevalence was also found among non-Latino blacks (23.5) and Latinos (8.2) compared with non-Latino whites (1.8) and non-Latino Asians (0.6) (p<0.0001). Incidence was highest among non-Latino blacks (2.4) compared with all other racial/ethnic groups. Similar relationships were observed for the secondary case definition. Conclusion/UNASSIGNED:Data from the MLSP provide epidemiological estimates for pDLE among the major racial/ethnic populations in the USA and reveal disparities in pDLE prevalence and incidence by sex and race/ethnicity among Manhattan residents.

Mothers giving birth to children with manifestations of neonatal lupus (NL) represent a unique population at risk for the development of clinically evident pathologic autoimmunity since many are asymptomatic and only become aware of anti-SSA/Ro positivity (anti-Ro+) based on heart block in their fetus. Accordingly, we hypothesized that the microbiome in saliva is associated with the development of autoreactivity and in some cases the progression in health status from benign to overt clinical disease including Sjögren's syndrome (SS) and systemic lupus erythematosus (SLE). The study comprised a clinical spectrum of anti-Ro+ mothers, all of whom gave birth to a child with NL: 9 were asymptomatic or had an undifferentiated autoimmune disease (Asym/UAS) and 16 fulfilled criteria for SS and/or SLE. Microbial diversity was reduced across all levels from kingdom to species for the anti-Ro+ mothers vs healthy controls; however, there were no significant differences between Asym/UAS and SS/SLE mothers. Relative abundance of Proteobacteria and more specifically class Betaproteobacteria decreased with clinical severity (healthy controls < Asym/UAS < SS/SLE). These ordered differences were maintained through the taxonomic hierarchy to three genera (Lautropia, Comamonas, and Neisseria) and species within these genera (L. mirabilis, N. flavescens and N. oralis). Biometric analysis comparing von Willebrand Factor domains present in human Ro60 with L. mirabilis proteins support the hypothesis of molecular mimicry. These data position the microbiome in the development of anti-Ro reactivity and subsequent clinical spectrum of disease.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by pathologic T cell-B cell interactions and autoantibody production. Defining the T cell populations that drive B cell responses in SLE may enable design of therapies that specifically target pathologic cell subsets. Here we evaluated the phenotypes of CD4+ T cells in the circulation of 52 SLE patients drawn from multiple cohorts and identified a highly expanded PD-1hi CXCR5- CD4+ T cell population. Cytometric, transcriptomic, and functional assays demonstrated that PD-1hi CXCR5- CD4+ T cells from SLE patients are T peripheral helper (Tph) cells, a CXCR5- T cell population that stimulates B cell responses via IL-21. The frequency of Tph cells, but not Tfh cells, correlated with both clinical disease activity and the frequency of CD11c+ B cells in SLE patients. PD-1hi CD4+ T cells were found within lupus nephritis kidneys and correlated with B cell numbers in kidney. Both IL-21 neutralization and CRISPR-mediated deletion of MAF abrogated the ability of Tph cells to induce memory B cell differentiation into plasmablasts in vitro. These findings identify Tph cells a highly expanded T cell population in SLE and suggest a key role for Tph cells in stimulating pathologic B cell responses.