Colton Center Projects

At NYU Langone’s Judith and Stewart Colton Center, our researchers conduct pilot projects and collect data for biomedical research to better understand the immunological basis of autoimmune disorders.

We pioneer basic science and translational research that drive advances in the diagnosis, treatment, and prevention of autoimmune diseases, such as ankylosing spondylitis, antiphospholipid syndrome, arthritis, lupus, Sjögren’s syndrome, and type 1 diabetes.

2018-19 Projects

“Evaluation of the Transcriptome of Non-Lesional, Non-Sun Exposed Skin to Provide   Insights into the Pathogenesis of Lupus Nephritis and Response to Therapy”
Principal investigators:  Jill Buyon, MD, Thomas Tuschl, PhD and Robert Clancy, PhD

A major factor in the association of mortality and SLE is lupus nephritis (LN), leading to acute or end-stage renal failure. Given the intense focus on new biologics for the treatment of LN, it is not surprising that the research community is eager for new pathologic insights and predictors of unresponsiveness. The identification of a marker which carries a poor prognosis would be highly useful in stratifying patients in clinical trials. Although there have been intense efforts to identify biomarkers in serum and urine from LN patients, these have not yet yielded sufficiently robust markers to replace the renal biopsy. Previous studies have shown that endothelial changes such as increased protein levels of membrane protein C receptor in patients with LN predicts poor responses to therapy. Furthermore, increased levels were noted in biopsies of non-lesional, non–sun-exposed skin of LN patients, suggesting that alterations in the microvasculature are widespread and extend to the dermal vasculature. Thus, 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.  While ongoing studies are exploiting single cell RNA sequencing to link phenotype to “biotype” and identify cell specific pathways in the kidney, this proposal addresses the hypothesis that these pathways may be reflected in uninvolved skin which is more likely to be serially biopsied. The aim of this pilot study is evaluate single-cell transcriptomes from biopsies of non-lesional, non-sun exposed skin temporally aligned with renal biopsies from patients with LN.  Associations will be explored in the context of:  a) biopsy class, activity and chronicity indices, and extent of tubulointerstitial disease b) renal outcome at 12 months.  This project leverages skin samples collected on patients with LN who are enrolled in the NIH funded Accelerating Medicines Partnership (AMP) RA/SLE network. The current proposal is to evaluate these crypreserved skin biopsies on the 10X Genomics Chromium scRNA-seq platform with droplet-based cell capture being nearly 10 fold higher than using previous approaches. This platform employs reverse transcription adapters equipped with unique molecular identifiers (UMIs) for more accurate counting of 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 and assess a novel approach to be able to serially follow cell-type resolved gene expression signatures, which may better correlate with renal outcomes than whole tissue or peripheral blood in patients with LN.

“Functional Genetics of IRF5 in Human Lupus”
Principal investigators: Timothy Niewold, MD and Jef Boeke, PhD

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

There are four common functional elements in the IRF5 gene, and 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(s) cannot be determined.

In our pilot project, we have used a novel DNA synthesis method in collaboration with the Boeke Laboratory and NYU Langone’s Institute for Systems Genetics 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 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 investigators: Boris Reizis, PhD

Elevated levels of type I interferons (interferon-a/b, IFN) 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 (the so-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 will use genetic reporters to visualize the ongoing production of IFN in experimental SLE and identify the IFN-producing cells in the lymphoid organs and in inflamed tissues such as the kidneys.

“Defining the antigenic landscape of MuSK autoantibodies to design therapies for Myasthenia Gravis”
Principal investigators: Steve Burden, PhD, Damian Ekiert, PhD and Gira Bhabha, PhD

Myasthenia gravis (MG) 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 with MG, the disease is caused by autoantibodies binding a protein, muscle-specific kinase (MuSK), which 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.

Drs. Bhabha, Burden, and Ekiert are studying how the autoantibodies bind the 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 patient tissues. The same approaches could be applied to any other autoimmune disease mediated by antibodies (e.g., lupus, RA, Guillain-Barre, etc.).
    
“Understanding the functional role of PNP polymorphism in Human SLE”
Principal investigators: Yogita Ghodke, PhD, Bruce Cronstein, MD and Tim Niewold, MD

Dr. Ghodke-Puranik was a lead investigator of a previous study that was the first to identify a variant of the PNP gene, which is essential to cellular DNA synthesis, as a lupus risk gene. Further studies demonstrated that the variant of the PNP gene associated with lupus disrupts DNA synthesis; the hypothesis of this pilot project is that this disruption causes fragments of the DNA to leak out from the cell, triggering the immune system and eventually resulting in lupus. Furthermore, because the PNP gene is also critical for metabolizing a chemical that helps the immune system to maintain balance, the pilot project also hypothesizes that a variant of the gene could also lead to the overactive immune response which is the hallmark of lupus.

Both hypotheses, if correct, would yield novel mechanisms of lupus pathogenesis; moreover, each has the potential for personalized therapeutic development. One of the Colton Center’s overarching goals in lupus 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,  for instance, is that some patients with lupus might be receiving drugs—such as azathioprine, a drug that interferes with DNA synthesis in the same way that the variant of the PNP gene does— that actually exacerbate the disease. 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 investigators: Theresa 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, however, physicians have to try a therapy and take the “watch and wait” approach to judge whether it’s working, which puts patients at risk of permanent joint damage.

Dr. Wampler Muskardin has demonstrated that it may be possible to predict which patients will respond to the inhibitors that are the most common treatment for rheumatoid arthritis by measuring their levels of type 1 interferons. Her work to date suggests that there is a precise degree of interferon activity which correlates to outcomes, which would enable physicians to make an objective, data-based decision on which therapy to recommend.  

“Investigating Cellular and Molecular Triggers of Disease Progression in Psoriatic Arthritis”
Principal investigators: Sergei Koralov, PhD and Jose Scher, MD

Approximately 30 percent of patients with psoriasis will eventually develop psoriatic arthritis, which presents a unique opportunity. If researchers can 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.
 
One of the major questions, and the subject of this study by Drs. Koralov and Scher, is to understand how cells of the adaptive immune system promote the progression from psoriasis to psoriatic arthritis. Drs. Koralov and Scher are working closely with colleagues at the NY Genome Center to take advantage of new high-throughput technology that enables them to simultaneously analyze the molecules on the surface of a cells, the RNA molecules being expressed inside the cell and to sequence the antigen specificity of T and B cells — thus providing unprecedented insight into the immune landscape of inflamed tissue. This work could provide a complete map of which cells are pivotal in the inflammatory process at the various tissues, and how they may interact with each other to break tolerance and promote disease.

“Exposure to phthalates in pregnant women with SLE: a proof-of-concept study”
Principal investigators: Leonardo Trasande, MD, MPP, Akhgar Ghassabian, MD, PhD, Jane Salmon, MD and Jill Buyon, MD

Phthalates are a group of non-persistent organic chemicals which are widely used in consumer products. Animal and in vitro studies have shown alterations in the immune system and susceptibility to autoimmunity as a result of exposure to phthalates. A recent report of the comparison between 58 lupus erythematous systemic (SLE) patients and 78 controls has shown that SLE patients had substantially higher levels of phthalates 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.

2017–18 Projects

“Microbiome and its Metabolites in Psoriatic Arthritis Pathogenesis”
Principal investigators: Jose U. Scher, MD, and Sergei B. Koralov, PhD

Our team examines how the intestinal and skin microbiomes and the metabolites these microbes produce contribute to the chronic inflammation that characterizes psoriatic arthritis (PsA). We study how these microbiomes and microbial metabolites differ between patients with PsA and healthy individuals and also changes in the microbiome and metabolites that take place during progression from psoriasis to PsA.

We also examine changes in circulating immune cells among patients with PsA and control cohorts to correlate the changes in microbiota and metabolites to functional changes in the immune compartment. We recently characterized a novel small animal model of PsA and are using this model to demonstrate and probe the causal link between changes in microbiota and the metabolites they produce and the chronic inflammatory response in the skin and joints of these animals.

Our hope is that these studies will produce novel insight into PsA pathogenesis and identify novel targets for new therapeutic approaches.

“Functional Genetics of Interferon Regulatory Factor 5 in Human Lupus”
Principal investigators: Timothy Niewold, MD, and Jef Boeke, PhD

We study the lupus risk gene interferon regulatory factor 5 (IRF5). In our previous work, we have shown that the risk variant of IRF5 is gain-of-function downstream of endosomal toll-like receptors. How IRF5 functions to cause SLE is not currently clear.

There are four common functional elements in the IRF5 gene, and the SLE-risk variant is a Neanderthal-derived haplotype that contains all four of these functional elements. These elements are in strong linkage disequilibrium with low haplotype diversity, 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(s) cannot be determined.

In our pilot project, we use a novel DNA synthesis method in collaboration with the Boeke Laboratory and NYU Langone’s Institute for Systems Genetics 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 to elucidate the molecular function of each element and potential synergy or interaction.

This will allow us to determine how these elements change the transcriptional output of IRF5, leading to SLE. This knowledge is crucial to developing personalized medicine strategies that target IRF5.  

“Translational Regulation of Autoimmune Suppressive Regulatory T Cells”
Principal investigators: Robert Schneider, PhD, and Adam Mor, MD, PhD

Regulatory T cells (Tregs) suppress the activation of other immune cells by both contact-dependent and independent mechanisms, thereby maintaining immune system homeostasis, inhibiting effector T cells in the periphery, controlling excessive responses to foreign antigens, and preventing autoimmune disease. When Treg function is impaired, autoimmune diseases arise both in patients and in mouse models.

Although it is well established that Treg production increases when the enzyme mTOR is inhibited—in fact, mTOR inhibitor drugs are sometimes used in kidney transplant recipients to prevent organ rejection—there are still many questions about the exact nature of the connection between mTOR and Treg production.

Our research has helped us better understand this connection with data showing a novel translational reprogramming mechanism that promotes Treg development and differentiation. We have found that disrupting the metabolic processes of mTOR is the key to Treg development. This disruption promotes the messenger RNA that “tells” undifferentiated, or naïve, T cells to become Tregs, while inhibiting messenger RNA that tells undifferentiated T cells to become other types.

We seek to understand, and ultimately target with drugs, the crucial intracellular molecular translational control signals that are essential for promoting and impairing Treg development and function.

“Understanding the Role of Calcium Ion Signaling in the Pathogenesis of Sjögren’s Syndrome”
Principal investigators: Stefan Feske, MD, and Rodrigo S. Lacruz, MSc, PhD

In Sjögren’s syndrome, a condition that affects as many as 4 million people in the United States, the moisture-producing glands of the body are impaired, which leads to symptoms such as excessive dryness of the salivary and tear ducts, profound fatigue, chronic pain, major organ involvement, and neuropathies and lymphomas. Approximately 50 percent of patients develop complications, including non-Hodgkin’s B-cell lymphoma.

Although Sjögren’s syndrome is considered an autoimmune disease, the reason why autoimmunity develops—for instance, in response to a viral infection—is not understood. However, recent discoveries indicate that genetic and environmental factors precipitate Sjögren’s syndrome and that subsequent activation of the adaptive immune system starts the cycle of inflammation and gland destruction.
 
In preliminary data, we found an unexpected link between the onset of Sjögren’s syndrome and the way that T cells process calcium signals. Calcium ions are crucial to the biological processes of all cell types. In T cells, calcium ions flow into the cell through a channel that is regulated by several proteins: ORAI1, STIM1, and STIM2.

When any of these proteins is deleted, T cells cannot properly process calcium ions, which leads to the autoimmune inflammation of the salivary glands that characterizes Sjögren’s syndrome.

2016–17 Projects

“The Microbiome and Its Metabolites in Psoriatic Arthritis Pathogenesis”
Principal investigators: Jose U. Scher, MD, and Sergei Koralov, PhD

Our team investigates the microbiome and its metabolites in psoriatic arthritis pathogenesis. We have demonstrated in mice a possible role for medium-chain fatty acidsupplementation in the progression of autoimmune disease.

We are conducting early intervention, proof-of-principle trials in healthy humans to assess the potential translational implications of these findings.

“Protein Engineering of a Nuclease for the Rational Immunotherapy of Systemic Lupus Erythematosus”
Primary investigators: Boris Reizis, PhD, and Timothy J. Cardozo, MD, PhD

A collaboration between the Boris Reizis Laboratory, which specializes in experimental immunology, and the Cardozo Lab, which focuses on protein engineering, our project focuses on DNase IL3, a unique secreted deoxyribonuclease associated with rare familial cases of human SLE.

With a model of the DNASE IL3 structure generated by the Cardozo lab, our team has characterized unique properties and endogenous DNA substrate of DNASE IL3. We have created a proof of principle for the delivery of exogenous DNASE IL3 to ameliorate anti–double-stranded DNA response. Because DNASE IL3 is an endogenous human serum protein, we hypothesize that its delivery as a biologic would be a safe and specific therapeutic strategy in SLE.

“Isolation of Novel Members of the Gut Microbiota that Mediate Resistance to Autoimmunity”
Primary investigators: Ken H. Cadwell, PhD, and P’ng Loke, PhD

Our team is investigating the hypothesis that an increase in the incidence of autoimmune diseases is associated with changes in the environment, such as decreased exposure to helminths and alterations to the gut microbiota.

Previously, we found that infecting mice that have NOD2 mutations with helminths induces expansion of Clostridiales species, which reverse intestinal disease by inhibiting Bacteroides vulgatus colonization. Helminth infections in the indigenous people of Malaysia have been associated with similar alterations in gut microbiota and suggest an antagonistic relationship between Clostridiales and inflammatory bacteria in humans.

Our research will isolate novel Clostridiales strains from a cohort of individuals with helminth infection and test their ability to suppress inflammation. This information may reveal strategies to improve the safety and efficacy of ongoing efforts to therapeutically target the microbiota in patients with autoimmune diseases.

“Epigenetics of Antibiotic-Induced Type 1 Diabetes in a Nonobese Diabetic Mouse Model”
Primary investigator: Martin Blaser, MD

Type 1 diabetes is a classic autoimmune disease that usually develops in early life. The substantial increase in the disease’s prevalence since World War II indicates the importance of exogenous influences. We are exploring the hypothesis that changes in human microbiome have significant immunological effects.

Our team has established a model that accelerates type 1 diabetes and has developed insights regarding possible mechanisms of disease. We now seek to extend these observations to better understand and ultimately prevent type 1 diabetes, as well as to obtain general information about the microbiota and immune interactions that drive autoimmunity.

Nonobese diabetic mice spontaneously develop type 1 diabetes, and we have shown previously that we can accelerate the incidence with exposure to antibiotics in early life. We are now examining the cells of the intestinal wall to determine whether changes to them can be explained by interactions between the microbes altered by antibiotic exposure and the immune system. Such epigenetic changes might be crucial in the microbe–host interface and might possibly be blocked to delay or prevent the development of type 1 diabetes.

2014–2016 Projects

"The examination of microbiota-triggered adaptive immune responses in autoimmune disease"
Principal investigator:  Dan Littman, MD, PhD
The central hypothesis of these studies is that an altered gastrointestinal microbiome, or dysbiosis, is an important initiating factor in the development of inflammatory arthritis in genetically susceptible individuals. The potential impact of the studies could lead to novel treatment strategies to either prevent or treat diseases such as rheumatoid arthritis, psoriatic arthritis, and ankylosing spondylitis.   
Working with Dr. Steven Abramson and Dr. Jose Scher, the group previously reported a correlation of new onset rheumatoid arthritis (NORA) with colonization of the fecal microbiota with Prevotella copri. Based on results in a mouse model of spontaneous arthritis, which was triggered by colonization with the Th17 cell-inducing segmented filamentous bacteria (SFB), we are seeking to determine if P. copri likewise triggers disease. We have cultured multiple strains of P. copri from NORA patients and healthy controls and have prepared sequencing libraries from 96 strains that are currently being processed.
Dr. Littman’s group has also initiated collaboration with rheumatology groups at the University of Oxford and University College, London to sequence the microbiota of patients with RA, ankylosing spondylitis, and juvenile inflammatory arthritis.

The examination of microbiota-triggered immune responses in SLE and APS
Principal investigator:  Gregg Silverman, MD
The overarching goal is to investigate whether specific bacterial isolates in the intestines of people with systemic erythematosus lupus (SLE) contribute to their autoimmune pathogenesis and to disease flares. Working with Dr. Jill Buyon, Dr. Silverman has uncovered several important new findings in his group’s studies of whether specific bacterial isolates in the intestines of SLE patients contribute to their autoimmune pathogenesis and to disease flares. One such finding has led to a project invention for antimicrobial fecal IgA as a diagnostic for SLE.

The role of DNASE1L3 and microparticle-associated DNA in human SLE
Principal investigators:  Boris Reizis, PhD and Jill Buyon, MD
Drs. Buyon and Reizis, who are investigating the role of DNASE1L3 in systemic lupus erythematosus (SLE), developed a new assay to measure DNASE1L3 activity in human serum or plasma, as well as a new method to measure DNA concentration in circulating microparticles in human plasma. Their study has developed three novel readouts of anti-DNA reactivity in SLE, which may represent novel, pathogenetically relevant parameters of the disease and have diagnostic and/or prognostic potential. These findings have led to a provisional project invention under preparation for DNASE1L3 as a therapeutic agent.