Multi-ancestral GWAS identifies shared and Asian-specific loci for SLE and links type III interferon signaling and lysosomal function to the disease

Childhood-Onset Systemic Lupus Erythematosus (cSLE): An International Perspective

PURPOSE OF REVIEW

Childhood-onset systemic lupus erythematosus (cSLE) is a severe and potentially life-threatening chronic autoimmune disease. cSLE is more aggressive and has poorer outcomes than adult-onset disease. The global burden of cSLE is poorly understood, with most publications on cSLE originating from high-resourced settings. The reports from less resourced settings indicate high morbidity and mortality in these populations.

RECENT FINDINGS

In this article, we review the disparities in global access to rheumatology care and research for patients with cSLE. We highlight recent cSLE advances from all regions of the globe. We describe current obstacles to cSLE clinical care and research in all settings. Finally, we propose a path forward for high quality, equitable and accessible care to individuals with cSLE everywhere. Individuals with cSLE are at risk for morbidity and death, yet patients worldwide face challenges to adequate access to care and research. Sustained, collaborative efforts are needed to create pathways to improve care and outcomes for these patients.

IRF5 Variants Are Risk Factors for Systemic Lupus Erythematosus in Two Mexican Populations

INTRODUCTION

Interferon regulatory factor 5 ( IRF5 ) is one of the pivotal genes implicated in systemic lupus erythematosus (SLE) among diverse ethnic groups, including Europeans, Asians, Hispanics, and Africans. Notably, its significance appears particularly pronounced among Hispanic populations. Previous studies have identified several single-nucleotide variants within IRF5 , such as rs2004640G/T, rs2070197T/C, and rs10954213G/A, as associated with susceptibility to SLE among patients from Mexico City. However, the population of Yucatan, located in the Southeast of Mexico and characterized by a greater Amerindian genetic component, remains largely unexplored in this regard.

OBJECTIVES

Our study aimed to replicate the observed association between IRF5 variants and susceptibility to SLE among patients from Central Mexico and Yucatan. Furthermore, we investigated the impact of IRF5 rs59110799G/T, a variant that has not been previously studied in SLE individuals.

METHOD

Our study included 204 SLE patients and 160 controls from Central Mexico, as well as 184 SLE patients and 184 controls from Yucatan. All participants were females 18 years and older. We employed a TaqMan assay to detect the presence of the following single-nucleotide variants: rs2004640G/T, rs2070197T/C, rs10954213G/A, and rs59110799G/T. Furthermore, we utilized 2 distinct web tools and databases to predict the potential functional implications of IRF5 variants.

RESULTS

In SLE patients from Central Mexico, several IRF5 alleles showed significant associations with the disease following adjustment by the Bonferroni test: the rs2070197C allele (odds ratio [OR], 2.08), the rs10954213A allele (OR, 1.59), and the rs59110799G allele (OR, 1.71). Conversely, among patients from Yucatan, the following alleles showed associations: rs2004640T (OR, 1.51), rs2070197C (OR, 1.62), rs10954213A (OR, 1.67), and rs59110799G (OR, 1.44).

CONCLUSION

Our findings highlight genetic variations between Mexican populations and emphasize the role of IRF5 as a risk factor in SLE patients from both Central Mexico and Yucatan.

Multiple polygenic risk scores can improve the prediction of systemic lupus erythematosus in Taiwan

OBJECTIVE

To identify new genetic variants associated with SLE in Taiwan and establish polygenic risk score (PRS) models to improve the early diagnostic accuracy of SLE.

METHODS

The study enrolled 2429 patients with SLE and 48 580 controls from China Medical University Hospital in Taiwan. A genome-wide association study (GWAS) and PRS analyses of SLE and other three SLE markers, namely ANA, anti-double-stranded DNA antibody (dsDNA) and anti-Smith antibody (Sm), were conducted.

RESULTS

Genetic variants associated with SLE were identified through GWAS. Some novel genes, which have been previously reported, such as RCC1L and EGLN3, were revealed to be associated with SLE in Taiwan. Multiple PRS models were established, and optimal cut-off points for each PRS were determined using the Youden Index. Combining the PRSs for SLE, ANA, dsDNA and Sm yielded an area under the curve of 0.64 for the optimal cut-off points. An analysis of human leucocyte antigen (HLA) haplotypes in SLE indicated that individuals with HLA-DQA1*01:01 and HLA-DQB1*05:01 were at a higher risk of being classified into the SLE group.

CONCLUSIONS

The use of PRSs to predict SLE enables the identification of high-risk patients before abnormal laboratory data were obtained or symptoms were manifested. Our findings underscore the potential of using PRSs and GWAS in identifying SLE markers, offering promise for early diagnosis and prediction of SLE.

Non-coding DNA variants for risk in lupus

Systemic Lupus Erythematosus (SLE) is a multifactorial autoimmune disease that arises from a dynamic interplay between genetics and environmental triggers. The advent of sophisticated genomics technology has catalyzed a shift in our understanding of disease etiology, spotlighting the pivotal role of non-coding DNA variants in SLE pathogenesis. In this review, we present a comprehensive examination of the non-coding variants associated with SLE, shedding light on their role in influencing disease risk and progression. We discuss the latest methodological advancements that have been instrumental in the identification and functional characterization of these genomic elements, with a special focus on the transformative power of CRISPR-based gene-editing technologies. Additionally, the review probes into the therapeutic opportunities that arise from modulating non-coding regions associated with SLE. Through an exploration of the complex network of non-coding DNA, this review aspires to decode the genetic puzzle of SLE and set the stage for groundbreaking gene-based therapeutic interventions and the advancement of precision medicine strategies tailored to SLE management.

Association of genetic variation on X chromosome with systemic lupus erythematosus in both Thai and Chinese populations

OBJECTIVES

X chromosome has been considered as a risk factor for SLE, which is a prototype of autoimmune diseases with a significant sex difference (female:male ratio is around 9:1). Our study aimed at exploring the association of genetic variants in X chromosome and investigating the influence of trisomy X in the development of SLE.

METHODS

X chromosome-wide association studies were conducted using data from both Thai (835 patients with SLE and 2995 controls) and Chinese populations (1604 patients with SLE and 3324 controls). Association analyses were performed separately in females and males, followed by a meta-analysis of the sex-specific results. In addition, the dosage of X chromosome in females with SLE were also examined.

RESULTS

Our analyses replicated the association of TMEM187-IRAK1-MECP2, TLR7, PRPS2 and GPR173 loci with SLE. We also identified two loci suggestively associated with SLE. In addition, making use of the difference in linkage disequilibrium between Thai and Chinese populations, a synonymous variant in TMEM187 was prioritised as a likely causal variant. This variant located in an active enhancer of immune-related cells, with the risk allele associated with decreased expression level of TMEM187. More importantly, we identified trisomy X (47,XXX) in 5 of 2231 (0.22%) females with SLE. The frequency is significantly higher than that found in the female controls (0.08%; two-sided exact binomial test P=0.002).

CONCLUSION

Our study confirmed previous SLE associations in X chromosome, and identified two loci suggestively associated with SLE. More importantly, our study indicated a higher risk of SLE for females with trisomy X.

Rheumatological complaints in H syndrome: from inflammatory profiling to target treatment in a case study

BACKGROUND

H Syndrome is a rare genetic condition caused by biallelic pathogenic variants in the SLC29A3 gene. It is characterized by a wide range of clinical manifestations, many of which are related to the immune-rheumatological field. These include scleroderma-like skin changes, deforming arthritis, and enlarged lymph nodes. The condition also features cardiac and endocrine defects, as well as hearing loss, for which the immune pathogenesis appears less clear. Immunomodulatory medications have been shown to improve many symptoms in recent experiences.

CASE PRESENTATION

A 21-year-old girl was referred to our institute after being diagnosed with H syndrome. Her medical history was characterized by the development of finger and toe deformities, which developed since the first years of life and progressively worsened with clinodactyly. At 6 years of age, she was diagnosed with diabetes mellitus without typical autoantibodies and with bilateral sensorineural hearing loss. She also complained of frequent episodes of lymphadenopathy, sometimes with colliquation and growth retardation due to pancreatic insufficiency. It wasn't until the genetic diagnosis of H syndrome that the continual increase in acute phase reactants was noticed, suggesting that an immunological pathogenesis may be the source of her problems. During her visit to our institute, she reported serious pain in both feet and hands and difficulty walking due to knee arthritis and muscle contractures. Conventional therapy with steroid injection in affected joints and methotrexate only led to partial improvement. After a thorough assessment of her inflammatory profile showing a high interferon score, the girl received treatment with baricitinib. Furthermore, based on recent data showing that SLC29A3 deficiency results in interferon production because of Toll-like Receptor 7 activation in lysosomes, hydroxychloroquine was also added. The combination of the two drugs resulted for the first time in a rapid and persistent normalization of inflammatory markers, paralleled by a dramatic improvement in symptoms.

CONCLUSIONS

We describe the results of inhibiting IFN inflammation in H syndrome and discuss how JAK inhibitors and antimalarials might represent a mechanistically based treatment for this orphan drug disorder.

Targeting TLR Signaling Cascades in Systemic Lupus Erythematosus and Rheumatoid Arthritis: An Update

Evidence from animal models and human genetics implicates Toll-like Receptors (TLRs) in the pathogenesis of Systemic Lupus Erythematosus (SLE) and Rheumatoid Arthritis (RA). Endosomal TLRs sensing nucleic acids were proposed to induce lupus-promoting signaling in dendritic cells, B cells, monocytes, and macrophages. Ligation of TLR4 in synovial macrophages and fibroblast-like synoviocytes (FLSs) by endogenous ligands was suggested to induce local production of mediators that amplify RA synovitis. Inhibition of TLRs using antagonists or monoclonal antibodies (mAbs) that selectively prevent extracellular or endosomal TLR ligation has emerged as an attractive treatment strategy for SLE and RA. Despite the consistent success of selective inhibition of TLR ligation in animal models, DV-1179 (dual TLR7/9 antagonist) failed to achieve pharmacodynamic effectiveness in SLE, and NI-0101 (mAb against TLR4) failed to improve arthritis in RA. Synergistic cooperation between TLRs and functional redundancy in human diseases may require pharmacologic targeting of intracellular molecules that integrate signaling downstream of multiple TLRs. Small molecules inhibiting shared kinases involved in TLR signaling and peptidomimetics disrupting the assembly of common signalosomes ("Myddosome") are under development. Targeted degraders (proteolysis-targeting chimeras (PROTACs)) of intracellular molecules involved in TLR signaling are a new class of TLR inhibitors with promising preliminary data awaiting further clinical validation.

A Non-Coding Variant in SLC15A4 Modulates Enhancer Activity and Lysosomal Deacidification Linked to Lupus Susceptibility

Systemic lupus erythematosus (SLE) is a complex autoimmune disease with a strong genetic basis. Despite the identification of several single nucleotide polymorphisms (SNPs) near the SLC15A4 gene that are significantly associated with SLE across multiple populations, specific causal SNP(s) and molecular mechanisms responsible for disease susceptibility are unknown. To address this gap, we employed bioinformatics, expression quantitative trait loci (eQTLs), and 3D chromatin interaction analysis to nominate a likely functional variant, rs35907548, in an active intronic enhancer of SLC15A4. Through luciferase reporter assays followed by chromatin immunoprecipitation (ChIP)-qPCR, we observed significant allele-specific enhancer effects of rs35907548 in diverse cell lines. The rs35907548 risk allele T is associated with increased regulatory activity and target gene expression, as shown by eQTLs and chromosome conformation capture (3C)-qPCR. The latter revealed long-range chromatin interactions between the rs35907548 enhancer and the promoters of SLC15A4, GLTLD1, and an uncharacterized lncRNA. The enhancer-promoter interactions and expression effects were validated by CRISPR/Cas9 knock-out (KO) of the locus in HL60 promyeloblast cells. KO cells also displayed dramatically dysregulated endolysosomal pH regulation. Together, our data show that the rs35907548 risk allele affects multiple aspects of cellular physiology and may directly contribute to SLE.

A Non-Coding Variant in SLC15A4 Modulates Enhancer Activity and Lysosomal Deacidification Linked to Lupus Susceptibility

Systemic lupus erythematosus (SLE) is a complex autoimmune disease with a strong genetic basis. Despite the identification of several single nucleotide polymorphisms (SNPs) near the SLC15A4 gene that are significantly associated with SLE across multiple populations, specific causal SNP(s) and molecular mechanisms responsible for disease susceptibility are unknown. To address this gap, we employed bioinformatics, expression quantitative trait loci (eQTLs), and 3D chromatin interaction analysis to nominate a likely functional variant, rs35907548, in an active intronic enhancer of SLC15A4 . Through luciferase reporter assays followed by chromatin immunoprecipitation (ChIP)-qPCR, we observed significant allele-specific enhancer effects of rs35907548 in diverse cell lines. The rs35907548 risk allele T is associated with increased regulatory activity and target gene expression, as shown by eQTLs and chromosome conformation capture (3C)-qPCR. The latter revealed long-range chromatin interactions between the rs35907548 enhancer and the promoters of SLC15A4, GLTLD1 , and an uncharacterized lncRNA. The enhancer-promoter interactions and expression effects were validated by CRISPR/Cas9 knock-out (KO) of the locus in HL60 promyeloblast cells. KO cells also displayed dramatically dysregulated endolysosomal pH regulation. Together, our data show that the rs35907548 risk allele affects multiple aspects of cellular physiology and may directly contribute to SLE.

TAOK3 limits age-associated inflammation by negatively modulating macrophage differentiation and their production of TNFα

BACKGROUND

Human aging is characterized by a state of chronic inflammation, termed inflammaging, for which the causes are incompletely understood. It is known, however, that macrophages play a driving role in establishing inflammaging by promoting pro-inflammatory rather than anti-inflammatory responses. Numerous genetic and environmental risk factors have been implicated with inflammaging, most of which are directly linked to pro-inflammatory mediators IL-6, IL1Ra, and TNFα. Genes involved in the signaling and production of those molecules have also been highlighted as essential contributors. TAOK3 is a serine/threonine kinase of the STE-20 kinase family that has been associated with an increased risk of developing auto-immune conditions in several genome-wide association studies (GWAS). Yet, the functional role of TAOK3 in inflammation has remained unexplored.

RESULTS

We found that mice deficient in the serine/Threonine kinase Taok3 developed severe inflammatory disorders with age, which was more pronounced in female animals. Further analyses revealed a drastic shift from lymphoid to myeloid cells in the spleens of those aged mice. This shift was accompanied by hematopoietic progenitor cells skewing in Taok3^-/- mice that favored myeloid lineage commitment. Finally, we identified that the kinase activity of the enzyme plays a vital role in limiting the establishment of proinflammatory responses in macrophages.

CONCLUSIONS

Essentially, Taok3 deficiency promotes the accumulation of monocytes in the periphery and their adoption of a pro-inflammatory phenotype. These findings illustrate the role of Taok3 in age-related inflammation and highlight the importance of genetic risk factors in this condition.

A review of genetic risk in systemic lupus erythematosus

INTRODUCTION

Systemic Lupus Erythematosus (SLE) is a complex multisystem autoimmune disease with a wide range of signs and symptoms in affected individuals. The utilization of genome-wide association study (GWAS) technology has led to an explosion in the number of genetic risk factors mapped for autoimmune diseases, including SLE.

AREAS COVERED

In this review, we summarize the more recent genetic risk loci mapped in SLE, which bring the total number of loci mapped to approximately 200. We review prioritization analyses of the associated variants and experimental validation of the putative causal variants. This includes the implementation of new bioinformatic techniques to align genomic and functional data and the use of transcriptomics with single-cell RNA-sequencing, CRISPR genome editing, and Massive Parallel Reporter Assays to analyze non-coding regulatory genetics.

EXPERT OPINION

Despite progress in identifying more genetic risk loci and variant-gene pairs for SLE, understanding its pathogenesis and applying findings clinically remains challenging. The polygenic risk score (PRS) has been used as an application of SLE genetics, but with limited performance in non-EUR populations. In the next few years, advancements in proteomics, post-translational modification estimation, and whole-genome sequencing will enhance disease understanding.

Treatment of lupus nephritis: consensus, evidence and perspectives

Despite the continuing development of immunomodulatory agents and supportive care, the prognosis associated with lupus nephritis (LN) has not improved substantially in the past decade, with end-stage kidney disease still developing in 5-30% of patients within 10 years of LN diagnosis. Moreover, inter-ethnic variation in the tolerance of, clinical response to and level of evidence regarding various therapeutic regimens for LN has led to variation in treatment prioritization in different international recommendations. Modalities that better preserve kidney function and reduce the toxicities of concomitant glucocorticoids are unmet needs in the development of therapeutics for LN. In addition to the conventional recommended therapies for LN, there are newly approved treatments as well as investigational drugs in the pipeline, including the newer generation calcineurin inhibitors and biologic agents. In view of the heterogeneity of LN in terms of clinical presentation and prognosis, the choice of therapies depends on a number of clinical considerations. Molecular profiling, gene-signature fingerprints and urine proteomic panels might enhance the accuracy of patient stratification for treatment personalization in the future.

Control of naive and effector CD4 T cell receptor repertoires by rheumatoid-arthritis-risk HLA alleles

OBJECTIVE

Human Leukocyte Antigen (HLA) alleles regulate susceptibility to rheumatoid arthritis (RA) and immune-mediated diseases. This study aims to elucidate the impact of HLA alleles to T cell subsets.

METHODS

We performed genome-wide and HLA allele association analysis for T cell receptor (TCR) beta chain repertoire in 13 purified T cell subsets from the ImmuNexUT database, consisting of 407 donors with ten immune-mediated diseases and healthy controls.

RESULTS

HLA class II alleles were associated with TRBV gene usage and the public clones of CD4 T cells, while HLA class I alleles were associated with CD8 T cells. RA-risk and immune-mediated diseases-risk HLA alleles were associated with TRBV gene usage of naive and effector CD4 T cell subsets and public clones accumulating in Th17. Clonal diversity was independent of HLA alleles and was correlated with transcriptome changes that reflect TCR signaling.

CONCLUSION

This study revealed in vivo evidence that both HLA alleles and environmental factors shape naive and effector TCR repertoires in RA and immune-mediated diseases patients.

A Study on MDA5 Signaling in Splenic B Cells from an Imiquimod-Induced Lupus Mouse Model with Proteomics

INTRODUCTION

Several environmental stimuli may influence lupus, particularly viral infections. In this study, we used an imiquimod-induced lupus mouse model focused on the TLR7 pathway and proteomics analysis to determine the specific pathway related to viral infection and the related protein expressions in splenic B cells to obtain insight into B-cell responses to viral infection in the lupus model.

MATERIALS AND METHODS

We treated FVB/N wild-type mice with imiquimod for 8 weeks to induce lupus symptoms and signs, retrieved splenocytes, selected B cells, and conducted the proteomic analysis. The B cells were co-cultured with CD40L+ feeder cells for another week before performing Western blot analysis. Panther pathway analysis was used to disclose the pathways activated and the protein-protein interactome was analyzed by the STRING database in this lupus murine model.

RESULTS

The lupus model was well established and well demonstrated with serology evidence and pathology proof of lupus-mimicking organ damage. Proteomics data of splenic B cells revealed that the most important activated pathways (fold enrichment > 100) demonstrated positive regulation of the MDA5 signaling pathway, negative regulation of IP-10 production, negative regulation of chemokine (C-X-C motif) ligand 2 production, and positive regulation of the RIG-I signaling pathway. A unique protein-protein interactome containing 10 genes was discovered, within which ISG15, IFIH1, IFIT1, DDX60, and DHX58 were demonstrated to be downstream effectors of MDA5 signaling. Finally, we found B-cell intracellular cytosolic proteins via Western blot experiment and continued to observe MDA5-related pathway activation.

CONCLUSION

In this experiment, we confirmed that the B cells in the lupus murine model focusing on the TLR7 pathway were activated through the MDA5 signaling pathway, an important RNA sensor implicated in the detection of viral infections and autoimmunity. The MDA5 agonist/antagonist RNAs and the detailed molecular interactions within B cells are worthy of further investigation for lupus therapy.

Random forests algorithm boosts genetic risk prediction of systemic lupus erythematosus

Patients with systemic lupus erythematosus (SLE) present varied clinical manifestations, posing a diagnostic challenge for physicians. Genetic factors substantially contribute to SLE development. A polygenic risk scoring (PRS) model has been used to estimate the genetic risk of SLE in individuals. However, this approach assumes independent and additive contribution of genetic variants to disease development. We aimed to improve the accuracy of SLE prediction using machine-learning algorithms. We applied random forest (RF), support vector machine (SVM), and artificial neural network (ANN) to classify SLE cases and controls using the data from our previous genome-wide association studies (GWAS) conducted in either Chinese or European populations, including a total of 19,208 participants. The overall performances of these predictors were assessed by the value of area under the receiver-operator curve (AUC). The analyses in the Chinese GWAS showed that the RF model significantly outperformed other predictors, achieving a mean AUC value of 0.84, a 13% improvement upon the PRS model (AUC = 0.74). At the optimal cut-off, the RF predictor reached a sensitivity of 84% with a specificity of 68% in SLE classification. To validate these results, similar analyses were repeated in the European GWAS, and the RF model consistently outperformed other algorithms. Our study suggests that the RF model could be an additional and powerful predictor for SLE early diagnosis.

Regulatory strategies limiting endosomal Toll-like receptor activation in B cells

The recognition of pathogen-associated nucleic acid (NA) promotes effective immunity against invading pathogens. However, endosomal Toll-like receptor (TLR) activation by self-NA also underlies the pathogenesis of systemic autoimmune diseases, such as systemic lupus erythematosus (SLE). For this reason, the activation thresholds of NA-sensing TLRs must be tightly regulated to balance protective and pathogenic immune responses. In this study, we will provide an overview of the evolutionary mechanisms designed to limit the aberrant activation of endosomal TLRs by self-ligands, focusing on four broad strategies. These include the following: 1) the production of nucleases able to degrade self-DNA and RNA; 2) the cell-specific regulation of endosomal TLR expression; 3) the spatial and temporal control of TLR positioning at a sub-cellular level; and 4) the modulation of downstream TLR signaling cascades. Given the critical role of B cells in lupus pathogenesis, where possible, we will describe evidence for B cell-specific induction of these regulatory mechanisms. We will also highlight our own work showing how modulation of B cell endolysosomal flux tunes NA-sensing TLR activation signals. In the face of inevitable generation of self-NA during normal cellular turnover, these parallel mechanisms are vital to protect against pathogenic inflammation.