Alterations in KLRB1 gene expression and a Scandinavian multiple sclerosis association study of the KLRB1 SNP rs4763655

The shared circulating diagnostic biomarkers and molecular mechanisms of systemic lupus erythematosus and inflammatory bowel disease

Background

Systemic lupus erythematosus (SLE) is a multi-organ chronic autoimmune disease. Inflammatory bowel disease (IBD) is a common chronic inflammatory disease of the gastrointestinal tract. Previous studies have shown that SLE and IBD share common pathogenic pathways and genetic susceptibility, but the specific pathogenic mechanisms remain unclear.

Methods

The datasets of SLE and IBD were downloaded from the Gene Expression Omnibus (GEO). Differentially expressed genes (DEGs) were identified using the Limma package. Weighted gene coexpression network analysis (WGCNA) was used to determine co-expression modules related to SLE and IBD. Pathway enrichment was performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis for co-driver genes. Using the Least AbsoluteShrinkage and Selection Operator (Lasso) regressionand Support Vector Machine-Recursive Feature Elimination (SVM-RFE), common diagnostic markers for both diseases were further evaluated. Then, we utilizedthe CIBERSORT method to assess the abundance of immune cell infiltration. Finally,we used the single-cell analysis to obtain the location of common diagnostic markers.

Results

71 common driver genes were identified in the SLE and IBD cohorts based on the DEGs and module genes. KEGG and GO enrichment results showed that these genes were closely associated with positive regulation of programmed cell death and inflammatory responses. By using LASSO regression and SVM, five hub genes (KLRF1, GZMK, KLRB1, CD40LG, and IL-7R) were ultimately determined as common diagnostic markers for SLE and IBD. ROC curve analysis also showed good diagnostic performance. The outcomes of immune cell infiltration demonstrated that SLE and IBD shared almost identical immune infiltration patterns. Furthermore, the majority of the hub genes were commonly expressed in NK cells by single-cell analysis.

Conclusion

This study demonstrates that SLE and IBD share common diagnostic markers and pathogenic pathways. In addition, SLE and IBD show similar immune cellinfiltration microenvironments which provides newperspectives for future treatment.

Natalizumab Treatment of Relapsing Remitting Multiple Sclerosis Has No Long-Term Effects on the Proportion of Circulating Regulatory T Cells

INTRODUCTION

Natalizumab (NTZ), a monoclonal antibody against the integrin α4β1 (VLA-4) found on activated T cells and B cells, blocks the interaction of this integrin with adhesion molecules of central nervous system (CNS) endothelial cells and lymphocyte migration through the blood-brain barrier, effectively preventing new lesion formation and relapses in multiple sclerosis (MS). Whether NTZ treatment has additional effects on the peripheral immune system cells, and how its actions compare with other MS disease-modifying treatments, have not been extensively investigated. In particular, its effect on the proportions of circulating regulatory T cells (Treg) is unclear.

METHODS

In this study, we investigated the effect of NTZ treatment in 12 patients with relapsing MS, at 6 and 12 months after the start of treatment. We evaluated the proportions of regulatory T cells (Treg), defined by flow cytometry as CD4+ CD25++ FoxP3+ cells and CD4+ CD25++ CD127- cells at these intervals. As an exploratory study, we also investigated the NTZ effects on the proportions of bulk T and B lymphocyte populations, and of those expressing novel the markers CD195 (CCR5), CD196 (CCR6), or CD161 (KLRB1), which are involved in MS pathogenesis but have been studied less in the context of MS treatment. The effects of NTZ were compared to those obtained with 11 patients under interferon-beta-1a (IFN-β1a) treatment, and against 9 healthy volunteers.

RESULTS

We observed a transient increment in the proportion of Treg cells at 6 months, which was not sustained at 12 months. We observed a reduction in the proportion of T cells expressing CD195 (CCR5) and CD161 (KLRB1) subsets of T cells.

CONCLUSION

We conclude that NTZ does not have an effect on the proportion of Treg cells over 1 year, but it may affect the expression of molecules important for some aspects MS pathogenesis, in a manner that is not shared with IFN-β1a.

Immune cell-specific smoking-related expression characteristics are revealed by re-analysis of transcriptomes from the CEDAR cohort

Introduction

Smoking is known to affect whole-blood expression and methylation profiles. Although whole-genome methylation studies indicated that effects observed in blood may be driven by changes within leukocyte subtypes, these phenomena have not been explored using expression profiling.

Material and methods

This study reanalyzed data from the Correlated Expression and Disease Association Research (CEDAR) patient cohort recruited by Momozawa et al. (E-MTAB-6667). Data from gene expression profiling of immunomagnetically sorted CD4⁺, CD8⁺, CD14⁺, CD15⁺, and CD19⁺ cells were processed. Differential expression analyses were conducted in each immune cell type, followed by gene ontology analysis and supplementary investigations.

Results

Ninety-four differentially expressed genes were found (CD8⁺ n = 58, CD14⁺ n = 20, CD4⁺ n = 14, CD19⁺ n = 2). Two key smoking-related genes were overexpressed in specific cell types: LRRN3 (CD4⁺, CD8⁺) and MMP25 (CD8⁺, CD14⁺). In CD4⁺ cells smoking was associated with reduced expression of the NK cell receptor KLRB1, suggesting CD4⁺ subpopulation shifts and differences in interferon signaling (reduced IRF1 and IL18RAP in smokers). Key results and their integration with an immune protein-protein interaction network revealed that smoking influences integrins in CD8⁺ cells (ITGB7, ITGAL, ITGAM, ITGB2). C-type lectin CLEC4A was reduced in CD8⁺ cells and CLEC10A was increased in CD14⁺ cells from smokers; moreover, CLEC5A (CD8⁺), CLEC7A (CD8⁺) and CLEC9A (CD19⁺) were related to smoking in supplementary analyses. CD14⁺ cells from smokers exhibited overexpression of LDLR and the formyl peptide receptor FPR3.

Conclusions

Smoking specifically alters vital immune regulation genes in lymphocyte subtypes, especially CD4⁺, CD8⁺ and CD14⁺ cells.

Identifying CNS-colonizing T cells as potential therapeutic targets to prevent progression of multiple sclerosis

BACKGROUND

Multiple sclerosis (MS), an autoimmune disease of the central nervous system (CNS), can be suppressed in its early stages but eventually becomes clinically progressive and unresponsive to therapy. Here, we investigate whether the therapeutic resistance of progressive MS can be attributed to chronic immune cell accumulation behind the blood-brain barrier (BBB).

METHODS

We systematically track CNS-homing immune cells in the peripheral blood of 31 MS patients and 31 matched healthy individuals in an integrated analysis of 497,705 single-cell transcriptomes and 355,433 surface protein profiles from 71 samples. Through spatial RNA sequencing, we localize these cells in post mortem brain tissue of 6 progressive MS patients contrasted against 4 control brains (20 samples, 85,000 spot transcriptomes).

FINDINGS

We identify a specific pathogenic CD161+/lymphotoxin beta (LTB)+ T cell population that resides in brains of progressive MS patients. Intriguingly, our data suggest that the colonization of the CNS by these T cells may begin earlier in the disease course, as they can be mobilized to the blood by usage of the integrin-blocking antibody natalizumab in relapsing-remitting MS patients.

CONCLUSIONS

As a consequence, we lay the groundwork for a therapeutic strategy to deplete CNS-homing T cells before they can fuel treatment-resistant progression.

FUNDING

This study was supported by funding from the University Medical Center Hamburg-Eppendorf, the Stifterverband für die Deutsche Wissenschaft, the OAK Foundation, Medical Research Council UK, and Wellcome.

Genetic polymorphisms of C-type lectin receptors in Behcet's disease in a Chinese Han population

C-type lectin receptors (CLRs) have been demonstrated to be involved in several autoimmune diseases. The role of CLRs in Behcet’s disease (BD) is unknown and thus was the purpose of this study. A two-stage association study was carried out and a total of 766 BD patients and 1674 healthy controls were recruited. Genotyping of 14 SNPs of 13 genes in CLRs was carried out by iPLEX Gold genotyping or polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay. The expression of mannose binding lectin 2 (MBL2) and killer cell lectin like receptor C4 (KLRC4) was measured by Real-time PCR. Significantly increased frequencies of the A allele as well as AA genotype of rs1800450 in MBL2 (Pc = 2.50 × 10⁻⁶, OR = 1.494; Pc = 2.24 × 10⁻⁶,OR = 2.899; respectively) and TT genotype of rs2617170 in KLRC4 (Pc = 2.53 × 10⁻⁶, OR = 1.695) and decreased frequencies of GG genotype of rs1800450 (Pc = 1.56 × 10−3, OR = 0.689) and C allele as well as CC genotype of rs2617170 (Pc = 2.05 × 10−9,OR = 0.664; Pc = 1.20 × 10−5, OR = 0.585; respectively) were observed in BD. Two variants, p.Gly54Asp (rs1800450) and p.Asn104Ser (rs2617170) affect MBL2 and KLRC4 protein stability and expression. Our study demonstrates that the MBL2/rs1800450 and KLRC4/rs2617170 are susceptibility factors for BD in a Chinese Han population.

The Norwegian Multiple Sclerosis Registry and Biobank

Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system with unknown cause and various benefits from disease modifying therapies. Systematic recording of data into national MS registries is therefore needed to optimize treatment and define the pathogenesis of the disease. The Norwegian MS Registry and Biobank was established for systematic collection of clinical and epidemiological data, as well as biological samples. Data collection is based on informed consent from the individual patients and recordings by treating neurologists. All researchers have, by application, access to data and biological samples from the Norwegian Multiple Sclerosis Registry and Biobank. By this combined effort from both patients and healthcare personnel, the Registry and Biobank aims to facilitate research for improved understanding of disease mechanisms and improved health care in MS.

The c.503T>C Polymorphism in the Human KLRB1 Gene Alters Ligand Binding and Inhibitory Potential of CD161 Molecules

Studying genetic diversity of immunologically relevant molecules can improve our knowledge on their functional spectrum in normal immune responses and may also uncover a possible role of different variants in diseases. We characterized the c.503T>C polymorphism in the human KLRB1 gene (Killer cell lectin-like receptor, subfamily B, member 1) coding for the cell surface receptor CD161. CD161 is expressed by subsets of CD4⁺ and CD8⁺ T cells and the great majority of CD56⁺ natural killer (NK) cells, acting as inhibitory receptor in the latter population. Genotyping a cohort of 118 healthy individuals revealed 40% TT homozygotes, 46% TC heterozygotes, and 14% carriers of CC. There was no difference in the frequency of CD161 expressing CD4⁺ and CD8⁺ T cells between the different genotypes. However, the frequency of CD161⁺ NK cells was significantly decreased in CC carriers as compared to TT homozygotes. c.503T>C causes an amino acid exchange (p.Ile168Thr) in an extracellular loop of the CD161 receptor, which is regarded to be involved in binding of its ligand Lectin-like transcript 1 (LLT1). Binding studies using soluble LLT1-Fc on 293 transfectants over-expressing CD161 receptors from TT or CC carriers suggested diminished binding to the CC variant. Furthermore, triggering of CD161 either by LLT1 or anti-CD161 antibodies inhibited NK cell activation less effectively in cells from CC individuals than cells from TT carriers. These data suggest that the c.503T>C polymorphism is associated with structural alterations of the CD161 receptor. The regulation of NK cell homeostasis and activation apparently differs between carriers of the CC and TT variant of CD161.

Effect of natalizumab on circulating CD4+ T-cells in multiple sclerosis

In multiple sclerosis (MS), treatment with the monoclonal antibody natalizumab effectively reduces the formation of acute lesions in the central nervous system (CNS). Natalizumab binds the integrin very late antigen (VLA)-4, expressed on the surface of immune cells, and inhibits VLA-4 dependent transmigration of circulating immune-cells across the vascular endothelium into the CNS. Recent studies suggested that natalizumab treated MS patients have an increased T-cell pool in the blood compartment which may be selectively enriched in activated T-cells. Proposed causes are sequestration of activated T-cells due to reduced extravasation of activated and pro-inflammatory T-cells or due to induction of VLA-4 mediated co-stimulatory signals by natalizumab. In this study we examined how natalizumab treatment altered the distribution of effector and memory T-cell subsets in the blood compartment and if T-cells in general or myelin-reactive T-cells in particular showed signs of increased immune activation. Furthermore we examined the effects of natalizumab on CD4(+) T-cell responses to myelin in vitro. Natalizumab-treated MS patients had significantly increased numbers of effector-memory T-cells in the blood. In T-cells from natalizumab-treated MS patients, the expression of TNF-α mRNA was increased whereas the expression of fourteen other effector cytokines or transcription factors was unchanged. Natalizumab-treated MS patients had significantly decreased expression of the co-stimulatory molecule CD134 on CD4(+)CD26(HIGH) T-cells, in blood, and natalizumab decreased the expression of CD134 on MBP-reactive CD26(HIGH)CD4(+) T-cells in vitro. Otherwise CD4(+) T-cells from natalizumab-treated and untreated MS patients showed similar responses to MBP. In conclusion natalizumab treatment selectively increased the effector memory T-cell pool but not the activation state of T-cells in the blood compartment. Myelin-reactive T-cells were not selectively increased in natalizumab treated MS.

Regulatory NK cells in autoimmune disease

As major components of innate immunity, NK cells not only exert cell-mediated cytotoxicity against tumor cells or infected cells, but also act to regulate the function of other immune cells by secretion of cytokines and chemokines, thus providing surveillance in early defense against viruses, intracellular bacteria and cancer cells. However, the effector function of NK cells must be exquisitely controlled in order to prevent inadvertent attack against self normal cells. The activity of NK cells is defined by integration of signals coming from inhibitory and activation receptors. Inhibitory receptors not only distinguish healthy from diseased cells by recognize self-MHC class I molecules on cell surfaces with "missing-self" model, but also provide an educational signal that generates functional NK cells. NK cells enrich in immunotolerance organ and recent findings of different regulatory NK cell subsets have indicated the unique role of NK cells in maintenance of homeostasis. Once the self-tolerance is broken, autoimmune response may occur. Although data has demonstrated that NK cells play important role in autoimmune disorders, NK cells seemed to act as a two edged weapon and play opposite roles with both regulatory and inducer activity even in the same disease. The precise role and regulatory mechanisms need to be further determined. In this review, we focus on recent research on the association of NK cells and antoimmune diseases, particularly the genetic correlation, the immune tolerance and misrecognition of NK cells, the regulatory function of NK cells, and their potential role in autoimmunity.