Autoimmunity
Abstract
More than 90% of autoimmune-associated variants are located in noncoding regions, leading to challenges in deciphering the underlying causal roles of functional variants and genes and biological mechanisms. Therefore, to reduce the gap between traditional genetic findings and mechanistic understanding of disease etiologies and clinical drug development, it is important to translate systematically the regulatory mechanisms underlying noncoding variants. Here, we prioritized functional noncoding SNPs with regulatory gene targets associated with 19 autoimmune diseases by incorporating hundreds of immune cell–specific multiomics data. The prioritized SNPs are associated with transcription factor (TF) binding, histone modification, or chromatin accessibility, indicating their allele-specific regulatory roles. Their target genes are significantly enriched in immunologically related pathways and other known immunologically related functions. We found that 90.1% of target genes are regulated by distal SNPs involving several TFs (e.g., the DNA-binding protein CCCTC-binding factor [CTCF]), suggesting the importance of long-range chromatin interaction in autoimmune diseases. Moreover, we predicted potential drug targets for autoimmune diseases, including 2 genes (NFKB1 and SH2B3) with known drug indications on other diseases, highlighting their potential drug repurposing opportunities. Taken together, these findings may provide useful information for future experimental follow-up and drug applications on autoimmune diseases.
Authors
Xiao-Feng Chen, Ming-Rui Guo, Yuan-Yuan Duan, Feng Jiang, Hao Wu, Shan-Shan Dong, Xiao-Rong Zhou, Hlaing Nwe Thynn, Cong-Cong Liu, Lin Zhang, Yan Guo, Tie-Lin Yang
Abstract
Background: Baseline expression of FCRL5, a marker of naïve and memory B cells, was shown to predict response to rituximab (RTX) in rheumatoid arthritis. This study investigated baseline expression of FCRL5 as a potential biomarker of clinical response to RTX in granulomatosis with polyangiitis (GPA) and microscopic polyangiitis (MPA). Methods: A previously validated RT-qPCR-based platform was used to assess FCRL5 expression in patients with GPA/MPA (RAVE trial, NCT00104299). Results: Baseline FCRL5 expression was significantly higher in patients achieving complete response (CR) at 6, 12, and 18 months, independent of other clinical and serological variables, among those randomized to RTX but not CYC/AZA. Patients with baseline FCRL5 expression ≥ 0.01 expression units (termed FCRL5hi) exhibited significantly higher CR rates at 6, 12, and 18 months as compared to FCRL5low subjects (84% vs 57% p=0.016, 68% vs 40% p=0.02 and 68% vs 29% p=0.0009, respectively). Conclusion: Our data taken together suggest that FCRL5 is a biomarker of B cell lineage associated with increased achievement and maintenance of complete remission among patients treated with RTX and warrant further investigation in a prospective manner.
Authors
Kasia Owczarczyk, Matthew D. Cascino, Cecile Holweg, Gaik W. Tew, Ward Ortmann, Timothy W. Behrens, Thomas Schindler, Carol A. Langford, E. William St. Clair, Peter A. Merkel, Robert Spiera, Philip Seo, Cees G.M. Kallenberg, Ulrich Specks, Noha Lim, John H. Stone, Paul Brunetta, Marco Prunotto
Abstract
Scleroderma is a devastating fibrotic autoimmune disease. Current treatments are partly effective in preventing disease progression but do not remove fibrotic tissue. Here, we evaluated whether scleroderma fibroblasts take advantage of the “don’t-eat-me-signal” CD47 and whether blocking CD47 enables the body’s immune system to get rid of diseased fibroblasts. To test this approach, we used a Jun-inducible scleroderma model. We first demonstrated in patient samples that scleroderma upregulated transcription factor JUN and increased promoter accessibilities of both JUN and CD47. Next, we established our scleroderma model, demonstrating that Jun mediated skin fibrosis through the hedgehog-dependent expansion of CD26+Sca1– fibroblasts in mice. In a niche-independent adaptive transfer model, JUN steered graft survival and conferred increased self-renewal to fibroblasts. In vivo, JUN enhanced the expression of CD47, and inhibiting CD47 eliminated an ectopic fibroblast graft and increased in vitro phagocytosis. In the syngeneic mouse, depleting macrophages ameliorated skin fibrosis. Therapeutically, combined CD47 and IL-6 blockade reversed skin fibrosis in mice and led to the rapid elimination of ectopically transplanted scleroderma cells. Altogether, our study demonstrates the efficiency of combining different immunotherapies in treating scleroderma and provides a rationale for combining CD47 and IL-6 inhibition in clinical trials.
Authors
Tristan Lerbs, Lu Cui, Megan E. King, Tim Chai, Claire Muscat, Lorinda Chung, Ryanne Brown, Kerri Rieger, Tyler Shibata, Gerlinde Wernig
Abstract
Gene expression signatures can stratify patients with heterogeneous diseases, such as systemic lupus erythematosus (SLE), yet understanding the contributions of ancestral background to this heterogeneity is not well understood. We hypothesized that ancestry would significantly influence gene expression signatures and measured 34 gene modules in 1566 SLE patients of African ancestry (AA), European ancestry (EA), or Native American ancestry (NAA). Healthy subject ancestry-specific gene expression provided the transcriptomic background upon which the SLE patient signatures were built. Although standard therapy affected every gene signature and significantly increased myeloid cell signatures, logistic regression analysis determined that ancestral background significantly changed 23 of 34 gene signatures. Additionally, the strongest association to gene expression changes was found with autoantibodies, and this also had etiology in ancestry: the AA predisposition to have both RNP and dsDNA autoantibodies compared with EA predisposition to have only anti-dsDNA. A machine learning approach was used to determine a gene signature characteristic to distinguish AA SLE and was most influenced by genes characteristic of the perturbed B cell axis in AA SLE patients.
Authors
Michelle D. Catalina, Prathyusha Bachali, Anthony E. Yeo, Nicholas S. Geraci, Michelle A. Petri, Amrie C. Grammer, Peter E. Lipsky
Abstract
Systemic sclerosis (SSc) is a heterogeneous autoimmune disorder that results in skin fibrosis, autoantibody production and internal organ dysfunction. We previously identified four ‘intrinsic’ subsets of SSc based upon skin gene expression that are found across organ systems. Gene expression regulators that underlie the SSc intrinsic subsets, or are associated with clinical covariates, have not been systematically characterized. Here we present a computational framework to calculate the activity scores of gene expression regulators and identify their associations with SSc clinical outcomes. We find regulator activity scores can reproduce the intrinsic molecular subsets with distinct sets of regulators identified for inflammatory, fibroproliferative and normal-like samples. Regulators most highly correlated with modified Rodnan skin score (MRSS) also varied by intrinsic subset. We identify a subgroup of fibroproliferative/inflammatory SSc patients with more severe pathophenotypes. We further identify a subgroup of SSc patients that had higher MRSS and increased likelihood of interstitial lung disease. Using an independent cohort, we show this group was most likely to show forced vital capacity decline over a period of 36 – 54 months. Our results demonstrate an association between the activation of regulators, gene expression subsets and clinical variables that can identify SSc patients with more severe disease.
Authors
Yue Wang, Jennifer M. Franks, Monica Yang, Diana M. Toledo, Tammara A. Wood, Monique Hinchcliff, Michael L. Whitfield
Abstract
Skin lesions in dermatomyositis (DM) patients are common, frequently refractory, and have prognostic significance. Histologically, DM lesions appear like cutaneous lupus erythematosus (CLE) lesions and frequently cannot be differentiated. We thus undertook to examine the transcriptional profile of DM biopsies and compared them to CLE lesions in order to identify unique features. Type I interferon (IFN) signaling, including upregulation of IFN kappa, was a common pathway in both DM and CLE, but CLE also exhibited other inflammatory pathways. Importantly, DM lesions could be distinguished from CLE by a 5-gene biomarker panel that included an upregulation of IL18. Using single-cell RNA-sequencing, we further identified keratinocytes as the main source of increased IL-18 in DM skin. The novel molecular signature identified in this study has significant clinical implications for differentiating DM from CLE lesions, and we have highlighted the potential role for IL-18 in the pathophysiology of DM skin disease.
Authors
Lam Tsoi, Mehrnaz Gharaee-Kermani, Celine C. Berthier, Tori Nault, Grace Hile, Shannon N. Estadt, Matthew T. Patrick, Rachael Wasikowski, Allison C. Billi, Lori Lowe, Tamra J. Reed, Johann Gudjonsson, J. Michelle Kahlenberg
Abstract
M3 muscarinic acetylcholine receptor (M3R) is one of the autoantigens associated with Sjögren’s syndrome (SS) and is localized in exocrine glands where disease specific inflammation occurs. The inflammatory lesion is characterized by infiltration of CD4+ T cells, including clonally expanded Th17 cells. We undertook this study to identify circulating M3R specific Th17 cells, and to determine functional properties of those cells. Using ELISpot method, we identified M3R reactive Th17 cells in the peripheral blood of patients with primary SS (pSS). Among examined 10 pSS, 10 healthy subjects (HS), and 5 IgG4-related disease (IgG4-RD) patients, M3R reactive IL-17 secreting cells were significantly increased in five pSS patients specifically. The commonest T cell epitope, which was analyzed and confirmed by co-culture of isolated CD4+ T cells with antigen presenting cells plus M3R peptides in vitro, was peptide 83-95 of M3R. Peptide recognition was partly in HLA DR restricted manner, confirmed by blocking assay. M3R reactive Th17 cells positivity correlated with higher titers of anti-M3R antibodies, whose systemic disease activity score tended to be higher. Our studies highlight the role of tissue specific autoantigen derived circulating Th17 cells in pSS, for which further work might lead to antigen specific targeted therapy.
Authors
Saori Abe, Hiroto Tsuboi, Hanae Kudo, Hiromitsu Asashima, Yuko Ono, Fumika Honda, Hiroyuki Takahashi, Mizuki Yagishita, Shinya Hagiwara, Yuya Kondo, Isao Matsumoto, Takayuki Sumida
Abstract
Rituximab, a B cell-depleting therapy, is indicated for treating a growing number of autoantibody-mediated autoimmune disorders. However, relapses can occur after treatment and autoantibody-producing B cell subsets may be found during relapses. It is not understood if these autoantibody-producing B cell subsets emerge from the failed depletion of pre-existing B cells or are generated de novo. To further define the mechanisms that cause post-rituximab relapse, we studied patients with autoantibody-mediated muscle-specific kinase (MuSK) myasthenia gravis (MG) who relapsed after treatment. We carried out single-cell transcriptional and B cell receptor (BCR) profiling on longitudinal B cell samples. We identified clones present prior to therapy that continued to persist during relapse. Persistent B cell clones included both antibody-secreting cells and memory B cells characterized by gene expression signatures associated with B cell survival. A subset of persistent antibody-secreting cells and memory B cells were specific for the MuSK autoantigen. These results demonstrate that rituximab is not fully effective at eliminating autoantibody-producing B cells and provide a mechanistic understanding of post-rituximab relapse in MuSK MG.
Authors
Ruoyi Jiang, Miriam L. Fichtner, Kenneth B. Hoehn, Minh C. Pham, Panos Stathopoulos, Richard J. Nowak, Steven H. Kleinstein, Kevin C. O'Connor
Abstract
Regulatory T cells (Tregs) play essential roles in maintaining immunological self-tolerance and preventing autoimmunity. The adoptive transfer of antigen-specific Tregs has been expected to be a potent therapeutic method for autoimmune diseases, severe allergy, and rejection in organ transplantation. However, effective Treg therapy has not yet been established because of the difficulty in preparing a limited number of antigen-specific Tregs. Chimeric antigen receptor (CAR) T cells have been shown to be a powerful therapeutic method for treating B cell lymphomas, but application of CAR to Treg-mediated therapy has not yet been established. Here, we generated CD19-targeted CAR (CD19-CAR) Tregs from human peripheral blood mononuclear cells (hPBMCs) and optimized the fraction of the Treg source as CD4+CD25+CD127lowCD45RA+CD45RO–. CD19-CAR Tregs could be expanded in vitro while maintaining Treg properties, including a high expression of the latent form of TGF-β. CD19-CAR Tregs suppressed IgG antibody production from primary B cell differentiation in vitro via a TGF-β-dependent mechanism. Unlike conventional CD19-CAR CD8+ T cells, CD19-CAR Tregs suppressed antibody production in immunodeficient mice that were reconstituted with hPBMCs with reducing the risk of graft-versus-host disease. Therefore, the adoptive transfer of CD19-CAR Tregs may provide a novel therapeutic method for treating autoantibody-mediated autoimmune diseases.
Authors
Yuki Imura, Makoto Ando, Taisuke Kondo, Minako Ito, Akihiko Yoshimura
Abstract
Patients with systemic lupus erythematosus (SLE) present a high incidence of atherosclerosis, which contributes significantly to morbidity and mortality in this autoimmune disease. An impaired balance between regulatory (Treg) and follicular helper (Tfh) CD4+ T cells is shared by both diseases. However, whether there are common mechanisms of CD4+ T cell dysregulation between SLE and atherosclerosis remains unclear. Pre-B cell leukemia transcription factor 1 isoform d (Pbx1d) is a lupus susceptibility gene that regulates Tfh cell expansion and Treg cell homeostasis. Here, we investigated the role of T cells overexpressing Pbx1d in low-density lipoprotein receptor–deficient (Ldlr–/–) mice fed with a high-fat diet, an experimental model for atherosclerosis. Pbx1d-transgenic T cells exacerbated some phenotypes of atherosclerosis, which were associated with higher autoantibody production, increased Tfh cell frequency, and impaired Treg cell regulation, in Ldlr–/– mice as compared with control T cells. In addition, we showed that dyslipidemia and Pbx1d-transgenic expression independently impaired the differentiation and function of Treg cells in vitro, suggesting a gene/environment additive effect. Thus, our results suggest that the combination of Pbx1d expression in T cells and dyslipidemia exacerbates both atherosclerosis and autoimmunity, at least in part through a dysregulation of Treg cell homeostasis.
Authors
Wei Li, Ahmed S. Elshikha, Caleb Cornaby, Xiangyu Teng, Georges Abboud, Josephine Brown, Xueyang Zou, Leilani Zeumer-Spataro, Brian Robusto, Seung-Chul Choi, Kristianna Fredenburg, Amy Major, Laurence Morel
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