Researchers at NYU Langone’s Judith and Stewart Colton Center for Autoimmunity received grant awards for the following projects in 2020.

Evaluation of the Transcriptome of Nonlesional, Non–Sun-exposed Skin to Provide Insights into the Pathogenesis of Lupus Nephritis and Response to Therapy

Principal investigators: Jill P. Buyon, MD; Thomas Tuschl, PhD; and Robert Clancy, PhD

Lupus nephritis that leads to acute or end-stage renal failure is a major factor in the association of systemic lupus erythematosus (SLE) with mortality. Given the intense focus on new biologics for the treatment of lupus nephritis, the research community is eager for new pathologic insights and predictors of treatment unresponsiveness. Identification of a biomarker associated with poor prognosis would be useful for stratifying patients in clinical trials.

Efforts to identify biomarkers in serum and urine from people with lupus nephritis have not yet yielded sufficiently robust markers to replace renal biopsy. Previous studies have shown that endothelial changes, such as increased levels of membrane protein C receptor, predict poor responses to therapy. Furthermore, increased levels of the protein were noted in nonlesional, non–sun-exposed skin biopsies from people with lupus nephritis, suggesting that alterations in the microvasculature are widespread and extend to the dermal vasculature.

Analysis of this more readily accessible tissue, even distant from the primary affected organ, may provide an opportunity to explore surrogates for renal tissue analyses. Although ongoing studies are examining single-cell RNA sequencing to link phenotype to biotype and to identify cell-specific pathways in the kidney, this proposal addresses the hypothesis that these pathways may be reflected in uninvolved skin that is more likely to be serially biopsied.

The aim of this pilot study is to evaluate single-cell transcriptomes from biopsies of nonlesional, non–sun-exposed skin that has been temporally aligned with renal biopsies from people with lupus nephritis. We plan to explore associations in the context of biopsy class, activity and chronicity indices, and extent of tubulointerstitial disease; and renal outcome at 12 months.

This project leverages skin samples collected from patients with lupus nephritis, who are enrolled in the National Institutes of Health–funded Accelerating Medicines Partnership Rheumatoid Arthritis/Systemic Lupus Erythematosus (AMP RA/SLE) Program. The current proposal is to evaluate these cryopreserved skin biopsies on the 10× Genomics Chromium scRNA-seq platform, which offers droplet-based cell capture that is nearly 10-fold higher than previous approaches. This platform employs reverse transcription adapters equipped with unique molecular identifiers that more accurately count transcripts captured per cell.

In sum, analysis of more readily accessible skin tissue is expected to provide insight regarding keratinocyte, fibroblast, endothelial, and other tissue–resident cell dysfunction. We hope this novel approach may be better able to serially follow cell type–resolved gene expression signatures that may better correlate with renal outcomes than whole tissue or peripheral blood in patients with lupus nephritis.

Functional Genetics of Interferon Regulatory Factor 5 in Human Lupus

Principal investigators: Timothy Niewold, MD, and Jef D. Boeke, PhD

We study the lupus risk gene interferon regulatory factor 5 (IRF5). In our earlier work, we have shown that the risk variant of IRF5 is gain-of-function downstream of endosomal toll-like receptors. The role of IRF5 gene variants in causing SLE is not currently clear.

There are four common functional elements in the IRF5 gene. The SLE risk variant is a Neanderthal-derived haplotype that contains all four of these functional elements. These elements typically come together in strong linkage disequilibrium, so the contribution of each element cannot be determined individually.

This presents a major limitation of genetic epidemiology—because the variants are not observed in isolation on human chromosomes, the causal element or elements cannot be determined.

In our pilot project, we have used a novel DNA synthesis method in collaboration with the Boeke Laboratory and the Institute for Systems Genetics at NYU Langone to solve this problem. We are creating synthetic IRF5 haplotypes, which are not found in nature, that contain each risk-associated variant in isolation, as well as in novel combinations. Our goal is to elucidate the molecular function of each element and potential synergy or interaction. We have made these elements and are working to put them into stem cells, which would then allow for testing of the different IRF5 alleles in various immune cell types.

Identifying the Source of Pathogenic Type I Interferon in Experimental Lupus

Principal investigator: Boris Reizis, PhD

Elevated levels of type I interferons (IFNs α and β) are thought to contribute to the pathogenesis of systemic lupus erythematosus (SLE) and represent an attractive target of emerging therapies for the disease. Despite the readily detectable expression of IFN-stimulated genes (also called IFN signature), the actual cellular origin of IFN in human SLE patients and in SLE-prone animals remains poorly defined.

The overall goal of this pilot project is to establish the cellular source of IFN in experimental models of SLE, specifically in SLE-driven kidney inflammation. We use genetic reporters to visualize the ongoing production of IFN in experimental SLE and identify the IFN-producing cells in the lymphoid organs, as well as in inflamed tissues such as the kidneys.

Defining the Antigenic Landscape of Muscle-Specific Kinase Autoantibodies to Design Therapies for Myasthenia Gravis

Principal investigators: Steven J. Burden, PhD; Damian C. Ekiert, PhD; and Gira Bhabha, PhD

Myasthenia gravis is an autoimmune disease of the neuromuscular system that causes muscle weakness and fatigue, resulting in difficulty swallowing; altered facial, neck, and limb movements; and impaired breathing.

In approximately 20 percent of patients, the disease is caused by autoantibodies binding to a protein—muscle-specific kinase (MuSK)—that is critical for synaptic differentiation and maintaining the connection between motor neurons and muscles. For this subset of patients, the disease can be severe, and the standard of care—immunosuppressants and blood plasma replacement—is less successful.

Dr. Bhabha, Dr. Burden, and Dr. Ekiert are studying how the autoantibodies bind to MuSK protein in the hopes that this knowledge may lead to the design of protein-based therapies to sequester the autoantibodies, allowing MuSK to carry out its normal function.

In the long term, if the project leads to an understanding of how autoantibodies recognize MuSK, this information could be used to design therapeutic proteins or small molecules that block the interaction and protect tissue. The same approaches could be applied to any other autoimmune disease mediated by antibodies, such as lupus, rheumatoid arthritis, Guillain-Barré, and others.

Understanding the Functional Role of Purine Nucleoside Phosphorylase NP Polymorphism in Human Systemic Lupus Erythematosus

Principal investigators: Yogita A. Ghodke, PhD; Bruce N. Cronstein, MD; and Timothy Niewold, MD

Dr. Ghodke was a lead investigator of the first study to identify a variant of purine nucleoside phosphorylase (PNP) as a lupus risk gene. PNP is essential to cellular DNA synthesis.

Additional studies have demonstrated that the variant of the PNP gene associated with lupus disrupts DNA synthesis. In this pilot project, we hypothesize that this disruption causes fragments of the DNA to leak out from the cell, which triggers the immune system and eventually results in lupus.

Because the PNP gene is also critical for metabolizing a chemical that helps the immune system to maintain balance, we also hypothesize that a variant of the gene may also lead to the overactive immune response that is the hallmark of lupus.

If correct, both hypotheses would yield novel mechanisms of lupus pathogenesis. Moreover, each has the potential for personalized therapeutic development. One of the Colton Center for Autoimmunity’s overarching goals in lupus research is to address the fact that the disease’s origins and development can be completely different from patient to patient, yet standard care is “one size fits all.”

One of the implications of this project is that some patients with lupus might be receiving drugs that actually exacerbate the disease. For example, the medication azathioprine interferes with DNA synthesis in the same way as the variant of the PNP gene. This project could help move the field toward diagnosing and treating patients based on their molecular and immunological profiles.

Type I Interferon as a Predictor of Treatment Response in Rheumatoid Arthritis

Principal investigator: Theresa L. Wampler Muskardin, MD

For patients with rheumatoid arthritis, receiving the right kind of treatment as early as possible is crucial. Remission within the first three months of therapy is the best predictor of remission at one year, so a delay in getting the correct treatment can significantly change the likelihood of a positive outcome.

Because there are currently no biomarkers to predict which treatment is best for a given patient, physicians try a therapy and take the “watch and wait” approach to judge whether it’s working. Because of this, patients are often at risk of permanent joint damage.

Dr. Wampler Muskardin has demonstrated that measuring levels of type I interferon may help predict which patients will respond to the inhibitors commonly used to treat rheumatoid arthritis. Her work to date suggests there is a precise degree of interferon activity that correlates with outcomes. This could enable physicians to make objective, data-based decisions about which therapy to recommend.

Investigating Cellular and Molecular Triggers of Disease Progression in Psoriatic Arthritis

Principal investigators: Sergei B. Koralov, PhD, and Jose U. Scher, MD

Approximately 30 percent of patients with psoriasis will eventually develop psoriatic arthritis, which presents a unique opportunity for potential treatments. If researchers are able to find biomarkers that indicate exactly when and how psoriasis turns into psoriatic arthritis, the discovery could lead to early intervention and prevention in a susceptible and readily identifiable population.

So far, however, researchers have made little progress in understanding the pathology that links the two conditions due to a limited understanding of the phenotypic, molecular, and cellular events underlying the transition from psoriasis to psoriatic arthritis.

One of the major questions, and the subject of this study by Dr. Koralov and Dr. Scher, is to understand how cells of the adaptive immune system promote the progression from psoriasis to psoriatic arthritis. The two are working closely with colleagues at the New York Genome Center to take advantage of new high-throughput technology.

This technology enables researchers to simultaneously analyze the molecules on the surface of cells and the RNA molecules being expressed inside the cell, as well as to sequence the antigen specificity of T and B cells. These insights provide unprecedented insight into the immune landscape of inflamed tissue.

This research could provide a complete map of the cells that are pivotal in the inflammatory process of various tissues and how these may interact with each other to break tolerance and promote disease.

Exposure to Phthalates in Pregnant Women with Systemic Lupus Erythematosus: A Proof-of-Concept Study

Principal investigators: Leonardo Trasande, MD, MPP; Akhgar Ghassabian, MD, PhD; Jane Salmon, MD; and Jill P. Buyon, MD

Phthalates are a group of organic chemicals that are widely used in consumer products and are considered nonpersistant, meaning that environmental damage attributed to these chemicals is reversible. Animal and in vitro studies have associated alterations in the immune system and susceptibility to autoimmunity with exposure to phthalates.

A recent comparison of 58 people with systemic lupus erythematous systemic (SLE) and 78 controls has shown that those with SLE had substantially higher levels of phthalate metabolites measured in banked serum than healthy controls. Phthalate exposure represents a special concern in pregnant women because of the evidence suggesting that phthalates can influence intrauterine fetal growth and birth outcomes.

The objective of this pilot project is to measure concentrations of phthalate metabolites in urine samples collected through pregnancy in a group of pregnant women with SLE and to compare their levels with existing data from a cohort of pregnant women from the general population, who had no underlying conditions.