FASGene Copy Numbers are Associated with Susceptibility to Behçet Disease and VKH Syndrome in Han Chinese

Comprehensive profiling of extracellular vesicles in uveitis and scleritis enables biomarker discovery and mechanism exploration

BACKGROUND

Uveitis and posterior scleritis are sight-threatening diseases with undefined pathogenesis and accurate diagnosis remains challenging.

METHODS

Two plasma-derived extracellular vesicle (EV) subpopulations, small and large EVs, obtained from patients with ankylosing spondylitis-related uveitis, Behcet's disease uveitis, Vogt-Koyanagi-Harada syndrome, and posterior scleritis were subjected to proteomics analysis alongside plasma using SWATH-MS. A comprehensive bioinformatics analysis was performed on the proteomic profiles of sEVs, lEVs, and plasma. Candidate biomarkers were validated in a new cohort using ELISA. Pearson correlation analysis was performed to analyze the relationship between clinical parameters and proteomic data. Connectivity map database was used to predict therapeutic agents.

RESULTS

In total, 3,668 proteins were identified and over 3000 proteins were quantified from 278 samples. When comparing diseased group to healthy control, the proteomic profiles of the two EV subgroups were more correlated with disease than plasma. Comprehensive bioinformatics analysis highlighted potential pathogenic mechanisms for these diseases. Potential biomarker panels for four diseases were identified and validated. We found a negative correlation between plasma endothelin-converting enzyme 1 level and mean retinal thickness. Potential therapeutic drugs were proposed, and their targets were identified.

CONCLUSIONS

This study provides a proteomic landscape of plasma and EVs involved in ankylosing spondylitis-related uveitis, Behcet's disease uveitis, Vogt-Koyanagi-Harada syndrome, and posterior scleritis, offers insights into disease pathogenesis, identifies valuable biomarker candidates, and proposes promising therapeutic agents.

Genetics in Behcet's Disease: An Update Review

Behcet's disease (BD) is one of the most vision-threatening clinical entities of uveitis. Although the etiopathogenesis of BD remains obscure, accumulating evidence has demonstrated that both genetic and environmental factors may contribute to the development of BD. Genome-wide association studies (GWAS) and candidate association studies have identified several genetic variants strongly associated with BD, including variants in human leukocyte antigen (HLA) -A02, -A03, -A24, -A26, -A31, -B15, -B27, -B35, -B49, -B51, -B57, -B58, -C0704, CIITA, ERAP1, MICA, IL1A-IL1B, IL10, IL12, IL23R, IL-23R/IL-12RB2, IL1RL1-IL18R1, STAT4, TFCP2L1, TRAF5, TNFAIP3, CCR1/CCR3, RIPK2, ADO-ZNF365-EGR2, KLRC4, LACC1, MEFV, IRF8, FUT2, CEBPB-PTPN1, ZMIZ1, RPS6KA4, IL10RA, SIPA1-FIBP-FOSL1, VAMP1, JRKL/CTCN5, IFNGR1 and miRNA-146a. Epigenetic modifications are also reported to play essential roles in the development of BD, including DNA methylation and histone modification. We review here the recent advances in the genetic and epigenetic factors associated with the BD pathogenesis.

An Update Evolving View of Copy Number Variations in Autoimmune Diseases

Autoimmune diseases (AIDs) usually share possible common mechanisms, i.e., a defect in the immune tolerance exists due to diverse causes from central and peripheral tolerance mechanisms. Some genetic variations including copy number variations (CNVs) are known to link to several AIDs and are of importance in the susceptibility to AIDs and the potential therapeutic responses to medicines. As an important source of genetic variants, DNA CNVs have been shown to be very common in AIDs, implying these AIDs may possess possible common mechanisms. In addition, some CNVs are differently distributed in various diseases in different ethnic populations, suggesting that AIDs may have their own different phenotypes and different genetic and/or environmental backgrounds among diverse populations. Due to the continuous advancement in genotyping technology, such as high-throughput whole-genome sequencing method, more susceptible variants have been found. Moreover, further replication studies should be conducted to confirm the results of studies with different ethnic cohorts and independent populations. In this review, we aim to summarize the most relevant data that emerged in the past few decades on the relationship of CNVs and AIDs and gain some new insights into the issue.

Polymorphisms rs763110 in FASL is linked to hepatitis C virus infection among high-risk populations

BACKGROUND

The Fas cell surface death receptor (FAS) and Fas ligand (FASL) can participate in the apoptosis of immune cells and target cells infected with a virus through the FAS-FASL signalling pathway. The decoy receptor 3 (DCR3) can competitively inhibit the binding of FAS to FASL. Our aim is to investigate the effect of single nucleotide polymorphisms (SNPs) in FAS, FASL and DCR3 on hepatitis C virus (HCV) infection.

METHODS

Four SNPs (rs763110 in FASL, rs1324551 and rs2234767 in FAS and rs2257440 in DCR3) were genotyped in 1495 controls free of HCV, 522 individuals with spontaneous HCV clearance and 732 patients with hepatitis C virus infection. The RegulomeDB database and RNAfold web servers were used to explore potential biological functions of SNPs.

RESULTS

FASL rs763110 was associated with susceptibility to HCV infection, and not to CHC. The odds ratio (95% confidence interval) of HCV infection in high-risk populations carrying FASL rs763110-TT was 1.82 (1.36-2.51, P < 0.001) compared to that of CC genotypes and 1.93 (1.43-2.60, P < 0.001) higher than that of CC + CT genotypes. Based on computer simulation, FASL rs763110-T may affect the transcription of mRNA by affecting the binding of a transcription factor, leading to structural changes in mRNA.

CONCLUSION

The genetic variant in FASL is linked with HCV infection, but not to spontaneous HCV clearance.

Epigenome-wide association study identifies Behçet's disease-associated methylation loci in Han Chinese

OBJECTIVE

The aetiology of Behçet's disease (BD), known as a systemic vasculitis, is not completely understood. Increasing evidence suggests that aberrant DNA methylation may contribute to the pathogenesis of BD. The aim of this epigenome-wide association study was to identify BD-associated methylation loci in Han Chinese.

METHODS

Genome-wide DNA methylation profiles were compared between 60 BD patients and 60 healthy controls using the Infinium Human Methylation 450 K Beadchip. BD-associated methylation loci were validated in 100 BD patients and 100 healthy controls by pyrosequencing. Gene expression and cytokine production was quantified by real-time PCR and ELISA.

RESULTS

A total of 4332 differentially methylated CpG sites were associated with BD. Five differentially methylated CpG sites (cg03546163, cg25114611, cg20228731, cg23261343 and cg14290576) revealed a significant hypomethylation status across four different genes (FKBP5, FLJ43663, RUNX2 and NFIL3) and were validated by pyrosequencing. Validation results showed that the most significant locus was located in the 5'UTR of FKBP5 (cg03546163, P = 3.81E-13). Four CpG sites with an aberrant methylation status, including cg03546163, cg25114611, cg23261343 and cg14290576, may serve as a diagnostic marker for BD (area under the receiver operating curve curve = 83.95%, 95% CI 78.20, 89.70%). A significantly inverse correlation was found between the degree of methylation at cg03546163 as well as cg25114611 and FKBP5 mRNA expression. Treatment with a demethylation agent, 5-Aza-2'-deoxycytidine resulted in an increase of FKBP5 mRNA expression and a stimulated IL-1β production.

CONCLUSION

Our findings suggest that aberrant DNA methylation, independently of previously known genetic variants, plays a vital role in the pathogenesis of BD.

TRIAL REGISTRATION

Chinese Clinical Trial Registry, chictr.org.cn, ChiCTR-CCC-12002184.

Associations between TNFSF4, TNFSF8 and TNFSF15 and Behçet's disease but not VKH syndrome in Han Chinese

The present study was designed to explore the interrelationship between single nucleotide polymorphisms (SNP) of the tumor necrosis factor superfamily (TNFSF) and its respective receptor superfamily (TNFRSF) genes and Behcet's disease (BD) and Vogt-Koyanagi-Harada syndrome (VKH) in Han Chinese. The study sample included 796 patients with BD, 792 patients with VKH syndrome, and 1604 healthy controls. The genotyping of 35 SNPs was performed by MassARRAY platform (Sequenom), iPLEX Gold Assay, PCR-restriction fragment length polymorphism assay and TaqMan SNP assay. The mRNA expression levels of TNFSF4, TNFSF8 and TNFSF15 were analyzed by real-time PCR. The IL-6 and TNF-α expression levels were measured by ELISA. The A allele and AA genotype frequencies of TNFSF4/rs1234313 were significantly increased, and the GG genotype frequency of rs1234313 was decreased in subjects with BD. Significantly lower frequencies of the C allele and the CC genotype and higher frequencies of the TT and CT genotypes of TNFSF15/rs4246905 were observed in BD patients. A decreased frequency of the A allele of TNFSF8/rs7028891 was observed in BD patients. The expression of TNFSF15 in CT carriers was significantly higher than that in CC/TT individuals. Increased IL-6 expression and TNF-α production were found in the TNFSF15 CT carriers compared with the CC/TT genotype carriers. No significant differences were observed between the VKH patients and controls. This study indicates that TNFSF4, TNFSF15 and TNFSF8 may participate in the susceptibility to BD among Han Chinese.

Genetic analysis of innate immunity in Behcet's disease identifies an association with IL-37 and IL-18RAP

Interleukin-1 (IL-1) and the IL-1 receptor (IL-1R) family play an important role in the pathogenesis of inflammatory diseases. This study aimed to investigate the association between single nucleotide polymorphisms (SNP) of IL-1 and IL-1R family genes with Vogt-Koyanagi-Harada (VKH) and Behcet’s disease (BD) in Han Chinese. The case-control study was divided into two stages and included 419 VKH cases, 1063 BD cases and 1872 healthy controls. The MassARRAY platform (Sequenom), iPLEX Gold Assay and TaqMan SNP assays were used to score genotypes of 24 SNPs. The expression of IL-37 and IL-18Rap was measured by ELISA and real-time PCR in genotyped healthy individuals. A significantly lower frequency of the AG genotype, and a higher frequency of the GG genotype and G allele of IL-37/rs3811047 were observed in BD as compared to controls. AA genotype and A allele frequency of IL-18RAP/rs2058660 was significantly decreased in BD as compared to controls. Functional studies performed in healthy controls showed that rs3811047 AG genotype carriers had a higher IL-37 gene expression in peripheral blood mononuclear cells (PBMCs) than GG carriers. GG carriers showed a higher cytokine expression as compared to AG carriers. No association was detected between the tested SNPs and VKH.

The potential of genetically guided treatment in Behçet's disease

Continuous identification of specific targets and candidate genes together with novel approaches offers new promises for the future of gene therapy design in Behçet's disease (BD). Personalized medicine based on pharmacogenomics is being developed at the clinical stage to improve treatment response. Screening the whole gene and regulatory regions is important when searching for novel variants associated with such complex diseases. Different host genetic factors play significant roles in susceptibility to BD. Thus, identifying these genes responsible for susceptibility and resistance to BD may offer a notable contribution toward understanding its pathogenesis, and may lead to the development of novel prophylactic and treatment strategies. Evidenced-based treatment strategy is recommended for the management in BD patients. This review sheds light on the immunopathogenesis and pharmacogenetics of BD with special attention to the treatment targeting gene polymorphisms. In conclusion, the potential of genetically guided treatment in BD takes us back to the future for an accurate management strategy of this serious rheumatic disease. The ongoing discovery of pivotal genes related to the susceptibility, manifestations, disease activity and treatment options provide substantial hope to the reduced frequency of BD, effective control and improvement in the prognosis. Targeted gene therapy could be a leading option in the treatment armamentarium of BD.

Identification of susceptibility SNPs in IL10 and IL23R-IL12RB2 for Behçet's disease in Han Chinese

BACKGROUND

Although previous genome-wide association studies in various cohorts have identified several susceptibility loci underlying Behçet's disease (BD), this has not yet led to a breakthrough in the management of BD.

OBJECTIVE

This study aimed to further investigate the association of 26 candidate single nucleotide polymorphisms with previous genome-wide association studies-identified nearly positive P values (5.0 × 10^-8 < P < 1.0 × 10^-5) in Chinese Han patients with BD.

METHODS

A case-control association study was performed in 1206 patients with BD and 2475 healthy controls. Genotyping was performed using iPLEX Gold genotyping assay. Gene expression and cytokine production was quantified by real-time PCR and ELISA.

RESULTS

The results showed that significantly higher frequencies of the IL23R-IL12RB2/rs924080 TT genotype (P = 2.03 × 10^-8; odds ratio [OR] = 1.50), IL23R-IL12RB2/rs12141431 CC genotype (P = 2.18 × 10^-8; OR = 1.53), IL10/rs1800871 TT genotype (P = 5.88 × 10^-8; OR = 1.47), and IL10/rs3024490 TT genotype (P = 2.80 × 10^-5; OR = 1.34) were found in BD. Functional experiments showed an increased IL23R expression and IL-17 production in rs12141431/CC genotype carriers compared with GG genotype carriers. A decreased IL10 expression and IL-10 production was observed in rs3024490/TT genotype carriers as compared with GG genotype carriers.

CONCLUSIONS

Our findings not only confirmed the association of IL10/rs1800871 and IL23R-IL12RB2/rs924080 with BD but also identified 2 susceptibility single nucleotide polymorphisms in IL10 and IL23R-IL12RB2 (rs3024490 and rs12141431) with BD in Han Chinese.

Analysis of receptor tyrosine kinase genetics identifies two novel risk loci in GAS6 and PROS1 in Behçet's disease

The TAM kinase (Tyro3, Axl, Mer) and its two ligands (Gas6 and protein S) have been shown to play an important regulatory role in the innate immune response. The present study aimed to investigate whether the tag single-nucleotide polymorphisms (tag SNPs) of these 5 protein-coding genes are associated with Behçet’s disease (BD). A two-stage association study was performed in a total of 907 BD patients and 1780 healthy controls. Altogether 32 polymorphisms were tested, using a Sequenom MassARRAY genotyping method in the first stage and a PCR-restriction fragment length polymorphism (PCR-RFLP) assay in the replication phase. Real-time PCR was performed to test the relative mRNA expression level of GAS6 and PROS1 from different SNP genotyped healthy individuals. The frequency of the C allele and CC genotype of rs9577873 in GAS6 (P_c = 4.92 × 10⁻⁵, P_c = 1.91 × 10⁻⁵, respectively) and A allele and AA genotype of rs4857037 in PROS1 (P_c = 1.85 × 10⁻⁶, P_c = 4.52 × 10⁻⁷, respectively) were significantly increased in BD. GAS6 expression in CC carriers of rs9577873 was significantly lower than that in CT/TT individuals (P = 0.001). Decreased expression of GAS6 and increased pro-inflammatory cytokines (IL-6 and IFN-γ: P = 4.23 × 10⁻⁴, P = 0.011, respectively) in individuals carrying the CC genotype suggest that the TAM-GAS6/PROS1 signal pathway may be involved in the pathogenesis of BD.

Methylation Status of Alu and LINE-1 Interspersed Repetitive Sequences in Behcet's Disease Patients

Behcet's Disease (BD) is a multisystem chronic inflammatory disease. The pathology is believed to involve both genetic susceptibility and environmental factors. Hypomethylation leading to activation of interspersed repetitive sequences (IRSs) such as LINE-1 and Alu contributes to the pathologies of autoimmune diseases and cancer. Herein, the epigenetic changes of IRSs in BD were evaluated using combined bisulfite restriction analysis-interspersed repetitive sequences (COBRA-IRS). DNA from neutrophils and peripheral blood mononuclear cells (PBMCs) of BD patients with ocular involvement that were in active or inactive states and healthy controls were used to analyze LINE-1 and Alu methylation levels. For Alu sequences, significant differences were observed in the frequency of ^uC^uC alleles between PBMCs of patients and controls (p = 0.03), and between inactive patients and controls (p = 0.03). For neutrophils, the frequency of ^uC^uC was significantly higher between patients and controls (p = 0.006) and between inactive patients and controls (p = 0.002). The partial methylation (^uC^mC + ^mC^uC) frequencies of Alu between inactive patients and control samples also differed (p = 0.02). No statistically significant differences for LINE-1 were detected. Thus, changes in the methylation level of IRS elements might contribute to the pathogenesis of BD. The role of Alu transcripts in BD should be investigated further.

Vogt-Koyanagi-Harada disease: Novel insights into pathophysiology, diagnosis and treatment

Vogt-Koyanagi-Harada (VKH) disease is one of the major vision-threatening diseases in certain populations, such as Asians, native Americans, Hispanics and Middle Easterners. It is characterized by bilateral uveitis that is frequently associated with neurological (meningeal), auditory, and integumentary manifestations. Although the etiology and pathogenesis of VKH disease need to be further elucidated, it is widely accepted that the clinical manifestations are caused by an autoimmune response directed against melanin associated antigens in the target organs, i.e. the eye, inner ear, meninges and skin. In the past decades, accumulating evidence has shown that genetic factors, including VKH disease specific risk factors (HLA-DR4) and general risk factors for immune mediated diseases (IL-23R), dysfunction of immune responses, including the innate and adaptive immune system and environmental triggering factors are all involved in the development of VKH disease. Clinically, the criteria of diagnosis for VKH disease have been further improved by the employment of novel imaging techniques for the eye. For the treatment, early and adequate corticosteroids are still the mainstream regime for the disease. However, immunosuppressive and biological agents have shown benefit for the treatment of VKH disease, especially for those patients not responding to corticosteroids. This review is focused on our current knowledge of VKH disease, especially for the diagnosis, pathogenesis (genetic factors and immune mechanisms), ancillary tests and treatment. A better understanding of the role of microbiome composition, genetic basis and ongoing immune processes along with the development of novel biomarkers and objective quantitative assays to monitor intraocular inflammation are needed to improve current management of VKH patients.

Genetic Variations of NLR family genes in Behcet's Disease

This study aimed to investigate whether single nucleotide polymorphisms (SNPs) of five NLR family genes (NOD1, NOD2, NLRP1, NLRP3 and CIITA) are associated with Behcet’s disease (BD) in a Chinese Han population. The study was carried out in 950 BD patients and 1440 controls for 19 SNPs in the selected NLR genes. In the first-stage study, significantly decreased frequencies of the CIITA//rs12932187 C allele (Pc = 1.668E-02) and NOD1//rs2075818 G allele (Pc = 4.694E-02) were found in BD patients as compared to controls . After performing a second stage validation study and combination of data we confirmed the association of CIITA//rs12932187 and NOD1//rs2075818 with BD. In CIITA//rs12932187, the frequencies of the CC genotype and C allele were significantly lower in BD than in controls (Pc = 3.331E-06; Pc = 6.004E-07, respectively). In NOD1//rs2075818, the GG genotype and G allele showed significantly decreased frequencies in BD patients when compared to controls (Pc = 1.022E-02; Pc = 6.811E-05, respectively). Functional experiments showed that carriers with the CC genotype in CIITA//rs12932187 had a lower CIITA mRNA expression level and an enhanced IL-10 secretion as compared to GG and CG carriers. This study provides evidence that the CIITA and NOD1 gene are involved in the susceptibility to Behcet’s disease.