Faculty Bibliography

Background/Purpose: Treatment of lupus nephritis relies on renal histopathological features. However, renal biopsies do not capture patient-specific active biological pathways. Urine proteomic biomarkers could revolutionize the diagnosis and management of lupus nephritis by predicting active intrarenal biological pathways and can be noninvasively monitored over time.
Method(s): One thousand proteins were quantified (RayBiotech) in a total of 112 longitudinal urine samples from 30 SLE patients with active lupus nephritis and 7 healthy controls (HC). The proteins and molecular pathways detected in the urine proteome at the time of biopsy were then analyzed with respect to lupus nephritis class, response to treatment after 1 year, histopathological features (activity and chronicity indeces), and trajectory over time (baseline and week 12, 26, and 52). The intrarenal expression of candidate biomarkers was evaluated using single cell transcriptomics of renal biopsies from patients with active lupus nephritis.
Result(s): There were 237 proteins (FDR < 10%) enriched in the urine of patients with lupus nephritis reflecting several molecular pathways involving chemotaxis, extracellular matrix remodeling, and activation of neutrophils and platelets. Hierarchical clustering using urine proteomics segregated SLE patients into 2 groups, with 80% of complete responders clustering together. This finding could not be similarly reproduced using standard features including baseline proteinuria, creatinine, histologic activity or chronicity scores, or class, indicating unique informative features of urine proteomics (Fig. 1). Patients with proliferative lupus nephritis (class III or IV) had stronger activation of chemotaxis pathways. IL-16 was the urinary protein most significantly increased in proliferative disease compared to membranous (FC 6, p=0.002) (Fig. 2A). Assessment of urine proteins that correlated with histologic activity kidney highlighted IL-16 as the single most strongly correlated protein with histologic activity (r=0.69, p=9.5.10-5; Fig. 2B). IL-16 concentration was independent of the amount of proteinuria and progressively diminished over time in patients who were responding to immunosuppression (Fig. 2C). Single cell RNA sequencing revealed significant intrarenal expression of IL16 by all infiltrating immune cells and highlighted IL16 as the second most expressed cytokine in lupus nephritis kidneys out of a compendium of 236 cytokines (Fig. 3A-B).
Conclusion(s): Urine proteomics can noninvasively identify active and biologically relevant pathways in lupus nephritis. Integrated urine proteomics and renal single cell transcriptomics revealed that IL-16, a CD4 ligand with chemotactic and proinflammatory functions, was one of the most expressed cytokine in lupus nephritis. As a urine proteomic biomarker, IL-16 may predict renal histological activity and could be monitored over time to assess response to immunosuppression. Urinary IL-16 is independent of proteinuria thus potentially providing actionable clinical information that is not captured by currently used biomarkers. Further studies are ongoing to validate these findings

Background/Purpose: Neonatal Lupus (NL) is a model of passively acquired autoimmunity conferred by exposure to maternal anti-Ro antibodies with major manifestations being congenital heart block (CHB) and/or cutaneous disease. This study was initiated to address the development of de novo autoimmunity in these children and identify associated clinical and genetic risk factors.
Method(s): In a retrospective cohort study of enrollees in the Research Registry for Neonatal Lupus (RRNL), 511 children exposed to anti-Ro in utero responded to a follow up questionnaire focused on symptoms of autoimmunity. Self-reported diseases were confirmed via medical record review. Bivariate analyses were performed with potential risk factors for the development of autoimmune disease (AD) and included the NL status per se, a disease severity score based on mortality risk factors, and maternal AD (inclusive of lupus, Sjogren's syndrome, psoriasis, rheumatoid arthritis, or thyroid disease). A subset of 99 CHB, 9 cutaneous, and 55 unaffected anti-Ro exposed RRNL individuals were genotyped at Class II HLA DRB1 and DQB1 four-digit alleles, which were assigned by imputation (HIBAG) or sequencing. Generalized estimating equations (logit link, exchangeable correlation) were used to test for associations between HLA alleles and the development of AD.
Result(s): Of the respondents, 182 offspring had CHB, 95 had cutaneous only NL and 234 were siblings without NL. Females comprised 53% and 80% were Caucasian. The mean age was 14.2+/-9.7; 4% age 0-2 years, 48% 2-13 years, and 47% > 13 years. An AD developed in 38 offspring (20 CHB, 7 cutaneous NL, 11 non-NL siblings; Table 1). The most prevalent AD was thyroid disease. The development of an AD was significantly associated with presence of CHB vs. cutaneous only or non-NL siblings (11% vs. 5%, p=0.033). The maternal health status did not influence the development of an AD in the child (7% mothers with AD vs. 6% asymptomatic mothers, p=0.67). Mean NL severity score was higher in offspring with AD (3.8+/-4.8 vs. 2.2+/-4.0, p= 0.031). Other markers of fetal CHB disease severity were associated with subsequent AD development, including in-utero exposure to fluorinated steroids (15% vs. 6%, p=0.088) and beta agonists such as terbutaline (23% vs. 9%, p=0.043). In the study of 163 RRNL cases with HLA data (20 with AD, 143 without), HLA DRB1*03:01 (OR 3.4, CI 1.46-7.90, p=0.0045), DQA1*05:01 (OR 3.39, CI 1.16-9.92, p=0.0262), and DQB1*02:01 (OR 4.28, CI 1.73-10.62, p=0.0017) were associated with increased risk of AD (of note, these loci are in high linkage disequilibrium). In contrast, these alleles were not significantly associated with development of CHB (99 CHB vs. 64 without).
Conclusion(s): The development of an autoimmune disease was more common in anti-Ro exposed children with CHB, greater NL severity, and MHC Class II haplotypes. These factors may relate to an inherent susceptibility to inflammation and fibrosis, occuring in utero and later in life

BACKGROUND:Experimental and clinical evidence support the role of macrophage Toll-like receptor signaling in maternal anti-SSA/Ro-mediated congenital heart block (CHB). OBJECTIVES/OBJECTIVE:Hydroxychloroquine (HCQ), an orally administered Toll-like receptor antagonist widely used in lupus including during pregnancy, was evaluated for efficacy in reducing the historical 18% recurrence rate of CHB. METHODS:This multicenter, open-label, single-arm, 2-stage clinical trial was designed using Simon's optimal approach. Anti-SSA/Ro-positive mothers with a previous pregnancy complicated by CHB were recruited (n = 19 Stage 1; n = 35 Stage 2). Patients received 400 mg daily of HCQ prior to completion of gestational week 10, which was maintained through pregnancy. The primary outcome was 2° or 3° CHB any time during pregnancy, and secondary outcomes included isolated endocardial fibroelastosis, 1° CHB at birth and skin rash. RESULTS:By intention-to-treat (ITT) analysis, 4 of 54 evaluable pregnancies resulted in a primary outcome (7.4%; 90% confidence interval: 3.4% to 15.9%). Because 9 mothers took potentially confounding medications (fluorinated glucocorticoids and/or intravenous immunoglobulin) after enrollment but prior to a primary outcome, to evaluate HCQ alone, 9 additional mothers were recruited and followed the identical protocol. In the per-protocol analysis restricted to pregnancies exposed to HCQ alone, 4 of 54 (7.4%) fetuses developed a primary outcome as in the ITT. Secondary outcomes included mild endocardial fibroelastosis (n = 1) and cutaneous neonatal lupus (n = 4). CONCLUSIONS:These prospective data support that HCQ significantly reduces the recurrence of CHB below the historical rate by >50%, suggesting that this drug should be prescribed for secondary prevention of fetal cardiac disease in anti-SSA/Ro-exposed pregnancies. (Preventive Approach to Congenital Heart Block With Hydroxychloroquine [PATCH]; NCT01379573).

AIMS/OBJECTIVE:Investigating human heart development and applying this to deviations resulting in disease is incomplete without molecular characterization of the cell types required for its normal functioning. We investigated fetal human heart single-cell transcriptomes from midgestational healthy and anti-Ro associated congenital heart block (CHB) samples, respectively. METHODS AND RESULTS/RESULTS:Three healthy fetal human hearts (19th-22nd week of gestation) and one fetal heart affected by autoimmune-associated CHB (21st week of gestation) were subjected to enzymatic dissociation using the Langendorff preparation to obtain single cell suspensions followed by 10x Genomics- and Illumina-based single cell RNA-sequencing (scRNA-seq). In addition to the myocytes, fibroblasts, immune cells, and other minor cell types, previously uncharacterized diverse subpopulations of endothelial cells were identified in the human heart. Differential gene expression analysis revealed increased and heterogeneous interferon responses in varied cell types the CHB heart compared to the healthy controls. In addition, we also identified matrisome transcripts enriched in CHB stromal cells that potentially contributing to extracellular matrix deposition and subsequent fibrosis. CONCLUSION/CONCLUSIONS:These data provide an information-rich resource to further understanding of human heart development, which, as illustrated by comparison to a heart exposed to a maternal autoimmune environment, can be leveraged to provide insight into the pathogenesis of disease. TRANSLATIONAL PERSPECTIVE/UNASSIGNED:This study provides a single cell transcriptomic atlas of cells obtained from healthy second trimester fetal hearts to further understand human heart development and impart insight into autoimmune associated congenital heart block. In addition to myocytes and fibroblasts, previously uncharacterized subpopulations of endothelial cells were identified. Leveraging an unprecedented opportunity, healthy heart transcriptomes were compared to an age matched anti-SSA/Ro exposed fetal heart with third degree block in which no maternal medications were taken. Differential gene expression analysis revealed a remarkable interferon response in many cell types of the diseased heart. In addition, matrisome transcripts were enriched in the stromal cells likely contributing to the extracellular matrix deposition and thereby fibrosis, a signature lesion of heart block. Thus, targeting the interferon pathway merits therapeutic consideration.

Lupus nephritis, one of the most serious manifestations of systemic lupus erythematosus (SLE), has both a heterogeneous clinical and pathological presentation. For example, proliferative nephritis identifies a more aggressive disease class that requires immunosuppression. However, the current classification system relies on the static appearance of histopathological morphology which does not capture differences in the inflammatory response. Therefore, a biomarker grounded in the disease biology is needed to understand the molecular heterogeneity of lupus nephritis and identify immunologic mechanism and pathways. Here, we analyzed the patterns of 1000 urine protein biomarkers in 30 patients with active lupus nephritis. We found that patients stratify over a chemokine gradient inducible by interferon-gamma. Higher values identified patients with proliferative lupus nephritis. After integrating the urine proteomics with the single-cell transcriptomics of kidney biopsies, it was observed that the urinary chemokines defining the gradient were predominantly produced by infiltrating CD8 T cells, along with natural killer and myeloid cells. The urine chemokine gradient significantly correlated with the number of kidney-infiltrating CD8 cells. These findings suggest that urine proteomics can capture the complex biology of the kidney in lupus nephritis. Patient-specific pathways may be noninvasively tracked in the urine in real time, enabling diagnosis and personalized treatment.

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

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.

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

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 : Despite the strong association of maternal anti-Ro60 autoantibodies in the development of SS, Neonatal Lupus (NL) and scLE, understanding causality is challenging given that the intracellular location of the target RNP antigen only becomes accessible to extracellular autoantibodies during cell death. While binding Y RNA is a property of Ro60 in dying cells, Ro60 contributes to events essential to proliferation including the degradation of non-coding RNAs. To define potentially targetable molecular events associated with Ro60 accessibility and their effects on proliferation, we evaluated two candidate chaperone Ro60 binding proteins, ZBP1 (also known as IGF2BP1, which has two RNA recognition domains and plays a role in nuclear export of protein) and PTBP1 (which binds RNA in heterogeneous nuclear complexes). Methods : Short hairpin (sh)RNA knockdown (KD) of both ZPB1 and PTBP1 was accomplished by using MISSION pLKO.1 derived lentiviral vehicles for targeted shRNA to yield each of the specific depletions in human fetal fibroblasts. Affinity purified anti-Ro60 antibodies (AP60) isolated from the serum of 2 mothers of children with cardiac NL and control IgG isolated from a healthy donor were used to evaluate Ro60 surface translocation in intact and apoptotic cells by flow cytometry. Fibroblast proliferation was determined using 5-ethynyl-2'-deoxyuridine (EdU) incorporation. Results : KD of targeted transcripts were confirmed by qPCR and western blot. Permeabilized KD and wildtype fi-broblasts demonstrated equivalent intracellular expression of Ro60. As expected, flow cytometry with AP60 revealed no surface staining of non-permeabilized wildtype or KD fibroblasts. The next set of experiments addressed binding of AP60 to polyHEMA-apoptotic fibroblasts. Staining with annexin V (a proxy of apoptosis) was uniformly consistent between the wildtype and KD cells. As expected, compared to non-apoptotic fibroblasts, AP60 but not control donor IgG readily bound the surface of wildtype apoptotic fibroblasts, supporting that Ro60 was indeed translocated during apoptosis (MFI of 97 + 5 vs 211 + 14, respectively; P< 0.05; N=3). In contrast, binding of AP60 was significantly attenuated in the ZPB1 KD fibroblasts (81.5 + 7; N = 3) vs anti-Ro binding of apoptotic wildtype fibroblasts(P< 0.05). However, the binding of AP60 was equivalent in the apoptotic PTBP1 KD fibroblasts (MFI of 203 + 6, N= 3, P=NS) compared to apoptotic wildtype fibroblasts. With regard to cell proliferation, the percent positive EdU cells of wildtype fetal fibroblasts, ZBP1 KD fibroblasts, and PTBP1 KD fibroblasts were 56%, 2% and 45%, respectively, a result suggesting that the loss of ZBP1 restrains cell cycle progression. Conclusion : ZBP1 represents a novel and required chaperone for the translocation of Ro60 to the cell surface during apoptosis in addition to contributing to cell proliferation. Given that Ro60 antigen accessibility is essential, not only to the generation of anti-Ro60 responses but also to the formation of surface immune complexes and subsequent tissue injury, ZBP1 may represent a newly targetable candidate to forestall both the initiation and sequelae of autoimmunity