Autoimmune risk loci of IL12RB2, IKZF1, XKR6, TMEM39A and CSK in Chinese patients with systemic lupus erythematosus

Systemic Lupus Erythematosus Patients with DNASE1L3·Deficiency Have a Distinctive and Specific Genic Circular DNA Profile in Plasma

Cell-free (cf) extrachromosomal circular DNA (eccDNA) has a potential clinical application as a biomarker. Systemic lupus erythematosus (SLE) is a systemic autoimmune disease with a complex immunological pathogenesis, associated with autoantibody synthesis. A previous study found that SLE patients with deoxyribonuclease 1-like 3 (DNASE1L3) deficiency exhibit changes in the frequency of short and long eccDNA in plasma compared to controls. Here, using the DifCir method for differential analysis of short-read sequenced purified eccDNA data based on the split-read signal of the eccDNA on circulomics data, we show that SLE patients with DNASE1L3 deficiency have a distinctive profile of eccDNA excised by gene regions compared to controls. Moreover, this profile is specific; cf-eccDNA from the top 93 genes is detected in all SLE with DNASE1L3 deficiency samples, and none in the control plasma. The top protein coding gene producing eccDNA-carrying gene fragments is the transcription factor BARX2, which is involved in skeletal muscle morphogenesis and connective tissue development. The top gene ontology terms are ‘positive regulation of torc1 signaling’ and ‘chondrocyte development’. The top Harmonizome terms are ‘lymphopenia’, ‘metabolic syndrome x’, ‘asthma’, ‘cardiovascular system disease‘, ‘leukemia’, and ‘immune system disease’. Here, we show that gene associations of cf-eccDNA can serve as a biomarker in the autoimmune rheumatic diseases.

Genome-wide association study identifies Sjögren's risk loci with functional implications in immune and glandular cells

Sjögren's disease is a complex autoimmune disease with twelve established susceptibility loci. This genome-wide association study (GWAS) identifies ten novel genome-wide significant (GWS) regions in Sjögren's cases of European ancestry: CD247, NAB1, PTTG1-MIR146A, PRDM1-ATG5, TNFAIP3, XKR6, MAPT-CRHR1, RPTOR-CHMP6-BAIAP6, TYK2, SYNGR1. Polygenic risk scores yield predictability (AUROC = 0.71) and relative risk of 12.08. Interrogation of bioinformatics databases refine the associations, define local regulatory networks of GWS SNPs from the 95% credible set, and expand the implicated gene list to >40. Many GWS SNPs are eQTLs for genes within topologically associated domains in immune cells and/or eQTLs in the main target tissue, salivary glands.

Role of Genetic Polymorphisms in IL12Rβ2 in Chronic Obstructive Pulmonary Disease

Background

Chronic obstructive pulmonary disease (COPD) is the most common chronic inflammatory airway disease. Il-12r beta 2 (IL-12Rβ2) is important for the production of pathogenic Th1 cells. We aimed to explore the association between IL-12Rβ2 genetic variants and COPD risk among southern Chinese Han population.

Methods

We recruited 996 participants to perform an association analysis through SNPStats online software. We used false-positive report probability analysis to detect whether the positive findings were noteworthy. Haploview 4.2 software and SNPStats were used to conduct the haplotype analysis and linkage disequilibrium. Finally, the interaction of SNP-SNP in COPD risk was evaluated by multi-factor dimensionality reduction.

Results

The study found evidence that genetic loci in IL-12Rβ2 (rs2201584, rs1874791, rs6679356, and rs3790567) were potentially associated with the COPD susceptibility. In particular, IL-12Rβ2-rs2201584 and -rs1874791 showed close associations with COPD risk in both overall and several stratified analyses. Overall analysis or several stratified analyses indicated that allele A or homozygous genotype AA of IL-12Rβ2-rs2201584 were risk factors for COPD (Allele A: OR (95% CI) = 1.23 (1.02–1.48), p = 0.033; genotype AA: OR (95% CI) = 1.76 (1.15–2.69), p = 0.009). The allele A or homozygous genotype AA of IL-12Rβ2- rs1874791 were also risk factors for COPD (Allele A: OR (95% CI) = 1.36 (1.10–1.68), p = 0.004; genotype AA: OR (95% CI) = 2.17 (1.18–3.99), p = 0.013).

Conclusion

Intronic variants in IL-12Rβ2 (rs2201584, rs1874791, rs6679356, and rs3790567) were associated with the COPD susceptibility. In particular, there were sufficient evidences that IL-12Rβ2-rs2201584 and -rs1874791 were associated with the increasing risk of COPD.

Immunology of IL-12: An update on functional activities and implications for disease

As its first identified member, Interleukin-12 (IL-12) named a whole family of cytokines. In response to pathogens, the heterodimeric protein, consisting of the two subunits p35 and p40, is secreted by phagocytic cells. Binding of IL-12 to the IL-12 receptor (IL-12R) on T and natural killer (NK) cells leads to signaling via signal transducer and activator of transcription 4 (STAT4) and subsequent interferon gamma (IFN-γ) production and secretion. Signaling downstream of IFN-γ includes activation of T-box transcription factor TBX21 (Tbet) and induces pro-inflammatory functions of T helper 1 (T_H1) cells, thereby linking innate and adaptive immune responses. Initial views on the role of IL-12 and clinical efforts to translate them into therapeutic approaches had to be re-interpreted following the discovery of other members of the IL-12 family, such as IL-23, sharing a subunit with IL-12. However, the importance of IL-12 with regard to immune processes in the context of infection and (auto-) inflammation is still beyond doubt. In this review, we will provide an update on functional activities of IL-12 and their implications for disease. We will begin with a summary on structure and function of the cytokine itself as well as its receptor and outline the signal transduction and the transcriptional regulation of IL-12 secretion. In the second part of the review, we will depict the involvement of IL-12 in immune-mediated diseases and relevant experimental disease models, while also providing an outlook on potential translational approaches.

XKR6 rs7014968 SNP Increases Serum Total Cholesterol Levels and the Risk of Coronary Heart Disease and Ischemic Stroke

The X Kell blood group complex subunit-related family member 6 (XKR6) gene single-nucleotide polymorphisms (SNPs) have been associated with serum lipid profiles and the risk of coronary heart disease (CHD) and ischemic stroke (IS) in several previous studies, but the association between the XKR6 rs7014968 SNP and serum lipid levels and the risk of CHD and IS has not been detected previously. This study aims to explore the association between the XKR6 rs7014968 SNP and serum lipid traits and the susceptibility to CHD and IS in the Guangxi Han Chinese population. Snapshot technology was used to determine the genotypes of the XKR6 rs7014968 SNP in 624 controls, 588 patients with CHD, and 544 patients with IS. The XKR6 rs7014968C allele carriers in the control group had higher serum total cholesterol (TC) levels than the C allele noncarriers (P = .025). The XKR6 rs7014968C allele carriers also had an increased risk of CHD and IS (P < .05-.01). Stratified analysis showed that the patients with the rs7014968C allele in the female, age >60 years, body mass index (BMI) >24 kg/m², and hypertension subgroups had a higher risk of CHD than those in the subgroup counterparts. The patients with the rs7014968C allele in the male, BMI > 24 kg/m², smoker, and hypertension subgroups also had a higher risk of IS than those in the subgroup counterparts. These results suggest that the XKR6 rs7014968 SNP is likely to increase the risk of CHD and IS by increasing serum TC levels in our study populations.

Transmembrane Protein 39A Promotes the Replication of Encephalomyocarditis Virus via Autophagy Pathway

Encephalomyocarditis virus (EMCV) causes encephalitis, myocarditis, neuropathy, reproductive disorders, and diabetes in animals. EMCV is known to induce cell autophagy; however, the molecular mechanisms underlying this remain unclear. Here, we show that the type III-transmembrane protein, transmembrane protein 39A (TMEM39A), plays a critical role in EMCV replication. We showed that EMCV GS01 strain infection upregulated TMEM39A expression. Importantly, EMCV induced autophagy in a range of host cells. The autophagy chemical inhibitor, 3-MA, inhibited EMCV replication and reduced TMEM39A expression. This is the first study demonstrating TMEM39A promoting the replication of EMCV via autophagy. Overall, we show that TMEM39A plays a positive regulatory role in EMCV proliferation and that TMEM39A expression is dependent on the autophagy pathway.

Genetic Variants in TMEM39A Gene Are Associated with Autoimmune Thyroid Diseases

Transmembrane protein 39A (TMEM39A) gene polymorphisms have been related to various autoimmune diseases, but the relationship between TMEM39A polymorphisms and autoimmune thyroid disease (AITD) remains unknown. This study was aimed at investigating whether the polymorphisms of the TMEM39A were associated with AITD in the Chinese Han population. A case-control study was performed in a total of 906 AITD patients and 744 healthy controls. Four single nucleotide polymorphisms, including rs1132200, rs12492609, rs2282175, and rs7629750, in TMEM39A were examined by polymerase chain reaction-ligase detection reaction. We found that the allele T of rs12492609 in TMEM39A was associated with AITD and Hashimoto's thyroiditis (HT) (p = 0.023; p = 0.028 respectively). Compared with controls, the frequency of haplotype CCA in AITD patients was higher than that in controls (p = 0.036), but the frequency of haplotype CTA in AITD and HT patients was lower than that in controls (p = 0.046; p = 0.047 respectively). In addition, the frequency of allele A at rs7629750 in AITD patients with onset age ≤18 years old was higher than that in AITD patients with onset age ≥19 (p = 0.046). Further, there was an obvious difference in the genotype distributions of rs12492609 and rs7629750 between HT patients with hypothyroidism and those without hypothyroidism (p = 0.034 and p = 0.023, respectively). Our study first reveals that the polymorphisms of the TMEM39A gene are associated with the susceptibility to AITD, especially for early-onset AITD and HT with hypothyroidism.

Investigation of multi-trait associations using pathway-based analysis of GWAS summary statistics

Background

Genome-wide association studies (GWAS) have been successful in identifying disease-associated genetic variants. Recently, an increasing number of GWAS summary statistics have been made available to the research community, providing extensive repositories for studies of human complex diseases. In particular, cross-trait associations at the genetic level can be beneficial from large-scale GWAS summary statistics by using genetic variants that are associated with multiple traits. However, direct assessment of cross-trait associations using susceptibility loci has been challenging due to the complex genetic architectures in most diseases, calling for advantageous methods that could integrate functional interpretation and imply biological mechanisms.

Results

We developed an analytical framework for systematic integration of cross-trait associations. It incorporates two different approaches to detect enriched pathways and requires only summary statistics. We demonstrated the framework using 25 traits belonging to four phenotype groups. Our results revealed an average of 54 significantly associated pathways (ranged between 18 and 175) per trait. We further proved that pathway-based analysis provided increased power to estimate cross-trait associations compared to gene-level analysis. Based on Fisher’s Exact Test (FET), we identified a total of 24 (53) pairs of trait-trait association at adjusted p_FET < 1 × 10^− 3 (p_FET < 0.01) among the 25 traits. Our trait-trait association network revealed not only many relationships among the traits within the same group but also novel relationships among traits from different groups, which warrants further investigation in future.

Conclusions

Our study revealed that risk variants for 25 different traits aggregated in particular biological pathways and that these pathways were frequently shared among traits. Our results confirmed known mechanisms and also suggested several novel insights into the etiology of multi-traits.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5373-7) contains supplementary material, which is available to authorized users.

Cereblon modulator iberdomide induces degradation of the transcription factors Ikaros and Aiolos: immunomodulation in healthy volunteers and relevance to systemic lupus erythematosus

OBJECTIVES

IKZF1 and IKZF3 (encoding transcription factors Ikaros and Aiolos) are susceptibility loci for systemic lupus erythematosus (SLE). The pharmacology of iberdomide (CC-220), a cereblon (CRBN) modulator targeting Ikaros and Aiolos, was studied in SLE patient cells and in a phase 1 healthy volunteer study.

METHODS

CRBN, IKZF1 and IKZF3 gene expression was measured in peripheral blood mononuclear cells (PBMC) from patients with SLE and healthy volunteers. Ikaros and Aiolos protein levels were measured by Western blot and flow cytometry. Anti-dsDNA and anti-phospholipid autoantibodies were measured in SLE PBMC cultures treated for 7 days with iberdomide. Fifty-six healthy volunteers were randomised to a single dose of iberdomide (0.03-6 mg, n=6 across seven cohorts) or placebo (n=2/cohort). CD19+ B cells, CD3+ T cells and intracellular Aiolos were measured by flow cytometry. Interleukin (IL)-2 and IL-1β production was stimulated with anti-CD3 and lipopolysaccharide, respectively, in an ex vivo whole blood assay.

RESULTS

SLE patient PBMCs expressed significantly higher CRBN (1.5-fold), IKZF1 (2.1-fold) and IKZF3 (4.1-fold) mRNA levels compared with healthy volunteers. Iberdomide significantly reduced Ikaros and Aiolos protein levels in B cells, T cells and monocytes. In SLE PBMC cultures, iberdomide inhibited anti-dsDNA and anti-phospholipid autoantibody production (IC50 ≈10 nM). Single doses of iberdomide (0.3-6 mg) in healthy volunteers decreased intracellular Aiolos (minimum mean per cent of baseline: ≈12%-28% (B cells); ≈0%-33% (T cells)), decreased absolute CD19+ B cells, increased IL-2 and decreased IL-1β production ex vivo.

CONCLUSIONS

These findings demonstrate pharmacodynamic activity of iberdomide and support its further clinical development for the treatment of SLE.

TRIAL REGISTRATION NUMBER

NCT01733875; Results.

Aiolos Overexpression in Systemic Lupus Erythematosus B Cell Subtypes and BAFF-Induced Memory B Cell Differentiation Are Reduced by CC-220 Modulation of Cereblon Activity

BAFF is a B cell survival and maturation factor implicated in the pathogenesis of systemic lupus erythematosus (SLE). In this in vitro study, we describe that soluble BAFF in combination with IL-2 and IL-21 is a T cell contact-independent inducer of human B cell proliferation, plasmablast differentiation, and IgG secretion from circulating CD27⁺ memory and memory-like CD27^-IgD^- double-negative (DN) B cells, but not CD27^-IgD⁺ naive B cells. In contrast, soluble CD40L in combination with IL-2 and IL-21 induces these activities in both memory and naive B cells. Blood from healthy donors and SLE patients have similar circulating levels of IL-2, whereas SLE patients exhibit elevated BAFF and DN B cells and reduced IL-21. B cell differentiation transcription factors in memory, DN, and naive B cells in SLE show elevated levels of Aiolos, whereas Ikaros levels are unchanged. Treatment with CC-220, a modulator of the cullin ring ligase 4-cereblon E3 ubiquitin ligase complex, reduces Aiolos and Ikaros protein levels and BAFF- and CD40L-induced proliferation, plasmablast differentiation, and IgG secretion. The observation that the soluble factors BAFF, IL-2, and IL-21 induce memory and DN B cell activation and differentiation has implications for extrafollicular plasmablast development within inflamed tissue. Inhibition of B cell plasmablast differentiation by reduction of Aiolos and Ikaros may have utility in the treatment of SLE, where elevated levels of BAFF and Aiolos may prime CD27⁺ memory and DN memory-like B cells to become Ab-producing plasmablasts in the presence of BAFF and proinflammatory cytokines.

Autophagy and inflammation

Autophagy is a homeostatic mechanism involved in the disposal of damaged organelles, denatured proteins as well as invaded pathogens through a lysosomal degradation pathway. Recently, increasing evidences have demonstrated its role in both innate and adaptive immunity, and thereby influence the pathogenesis of inflammatory diseases. The detection of autophagy machinery facilitated the measurement of autophagy during physiological and pathophysiological processes. Autophagy plays critical roles in inflammation through influencing the development, homeostasis and survival of inflammatory cells, including macrophages, neutrophils and lymphocytes; effecting the transcription, processing and secretion of a number of cytokines, as well as being regulated by cytokines. Recently, autophagy-dependent mechanisms have been studied in the pathogenesis of several inflammatory diseases, including infectious diseases, Crohn’s disease, cystic fibrosis, pulmonary hypertension, chronic obstructive pulmonary diseases and so on. These studies suggested that modulation of autophagy might lead to therapeutic interventions for diseases associated with inflammation. Here we highlight recent advances in investigating the roles of autophagy in inflammation as well as inflammatory diseases.

TMEM39A and Human Diseases: A Brief Review

Transmembrane Protein 39A (TMEM39A) is a member of TMEM family. The understanding about this protein is still limited. The earlier studies indicated that TMEM39A was a key mediator of autoimmune disease. TMEM39A seems to be involved in systemic lupus erythematosus and multiple sclerosis in numerous of populations. All of these works stop at insufficient information by using gene functioning methods such as: Genome-wide association studies (GWASs) and/or follow-up study. It is the fact that the less understood of TMEM39A actually is the attraction to the scientist in near future. In this review the current knowledge about TMEM39A and its possible roles in cell biology, physiology and pathology will be described.

Association of novel polymorphisms in TMEM39A gene with systemic lupus erythematosus in a Chinese Han population

BACKGROUND

This study aimed to assess the association between 14 single nucleotide polymorphisms (SNPs) in six genes (IRF8, TMEM39A, IKZF3, ORMDL3, GSDMB, and ZPBP2) and systemic lupus erythematosus (SLE) in a Chinese Han population sample.

METHODS

We carried out a case-control study of 415 patients with SLE and 470 healthy controls without autoimmune disease or cancer. DNA for genetic analysis was isolated from the blood of all subjects using standard phenol-chloroform method. TagSNPs were identified using genotype data from the panel (Han Chinese in Beijing) of the HapMap Project and were selected using the Haploview program. Genotyping assay was conducted using the Sequenom MassARRAY iPLEX Gold platform. The frequencies of the alleles and genotypes were calculated and analyzed. Association studies and haplotype analysis were also performed.

RESULTS

The genotypic frequencies of rs12493175 and rs13062955 were significantly different between the SLE patients and the healthy controls. Compared with the common homozygous genotype, the CT and CT + TT genotypes in rs12493175 and the AC and AC + AA genotypes in rs13062955 was observed to significantly reduce the risk of SLE. The haplotype analysis of TMEM39A polymorphisms showed that the CGTA haplotype frequency was significantly low in the SLE patients.

CONCLUSION

Our findings identified three novel associations in SNPs located in the TMEM39A gene associated with SLE susceptibility in a Chinese Han population.

Recognition of Transmembrane Protein 39A as a Tumor-Specific Marker in Brain Tumor

Transmembrane protein 39A (TMEM39A) belongs to the TMEM39 family. TMEM39A gene is a susceptibility locus for multiple sclerosis. In addition, TMEM39A seems to be implicated in systemic lupus erythematosus. However, any possible involvement of TMEM39A in cancer remains largely unknown. In the present report, we provide evidence that TMEM39A may play a role in brain tumors. Western blotting using an anti-TMEM39A antibody indicated that TMEM39A was overexpressed in glioblastoma cell lines, including U87-MG and U251-MG. Deep-sequencing transcriptomic profiling of U87-MG and U251-MG cells revealed that TMEM39A transcripts were upregulated in such cells compared with those of the cerebral cortex. Confocal microscopic analysis of U251-MG cells stained with anti-TMEM39A antibody showed that TMEM39A was located in dot-like structures lying close to the nucleus. TMEM39A probably located to mitochondria or to endosomes. Immunohistochemical analysis of glioma tissue specimens indicated that TMEM39A was markedly upregulated in such samples. Bioinformatic analysis of the Rembrandt knowledge base also supported upregulation of TMEM39A mRNA levels in glioma patients. Together, the results afford strong evidence that TMEM39A is upregulated in glioma cell lines and glioma tissue specimens. Therefore, TMEM39A may serve as a novel diagnostic marker of, and a therapeutic target for, gliomas and other cancers.