No association between E- and L-selectin genes and SLE: soluble L-selectin levels do correlate with genotype and a subset in SLE

Combined proteomics and single cell RNA-sequencing analysis to identify biomarkers of disease diagnosis and disease exacerbation for systemic lupus erythematosus

Introduction

Systemic lupus erythematosus (SLE) is a chronic autoimmune disease for which there is no cure. Effective diagnosis and precise assessment of disease exacerbation remains a major challenge.

Methods

We performed peripheral blood mononuclear cell (PBMC) proteomics of a discovery cohort, including patients with active SLE and inactive SLE, patients with rheumatoid arthritis (RA), and healthy controls (HC). Then, we performed a machine learning pipeline to identify biomarker combinations. The biomarker combinations were further validated using enzyme-linked immunosorbent assays (ELISAs) in another cohort. Single-cell RNA sequencing (scRNA-seq) data from active SLE, inactive SLE, and HC PBMC samples further elucidated the potential immune cellular sources of each of these PBMC biomarkers.

Results

Screening of the PBMC proteome identified 1023, 168, and 124 proteins that were significantly different between SLE vs. HC, SLE vs. RA, and active SLE vs. inactive SLE, respectively. The machine learning pipeline identified two biomarker combinations that accurately distinguished patients with SLE from controls and discriminated between active and inactive SLE. The validated results of ELISAs for two biomarker combinations were in line with the discovery cohort results. Among them, the six-protein combination (IFIT3, MX1, TOMM40, STAT1, STAT2, and OAS3) exhibited good performance for SLE disease diagnosis, with AUC of 0.723 and 0.815 for distinguishing SLE from HC and RA, respectively. Nine-protein combination (PHACTR2, GOT2, L-selectin, CMC4, MAP2K1, CMPK2, ECPAS, SRA1, and STAT2) showed a robust performance in assessing disease exacerbation (AUC=0.990). Further, the potential immune cellular sources of nine PBMC biomarkers, which had the consistent changes with the proteomics data, were elucidated by PBMC scRNAseq.

Discussion

Unbiased proteomic quantification and experimental validation of PBMC samples from two cohorts of patients with SLE were identified as biomarker combinations for diagnosis and activity monitoring. Furthermore, the immune cell subtype origin of the biomarkers in the transcript expression level was determined using PBMC scRNAseq. These findings present valuable PBMC biomarkers associated with SLE and may reveal potential therapeutic targets.

Silica Induction of Diverse Inflammatory Proteome in Lungs of Lupus-Prone Mice Quelled by Dietary Docosahexaenoic Acid Supplementation

Repeated short-term intranasal instillation of lupus-prone mice with crystalline silica (cSiO2) induces inflammatory gene expression and ectopic lymphoid neogenesis in the lung, leading to early onset of systemic autoimmunity and rapid progression to glomerulonephritis. These responses are suppressed by dietary supplementation with the ω-3 polyunsaturated fatty acid docosahexaenoic acid (DHA). Here, we tested the hypothesis that dietary DHA supplementation suppresses cSiO2-induced inflammatory proteins in bronchoalveolar alveolar lavage fluid (BALF) and plasma of lupus-prone mice. Archived tissue fluid samples were used from a prior investigation in which 6 wk-old lupus-prone female NZBWF1 mice were fed isocaloric diets containing 0 or 10 g/kg DHA for 2 wks and then intranasally instilled with 1 mg cSiO2 or vehicle once weekly for 4 wks. Cohorts were terminated at 1, 5, 9 or 13 wk post-instillation (PI). BALF and plasma from each cohort were analyzed by high density multiplex array profiling of 200 inflammatory proteins. cSiO2 time-dependently induced increases in the BALF protein signatures that were highly reflective of unresolved lung inflammation, although responses in the plasma were much less robust. Induced proteins in BALF included chemokines (e.g., MIP-2, MCP-5), enzymes (e.g., MMP-10, granzyme B), adhesion molecules (e.g., sE-selectin, sVCAM-1), co-stimulatory molecules (e.g., sCD40L, sCD48), TNF superfamily proteins (e.g., sTNFRI, sBAFF-R), growth factors (e.g., IGF-1, IGFBP-3), and signal transduction proteins (e.g., MFG-E8, FcgRIIB), many of which were blocked or delayed by DHA supplementation. The BALF inflammatory proteome correlated positively with prior measurements of gene expression, pulmonary ectopic lymphoid tissue neogenesis, and induction of autoantibodies in the lungs of the control and treatment groups. Ingenuity Pathway Analysis (IPA) revealed that IL-1β, TNF-α, and IL-6 were among the top upstream regulators of the cSiO2-induced protein response. Furthermore, DHA's effects were associated with downregulation of cSiO2-induced pathways involving i) inhibition of ARE-mediated mRNA decay, ii) bacterial and viral pattern recognition receptor activation, or iii) TREM1, STAT3, NF-κB, and VEGF signaling and with upregulation of PPAR, LXR/RXR and PPARα/RXRα signaling. Altogether, these preclinical findings further support the contention that dietary DHA supplementation could be applicable as an intervention against inflammation-driven autoimmune triggering by cSiO2 or potentially other environmental agents.

Effect of Interleukin-15 on CD11b, CD54, and CD62L Expression on Natural Killer Cell and Natural Killer T-Like Cells in Systemic Lupus Erythematosus

Adhesion molecules may play an important role in systemic lupus erythematosus (SLE) pathogenesis. We investigated the effect of interleukin- (IL-) 15 on CD11b, CD54, and CD62L expression on natural killer (NK) cells, T cells, and CD56⁺CD3⁺ NKT-like cells from SLE subjects and healthy controls. SLE patients had decreased circulating NK cells and NKT-like cells compared to controls. NK cells from SLE patients showed higher CD11b and CD62L expression compared to controls. IL-15 enhanced CD11b and CD54 but downregulated CD62L expression on NK cells from SLE patients. Similar observations were found for T cells and NKT-like cells. NK cells from SLE patients expressed higher CD56 than controls; both could be further enhanced by IL-15. IL-15 also enhanced CD56 expression of NKT-like cells from SLE patients. A greater degree of IL-15 induced downregulation of CD62L on NKT-like cells noted in SLE patients compared to controls. The percentage of CD11b expressing NK cells and the % inhibition of CD62L expression on NKT-like cells by IL-15 correlated with serum anti-dsDNA levels in SLE patients, respectively. Taken together, we demonstrated the dysfunctional NK and NKT-like cells in SLE patients with regard to CD11b and CD62L expression and their response to IL-15.

A novel splice variant of human L-selectin encodes a soluble molecule that is elevated in serum of patients with rheumatic diseases

L-selectin, a type I membrane protein, is a leukocyte adhesion molecule that mediates both lymphocyte homing to peripheral lymph nodes and leukocyte accumulation at sites of inflammation. L-selectin is rapidly shed from the cell surface after cellular activation, and the ectodomain thus released is thought to account for high levels of soluble L-selectin in serum. In this study, we report the identification of a novel, naturally occurring isoform of the human L-selectin gene. Sequence analysis revealed that this isoform is generated by an alternative splicing event: the 7th exon of the human L-selectin gene, which encodes the region containing the transmembrane domain, is excluded, predicting a soluble protein product. The mRNA for this splice variant was expressed in lymphoid organs, where conventional L-selectin mRNA was also expressed. Activating T cells increased the variant mRNA and its ratio to the membrane form. Soluble L-selectin translated from the variant mRNA was present in human serum, albeit at a much lower level than that arising from ectodomain shedding, and was markedly elevated in patients with various rheumatic diseases, including rheumatoid arthritis and systemic lupus erythematosus. These observations indicate that some of the soluble L-selectin present in human serum arises through alternative splicing, which may be upregulated during lymphocyte activation in patients with various clinical conditions.

Polymorphisms of inflammatory markers and risk of essential hypertension in Tatars from Russia

Essential hypertension (EH) is a common disease with a clear genetic component. Inflammation and endothelial dysfunction play a prominent role in the development of persistent blood pressure elevation. The aim of the current study was to detect an association between EH and polymorphic markers in genes encoding for molecules involved in the control of intercellular interactions during the inflammation process. We analysed SNPs in SELE, SELP, SELL, ICAM1, VEGFA, IL1B, IL6, IL10 and IL12B genes in a group of 534 men of Tatar ethnicity (217 patients with EH and 317 controls). Using a Markov chain Monte-Carlo-based approach (APSampler), we found genotype and allelic combinations associated with EH. The most significant associations were observed for SELE rs2076059*C-SELP rs6131*A-VEGFA -2549*I-IL1B rs16944*C (p = 3.42 × 10(-5), FDR q = 0.035) and SELE rs2076059*C-SELP rs6131*A-IL12B rs3212227*C-IL1B rs16944*C (p = 323 × 10(-4), FDR q = 0.035).

Multi-ethnic analysis reveals soluble L-selectin may be post-transcriptionally regulated by 3'UTR polymorphism: the Multi-Ethnic Study of Atherosclerosis (MESA)

L-Selectin is constitutively expressed on leukocytes and mediates their interaction with endothelial cells during inflammation. Previous studies on the association of soluble L-selectin (sL-selectin) with cardiovascular disease (CVD) are inconsistent. Genetic variants associated with sL-selectin levels may be a better surrogate of levels over a lifetime. We explored the association of genetic variants and sL-selectin levels in a race/ethnicity stratified random sample of 2,403 participants in the Multi-Ethnic Study of Atherosclerosis (MESA). Through a genome-wide analysis with additive linear regression models, we found that rs12938 on the SELL gene accounted for a significant portion of the protein level variance across all four races/ethnicities. To evaluate potential additional associations, elastic net models were used for variants located in the SELL/SELP/SELE genetic region and an additional two SNPs, rs3917768 and rs4987361, were associated with sL-selectin levels in African Americans. These variants accounted for a portion of protein variance that ranged from 4 % in Hispanic to 14 % in African Americans. To investigate the relationship of these variants with CVD, 6,317 subjects were used. No significant association was found between any of the identified SNPs and carotid intima-media thickness or presence of carotid plaque using linear and logistic regression, respectively. Similarly no significant results were found for coronary artery calcium or coronary heart disease events. In conclusion, we found that variants within the SELL gene are associated with sL-selectin levels. Despite accounting for a significant portion of the protein level variance, none of the variants was associated with clinical or subclinical CVD.

Assessment of the E-selectin rs5361 (561A>C) polymorphism and soluble protein concentration in acute coronary syndrome: association with circulating levels

Introduction. The acute coronary syndrome (ACS) is a complex disease where genetic and environmental factors are involved. E-selectin gene is a candidate for ACS progression due to its contribution in the inflammatory process and endothelial function. The rs5361 (561A>C) polymorphism in the E-selectin gene has been linked to changes in gene expression, affinity for its receptor, and plasmatic levels; therefore it is associated with an increased risk of cardiovascular disease. The aim of this study was to determine the association of the rs5361 polymorphism with ACS and to measure serum levels of soluble E-selectin (sE-selectin). Materials and Methods. 283 ACS patients and 205 healthy subjects (HS) from Western Mexico were included. The polymerase chain reaction-restriction fragment length polymorphism was used to determine the rs5361 polymorphism. The sE-selectin levels were measured by enzyme-linked immunosorbent assay. Results. Neither genotype nor allele frequencies of the rs5361 polymorphism showed statistical differences between groups. The sE-selectin levels were significantly higher in ACS patients compared to HS (54.58 versus 40.41 ng/ml, P = 0.02). The C allele had no effect on sE-selectin levels. Conclusions. The rs5361 E-selectin gene polymorphism is not a susceptibility marker for ACS in Western Mexico population. However, sE-selectin may be a biological marker of ACS.

Soluble L-Selectin as an Independent Biomarker of Bronchial Asthma

BACKGROUND

We sought to determine the association of plasma level of soluble L-selectin (sL-selectin) and F206L polymorphism of L-selectin with asthma.

METHODS

A total of 90 asthmatic patients and 90 sex- and age-matched healthy controls were enrolled. The plasma level of sL-selectin was measured by enzyme-linked immunosorbent assay (ELISA) method. An amplification refractory mutation system polymerase chain reaction was performed to detect F206L polymorphism of L-selectin.

RESULTS

The mean plasma levels of sL-selectin was significantly higher in the patients with asthma than the controls (2113 ± 466 vs. 1664 ± 322 ng/ml, P = 0.001). Logistic regression analysis after adjustment for age, sex, and body mass index demonstrated that plasma levels of sL-selectin are an independent biomarkers for asthma (odds ratio [OR], 1.86; 95% confidence interval [95% CI], 1.42-2.24). The area under the receiver operating characteristic (ROC) curve for sL-selectin was 0.792, 95% CI (0.732-0.862), P = 0.0001. Individuals with the minor homozygote of F206L polymorphism of L-selectin demonstrated a higher level of sL-selectin than the major homozygous (2319 ± 732 vs. 1917 ± 453 ng/ml, P = 0.02). No association was found between F206L polymorphism of L-selectin with asthma.

CONCLUSION

Our study suggests that plasma level of sL-selectin is an independent biomarker for asthma.

Association of cell adhesion molecule gene polymorphisms with recurrent aphthous stomatitis

BACKGROUND

Recurrent aphthous stomatitis (RAS) is a common oral ulcerative condition. At ulcer sites vascular adhesion molecule-1 (VCAM-1), E-selectin and intercellular adhesion molecule-1 (ICAM-1) are strongly expressed on blood vessels, and ICAM-1 is expressed on keratinocytes. Expression of these molecules would promote leukocyte accumulation and invasion of the epithelium. Thus, polymorphisms in these candidate genes might contribute to RAS susceptibility. We investigated whether the inheritance of specific selectin, ICAM and VCAM gene polymorphisms is associated with RAS susceptibility.

METHODS

Ninety-six RAS cases and 153 controls were recruited from a Jordanian population. Blood was collected for hematological investigations and genotyping. Six SNPs were genotyped: E-selectin rs5361 and rs1805193, L-selectin, rs2205849, ICAM-1 rs5498, ICAM-5 rs885743 and VCAM-1 rs1800821. Association was determined using chi-square and binary logistic regression analysis after correcting for confounding factors. Linkage disequilibrium was determined using the EH program, and the Phase 2.1 program was used to construct and compare haplotypes between cases and controls.

RESULTS

There was a significant association of the A allele (Pcorr  = 0.027), AA and AC genotypes (OR = 10.9 and 9.0, respectively) of the E-selectin rs5361 gene polymorphism and TAA haplotype (rs2205849, rs5361, and rs1805193, respectively; P = 0.03) with RAS. None of the other SNPs showed a significant association.

CONCLUSIONS

This is the first report to link inheritance of the A allele, AA and AC genotypes of the E-selectin rs5361 polymorphism with increased risk of RAS. Further studies in different patient cohorts are needed to confirm the association, and functional analyses might clarify the biological significance of the association.

Variation in the upstream region of P-Selectin (SELP) is a risk factor for SLE

Systemic lupus erythematosus (SLE) is a complex autoimmune disease. Genome-wide linkage studies implicated a region containing the adhesion molecule P-Selectin. This family-based study revealed two regions of association within P-Selectin. The strongest signal, from a 21.4-kb risk haplotype, stretched from the promoter into the first two consensus repeat (CR) regions (P=8 × 10⁻⁴), with a second association from a 14.6-kb protective haplotype covering CR 2–9 (P=0.0198). The risk haplotype is tagged by the rare C allele of rs3753306, which disrupts the binding site of the trans-activating transcription factor HNF-1. One other variant (rs3917687) on the risk haplotype was significant after permutation (P₁₀₀₀₀<1 × 10⁻⁵), replicated in independent pseudo case-control analysis and was significant by meta-analysis (P=4.37 × 10⁻⁶). A third associated variant on the risk haplotype (rs3917657) replicated in 306 US SLE families and was significant in a joint UK-SLE data set after permutation. The protective haplotype is tagged by rs6133 (a non-synonymous variant in CR8 (P=9.00 × 10⁻⁴), which also shows association in the pseudo case-control analysis (P=1.09 × 10⁻³) and may contribute to another signal in P-Selectin. We propose that polymorphism in the upstream region may reduce expression of P-Selectin, the mechanism by which this promotes autoimmunity is unknown, although it may reduce the production of regulatory T cells.

Carbohydrate recognition systems in autoimmunity

The immune system is a complex functional network of diverse cells and soluble molecules orchestrating innate and adaptive immunity. Biological information, to run these intricate interactions, is not only stored in protein sequences but also in the structure of the glycan part of the glycoconjugates. The spatially accessible carbohydrate structures that contribute to the cell's glycome are decoded by versatile recognition systems in order to maintain the immune homeostasis of an organism. Microbial carbohydrate structures are recognized by pathogen associated molecular pattern (PAMP) receptors of innate immunity including C-type lectins such as MBL, the tandem-repeat-type macrophage mannose receptor, DC-SIGN or dectin-1 of dendritic cells, certain TLRS or the TCR of NKT cells. Natural autoantibodies, a long known effector branch of this network-based operation, are effective to home in on non-self and self-glycosylation also. The recirculating pool of mammalian immune cells is recruited to inflammatory sites by a reaction pathway involving the self-carbohydrate-binding selectins as initial recognition step. Galectins, further key sensors reading the high-density sugar code, exert regulatory functions on activated T cells, among other activities. Autoimmune diseases are being associated with defined changes of glycosylation. This correlation deserves to be thoroughly studied on the levels of structural mimicry and dysregulation as well as effector molecules to devise innovative anti-inflammatory strategies. This review briefly summarizes data on sensor systems for carbohydrate epitopes and implications for autoimmunity.

Systemic lupus erythematosus: multiple immunological phenotypes in a complex genetic disease

Systemic lupus erythematosus (SLE) is a complex polygenic autoimmune disease characterized by the presence of anti-nuclear autoantibodies (ANAs) that are often detectable years prior to the onset of clinical disease. The disease is associated with a chronic activation of the immune system, with the most severe forms progressing to inflammatory damage that can impact multiple organ systems in afflicted individuals. Current therapeutic strategies poorly control disease manifestations and are generally immunosuppressive. Recent studies in human patient populations and animal models have associated elements of the innate immune system and abnormalities in the immature B lymphocyte receptor repertoires with disease initiation. A variety of cytokines, most notably type I interferons, play important roles in disease pathogenesis and effector mechanisms. The genetic basis for disease susceptibility is complex, and analyses in humans and mice have identified multiple susceptibility loci, several of which are located in genomic regions that are syntenic between humans and mice. The complexities of the genetic interactions that mediate lupus have been investigated in murine model systems by characterizing the progressive development of disease in strains expressing various combinations of susceptibility alleles. These analyses indicate that genetic epistasis dramatically impact disease development and support the feasibility of identifying molecular pathways that can suppress disease progression without completely impairing normal immune function.