Researchers at NYU Langone’s Judith and Stewart Colton Center for Autoimmunity received grant awards for the following projects in 2019.

Investigating the Role of the Long Noncoding RNA CHROME in Lupus

Principal investigators: Kathryn J. Moore, PhD, and Ashira Blazer, MD

For decades, researchers have ignored the “dark matter” of the genome—RNAs that are transcribed but that do not code for proteins, also called long noncoding RNAs (lncRNAs). lncRNAs comprise the majority of transcriptionally active regions of the human genome, yet fewer than 1 percent of human lncRNAs are functionally characterized.

Recent studies have shown that lncRNAs are potent regulators of gene expression and have important functions in both health and disease. We have discovered an lncRNA, called CHROME, that is expressed specifically in primates and is dysregulated in systemic lupus erythematosus (SLE). In SLE, immune complex formation and toll-like receptor ligation trigger the expression of interferon (IFN), which propagates autoimmune inflammation. 

Notably, genetic susceptibility to higher IFN production is linked to SLE development, and is associated with higher serum autoantibodies and increased disease activity.
Our preliminary data indicate that CHROME is elevated in the plasma of SLE patients compared with healthy controls. Mechanistic studies have revealed that CHROME regulates IFN-stimulated gene expression in monocytes and macrophages. Using chromatin isolation by RNA purification (ChIRP) to map RNA–protein and RNA–DNA interactions, we found that CHROME binds at the promoters of IFN-stimulated genes and interacts with the DNA helicase topoisomerase to promote gene expression.

We hypothesize that CHROME contributes to SLE activity through transcriptional regulation of IFN-stimulated genes. To test this hypothesis, we propose investigating the expression of CHROME in patients with SLE to identify the mechanisms by which CHROME is induced in SLE and to identify how CHROME regulates IFN-stimulated gene expression.
Understanding the role of primate-specific lncRNAs such as CHROME in orchestrating IFN signaling may identify mechanisms underlying SLE-characteristic immune dysregulation and novel therapeutic targets for intervention.

Osteopontin as a Target in Lupus Nephritis

Principal investigators: Amrutesh S. Puranik, PharmD, and Timothy Niewold, MD

Long-term lupus results in accumulation of immune complexes in the kidney, which in turn leads to cell death and decline in kidney function. This condition is called lupus nephritis. Earlier studies from the Niewold Lab have shown that high levels of osteopontin are associated with lupus nephritis.

Recently, we observed that osteopontin is natively expressed by certain types of macrophages in the kidney. These macrophages reside in the kidney at birth and perform functions that include consuming dead cells and debris generated in the kidney, thereby keeping other cells safe. Similarly, macrophages also preferentially take up the immune complexes that reach the kidney and prevent them from damaging other cells.

In this study, we evaluate the role of these osteopontin-expressing macrophages (OPN-macrophages) in lupus nephritis. We expect that in lupus nephritis, OPN-macrophages will have an inflammatory phenotype and be localized to sites of damage in nephritis. Because these macrophages are involved in the early immune complex–mediated stages of nephritis, these cells could be attractive targets for early intervention or prevention of nephritis. Our studies could suggest OPN-macrophages as novel therapeutic targets.

Optimizing Immunoglobulin-Like Transcript 7 and BDCA-2 Regulation of Plasmacytoid Cells in Systemic Lupus Erythematosus

Principal investigators: Mark A. Jensen, PhD, and Timothy Niewold, MD

Systemic lupus erythematosus (SLE) is a prototype systemic autoimmune disease characterized by rash, arthritis, nephritis, serosal inflammation, cytopenias, and autoantibodies that are directed against nuclear antigens.

A hyperactive, dysregulated type I interferon signaling pathway is thought to contribute to disease pathogenesis, and high levels of type I interferons can be detected in the blood of a subset of patients. Levels of type I interferons are stably increased in these patients and are associated with worse clinical disease.

Plasmacytoid dendritic cells (PDCs) are a type of white blood cell that becomes activated in SLE and are thought to contribute to disease pathogenesis. Activated PDCs produce type I interferons and inflammatory cytokines and become potent antigen-presenting cells that promote the autoreactive immune response. PDCs express several different inhibitory surface receptors and intracellular signaling pathways that regulate their activation, as well as blunt production of interferons and inflammatory cytokines.

We studied PDCs from a cohort of SLE patients and unaffected controls. We found that PDCs from patients with more severe disease express lower levels of a subset of regulatory receptors. This suggests that PDCs in these patients have become dysregulated, leading to their chronic activation.

This research project focuses on using combinatorial approaches to identify two or more different signaling pathways that together optimally regulate PDCs in SLE patients that have more severe disease. This strategy has the potential to define an optimal combination of agents for regulating PDC activation that could lead to a novel treatment approach for SLE and rapidly advance to the clinic.

Defining Gene Regulatory Networks in Autoimmune Disease

Principal investigators: Aravinda Chakravarti, PhD, and Timothy Niewold, MD

Recent genetic studies have identified hundreds of gene variations that are associated with risk for autoimmune disease. Despite great strides in mapping the regions of the genome linked to autoimmune diseases, we know little about the biology or functions of these risk factors.

Many of the gene variants identified do not change the structure of proteins, but instead are likely to change the expression of nearby genes. Thus, the inherited gene variants associated with autoimmune disease result in a regulatory network that changes gene expression and alters immune cell function.

In this project, we seek to systematically define the gene regulatory network in human immune cells and to understand how sequence polymorphisms, or other changes in regulatory elements, perturb this network. Combining our expertise in human molecular genetics, human immunology, and autoimmune disease pathogenesis, our team is uniquely poised to accomplish these goals.

Development of a Novel Light-Inducible Cre Recombinase to Track and Manipulate Migration of Self-Reactive T Cells

Principal investigators: Susan R. Schwab, PhD, and Sergei B. Koralov, PhD

It is increasingly clear that an immune response in one part of the body can shape a distinct immune response at a distant site. We know that interactions between the immune system and bacteria in the gut can have powerful effects on the course of autoimmune diseases that are spatially separated from the intestine, such as damage to the brain associated with multiple sclerosis or joint damage associated with arthritis.

Yet it remains far from clear how this occurs. A basic obstacle to understanding this problem is that we lack the tools to label cells in one part of the body and follow their movement to other sites, as well as the ability to manipulate cells in one part of the body and assess how this ultimately affects courses of disease.

To address these problems, we propose using a mouse that expresses a light-inducible Cre recombinase, which will allow us to alter gene expression in cells at a specific time and place using blue light to track the cells. As a proof of principle, we plan to use these mice to identify immune cells in the intestine and trace cell migration upon the induction of a murine model of multiple sclerosis.

We hypothesize that inflammation induces the release of immune cells from the gut, that these cells traffic to the central nervous system, and that their exit from the intestine requires expression of a homing receptor, sphingosine-1-phosphate receptor 1 (S1P1). The U.S. Food and Drug Administration (FDA)–approved drug, Gilenya®, inhibits S1P1.

Ultimately, we hope our study enables investigators to ask a wide range of fundamental questions about cell migration in autoimmune disease and to identify novel targets for therapy.

Novel Hematopoietic Stem Cell Transplant Strategies for the Treatment of Autoimmune Disease

Principal investigators: Christopher Y. Park, MD, PhD, and Doyun Park, MD

The cornerstone of therapy for autoimmune disorders is the elimination, or crippling, of immune cells that cause these disorders. However, current strategies frequently provide only temporary control of disease. Blood stem cell transplant holds the promise of resetting the immune system by allowing complete replacement of the blood system with normal cells.

This strategy has been explored as a treatment for severe and refractory autoimmune diseases. Although these studies strongly suggest that blood stem cell transplant can provide a significant clinical benefit, even for patients with advanced autoimmune disease, this approach has been limited to the investigational setting. Risks associated with transplant include short-term mortality from the procedure and long-term consequences, such as infertility and secondary cancers.

Developing strategies for blood stem cell transplant that reduce short- and long-term side effects and preserve, or even improve, immunologic remodeling after the procedure would likely promote its use as a treatment for lupus and other autoimmune diseases.

We plan to use animal models of autoimmune disease to test whether safer methods of performing transplants and providing specific subtypes of stem cells may better treat diseases with the goal of moving these approaches into the clinic.

Understanding Lupus Nephritis

Principal investigators: Jef D. Boeke, PhD; Jill P. Buyon, MD; Thomas Tuschl, PhD; Amrutesh S. Puranik, PharmD; Boris Reizis, PhD; and Timothy Niewold, MD

Lupus nephritis is one of the most feared complications of systemic lupus erythematosus (SLE). It arises without warning or symptoms and can rapidly progress to renal failure. Clinically, we monitor urine tests and kidney function, but this can only detect disease after it has begun. Treatment is still nonspecific immunosuppression, which carries a high risk of side effects.

We seek to address the challenges of lupus nephritis with the goal of developing a prognostic model and identifying novel targets for therapy. Our multidisciplinary team includes outstanding expertise in genetics, murine and human immunology, and clinical lupus pathogenesis.

We propose three main projects to address the genetic basis of the nephritis, immunological pathogenesis, and the prediction of disease in the clinic. These projects seek to accomplish the following objectives:

• understand the functional genetics of SLE-associated alleles that confer risk of nephritis
• examine the role of type I interferon in SLE nephritis
• develop a predictive model for lupus nephritis

These studies are designed to work together and leverage a number of previous research findings with the goal of bringing our research to the clinic. Our team of primary investigators have complementary areas of expertise to drive these projects to completion.

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

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

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

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

We are developing a pipeline to study how autoantibodies bind the MuSK protein. We hope that this knowledge may lead to the design of protein-based therapies to sequester autoantibodies and develop agonist antibodies to stimulate MuSK and allow the protein 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 antibodies, other proteins, or small molecules that block the interaction and protect patient tissues. The same approaches could be applied to any other autoimmune disease mediated by antibodies, including lupus, rheumatoid arthritis, Guillain-Barré syndrome, and more.