Genetics of Antiphospholipid Syndrome

Distribution of HLA-DRB1 Alleles in Patients With Antiphospholipid Syndrome and Their Association With Antiphospholipid Antibodies Presence and Damage Indexes

Antiphospholipid syndrome (APS) is frequently coexisting with systemic lupus erythematosus (SLE) and the knowledge on its genetic background is essential. The objective of this work was to assess distribution of human leukocyte antigen (HLA)-DRB1 alleles in patients with APS with or without SLE in the context of Polish population data. The study was performed in a group of 112 patients with APS and healthy subjects to assess the distribution of HLA-DRB1 alleles in patients with APS and their association with clinical characteristics of patients with APS-antiphospholipid antibodies (aPLs) presence and disease activity/damage indexes. The distribution of HLA-DRB1 alleles showed significant differences between patients with APS and healthy subjects. Allelic variant HLA-DRB1⁣ ∗ 1.15 was identified as risk alleles for APS observed in patients with APS (odds ratio (OR): 2.06 (1.27, 3.23), p=0, 004), while HLA-DRB1⁣ ∗ 1.07 showed significant protective association (OR: 0.37 (0.14-0.76), p=0, 006). In subgroup of patients with coexisting SLE allelic variants above were not identified as risk or protective, while protective association was described for HLA-DRB1⁣ ∗ 01, but not for patients in primary APS group. Presence of antibodies anti-β 2-glycoprotein-I (aβ 2GPI) IgA and against domain 1, anti-phosphatidylserine/prothrombin (aPS/PT) and anticardiolipin antibody (aCL) IgA all the antibodies which were negatively associated with HLA-DRB1⁣ ∗ 15.01 carriers, what was reported for the first time may be suitable in discussion about value of these antibodies in practice and scientific research. This study clearly shows that primary APS has a distinct HLA-DRB1 associations as compared with SLE with a strong positive association with HLA-DRB1⁣ ∗ 15.01 allele and a protective association with HLA-DRB1⁣ ∗ 07.01.

Genetic and genomic associations in antiphospholipid syndrome: A systematic review

BACKGROUND

Numerous genes have been associated with APS in the literature. In recent years, microRNA (miRNA) and long non-coding RNA (lncRNA) have also been shown to modulate the expression of APS-related genes.

OBJECTIVE

We performed a systematic review to identify all studies reporting on genetic mechanisms that have been shown to be associated with APS.

METHODS

An extensive literature search was performed in the PubMed, Cochrane and Web of Science databases gathering all available articles through February 2024. We only selected case-control studies that met inclusion criteria and that focused on genetic contributors and modifiers related to primary APS.

RESULTS

Sixty studies were selected for data extraction. Selected studies were grouped into 8 broad categories for review and analysis: (1) gene expression studies; (2) thrombophilia genotypes; (3) single nucleotide polymorphisms (SNPs); (4) interferon-inducible genes; (5) microRNA studies; (6) long non-coding RNA (lncRNA) studies; (7) DNA methylation studies; and (8) differential gene expression studies. Several genes have been identified as associated with APS by more than one approach, including TF, complement associated genes, and interferon-inducible genes. It has been demonstrated that miRNA and lncRNA may alter the expression of important genes in patients with APS.

CONCLUSION

This systematic review has helped highlight important genes implicated in APS. Most importantly, pathways such as thrombosis/hemostasis, complement and interferon appear to be involved. Further studies are needed to help uncover important genes that could serve as biomarkers.

A Genome-Wide Association Study Suggests New Susceptibility Loci for Primary Antiphospholipid Syndrome

OBJECTIVE

Primary antiphospholipid syndrome (PAPS) is a rare autoimmune disease characterized by the presence of antiphospholipid antibodies and the occurrence of thrombotic events and pregnancy complications. Our study aimed to identify novel genetic susceptibility loci associated with PAPS.

METHODS

We performed a genome-wide association study comprising 5,485 individuals (482 affected individuals) of European ancestry. Significant and suggestive independent variants from a meta-analysis of approximately 7 million variants were evaluated for functional and biological process enrichment. The genetic risk variability for PAPS in different populations was also assessed. Hierarchical clustering, Mahalanobis distance, and Dirichlet Process Mixtures with uncertainty clustering methods were used to assess genetic similarities between PAPS and other immune-mediated diseases.

RESULTS

We revealed genetic associations with PAPS in a regulatory locus within the HLA class II region near HLA-DRA and in STAT1-STAT4 with a genome-wide level of significance; 34 additional suggestive genetic susceptibility loci for PAPS were also identified. The disease risk allele near HLA-DRA is associated with overexpression of HLA-DRB6, HLA-DRB9, HLA-DQA2, and HLA-DQB2 in immune cells, vascular tissue, and nervous tissue. This association is independent of the association between PAPS and HLA-DRB1*1302. Functional analyses highlighted immune-related pathways in PAPS-associated loci. The comparison with other immune-mediated diseases revealed a close genetic relatedness to neuromyelitis optica, systemic sclerosis, and Sjögren syndrome, suggesting co-localized causal variations close to STAT1-STAT4, TNPO3, and BLK.

CONCLUSION

This study represents a comprehensive large-scale genetic analysis for PAPS and provides new insights into the genetic basis and pathophysiology of this rare disease.

Risk Factors for Antiphospholipid Antibodies and Antiphospholipid Syndrome

Persistence of serum antiphospholipid antibodies (aPL) is associated with a high thrombotic risk, both arterial and venous, and with pregnancy complications. Due to the potential morbidity and mortality associated with the presence of aPL, identifying and recognizing risk factors for the development of aPL and thrombosis in aPL carriers may help to prevent and reduce the burden of disease. Multiple elements are involved in the pathomechanism of aPL development and aPL-related thrombosis such as genetics, malignancy, and infections. This review will address the role of both well-known risk factors and their evolution, and of emerging risk factors, including COVID-19, in the development of aPL and thrombosis in aPL carriers.

An immunogenomic exome landscape of triple positive primary antiphospholipid patients

Primary antiphospholipid syndrome is characterized by thrombosis and autoantibodies directed against phospholipids or associated proteins. The genetic etiology of PAPS remains unknown. We enrolled 21 patients with thromboembolic events associated to lupus anticoagulant, anticardiolipin and anti β2 glycoprotein1 autoantibodies. We performed whole exome sequencing and a systematic variant-based analysis in genes associated with thrombosis, in candidate genes previously associated with APS or inborn errors of immunity. Data were compared to public databases and to a control cohort of 873 non-autoimmune patients. Variants were identified following a state-of-the-art pipeline. Enrichment analysis was performed by comparing with the control cohort. We found an absence of significant HLA bias and genetic heterogeneity in these patients, including when testing combinations of rare variants in genes encoding for proteins involved in thrombosis and of variants in genes linked with inborn errors of immunity. These results provide evidence of genetic heterogeneity in PAPS, even in a homogenous series of triple positive patients. At the individual scale, a combination of variants may participate to the breakdown of B cell tolerance and to the vessel damage.

Non-invasive imaging in antiphospholipid syndrome to assess subclinical coronary artery disease

Antiphospholipid antibody syndrome (usually named antiphospholipid syndrome, APS) is an autoimmune disorder seen mainly in young people. Clinically, APS is described by pregnancy complications and/or a hypercoagulable state, including the venous or arterial vasculature, and strongly related to antiphospholipid antibodies. Although several cardiac manifestations have been involved with APS, and accelerated atherosclerosis is present in this condition, little is known about cardiovascular (CV) risk and the relation between APS. Several studies have used imaging markers to associate them with the main clinical features of patients with APS and the probability of having subclinical atherosclerosis. However, it has not yet been established which markers are most related to the risk of developing CV diseases (CVD) in these patients. In this narrative review, we focus on non-invasive imaging markers that can predict CVD, including carotid intima-media thickness and carotid plaques assessed by carotid ultrasonography or coronary artery calcium score, which usually by computed tomography. We also examine the evidence about vascular function markers used in APS, such as arterial flow-mediated brachial dilation and artery stiffness measured by the velocity of the pulse wave. We present the current status of non-invasive imaging markers, which suggest the existence of subclinical atherosclerosis in patients with APS. However, new prospective research is required to identify the predictive value of these findings and their modification by current treatments for APS.

A genome-wide association study suggests new susceptibility loci for primary antiphospholipid syndrome

Objectives

Primary antiphospholipid syndrome (PAPS) is a rare autoimmune disease characterized by the presence of antiphospholipid antibodies and the occurrence of thrombotic events and pregnancy complications. Our study aimed to identify novel genetic susceptibility loci associated with PAPS.

Methods

We performed a genome-wide association study comprising 5,485 individuals (482 affected individuals) of European ancestry. Significant and suggestive independent variants from a meta-analysis of approximately 7 million variants were evaluated for functional and biological process enrichment. The genetic risk variability for PAPS in different populations was also assessed. Hierarchical clustering, Mahalanobis distance, and Dirichlet Process Mixtures with uncertainty clustering methods were used to assess genetic similarities between PAPS and other immune-mediated diseases.

Results

We revealed genetic associations with PAPS in a regulatory locus within the HLA class II region near HLA-DRA and in STAT4 with a genome-wide level of significance. 34 additional suggestive genetic susceptibility loci for PAPS were also identified. The disease risk allele in the HLA class II locus is associated with overexpression of HLA-DRB6 , HLA-DRB9 , HLA-DPB2 , HLA-DQA2 and HLA-DQB2 , and is independent of the association between PAPS and HLA-DRB1*1302 . Functional analyses highlighted immune and nervous system related pathways in PAPS-associated loci. The comparison with other immune-mediated diseases revealed a close genetic relatedness to neuromyelitis optica, systemic sclerosis, and Sjögren's syndrome, suggesting colocalized causal variations close to STAT4 , TNPO3 , and BLK .

Conclusions

This study represents a comprehensive large-scale genetic analysis for PAPS and provides new insights into the genetic basis and pathophysiology of this rare disease.

The ABCs of antiphospholipid syndrome

Antiphospholipid syndrome (APS) is a thromboinflammatory syndrome characterized by thrombotic, microvascular, obstetric, or non-thrombotic events in the setting of persistent antiphospholipid antibodies (aPL), namely anticardiolipin antibody (aCL), anti-β2 glycoprotein-I antibody (aβ2GPI), and lupus anticoagulant (LA). The diagnosis of APS requires careful assessment of the aPL profile, the clinical phenotype, and additional risk factors. The standard management of aPL-related thrombosis is anticoagulation, which is not effective for microvascular and non-thrombotic events. In parallel to our improved understanding of aPL-related mechanisms, the role of immunosuppression has been increasingly investigated. In this review, we summarize the basic concepts and future perspectives in APS.

Antiphospholipid syndrome: advances in diagnosis, pathogenesis, and management

Antiphospholipid syndrome (APS) is a thrombo-inflammatory disease propelled by circulating autoantibodies that recognize cell surface phospholipids and phospholipid binding proteins. The result is an increased risk of thrombotic events, pregnancy morbidity, and various other autoimmune and inflammatory complications. Although antiphospholipid syndrome was first recognized in patients with lupus, the stand alone presentation of antiphospholipid syndrome is at least equally common. Overall, the diagnosis appears to affect at least one in 2000 people. Studies of antiphospholipid syndrome pathogenesis have long focused on logical candidates such as coagulation factors, endothelial cells, and platelets. Recent work has shed light on additional potential therapeutic targets within the innate immune system, including the complement system and neutrophil extracellular traps. Vitamin K antagonists remain the mainstay of treatment for most patients with thrombotic antiphospholipid syndrome and, based on current data, appear superior to the more targeted direct oral anticoagulants. The potential role of immunomodulatory treatments in antiphospholipid syndrome management is receiving increased attention. As for many systemic autoimmune diseases, the most important future direction is to more precisely identify mechanistic drivers of disease heterogeneity in pursuit of unlocking personalized and proactive treatments for patients.

Whole blood transcriptome identifies interferon-regulated genes as key drivers in thrombotic primary antiphospholipid syndrome

OBJECTIVE

Pathogenesis of antiphospholipid syndrome (APS) isn't fully elucidated. We aimed to identify gene signatures characterizing thrombotic primary APS (thrPAPS) and subgroups at high risk for worse outcomes.

METHODS

We performed whole blood next-generation RNA-sequencing in 62 patients with thrPAPS and 29 age-/sex-matched healthy controls (HCs), followed by differential gene expression analysis (DGEA) and enrichment analysis. We trained models on transcriptomics data using machine learning.

RESULTS

DGEA of 12.306 genes revealed 34 deregulated genes in thrPAPS versus HCs; 33 were upregulated by at least 2-fold, and 14/33 were type I and II interferon-regulated genes (IRGs) as determined by interferome database. Machine learning applied to deregulated genes returned 79% accuracy to discriminate thrPAPS from HCs, which increased to 82% when only the most informative IRGs were analyzed. Comparison of thrPAPS subgroups versus HCs showed an increased presence of IRGs among upregulated genes in venous thrombosis (21/23, 91%), triple-antiphospholipid antibody (aPL) positive (30/50, 60%), and recurrent thrombosis (19/42, 45%) subgroups. Enrichment analysis of upregulated genes in triple-aPL positive patients revealed terms related to 'type I interferon signaling pathway' and 'innate immune response'. DGEA among thrPAPS subgroups revealed upregulated genes, including IRGs, in patients with venous versus arterial thrombosis (n = 11, 9 IRGs), triple-aPL versus non-triple aPL (n = 10, 9 IRGs), and recurrent versus non-recurrent thrombosis (n = 10, 3 IRGs).

CONCLUSION

Upregulated IRGs may better discriminate thrPAPS from HCs than all deregulated genes in peripheral blood. Taken together with DGEA data, IRGs are highly expressed in thrPAPS and high-risk subgroups of triple-aPL and recurrent thrombosis, with potential treatment implications.

Genetic variation in toll-like receptor 4 gene with primary antiphospholipid syndrome susceptibility: a cohort of Egyptian patients

Background

As toll-like receptor 4 (TLR4) plays important roles in cellular immunity and TLR4 polymorphisms have been shown to be associated with susceptibility to a range of diseases, the present study aimed to investigate the association between TLR4 gene polymorphisms and the incidence of primary antiphospholipid syndrome (PAPS).

Methods

Two TLR4 single nucleotide polymorphisms (rs4986790 and rs4986791) were assessed in 110 subjects of Egyptian ethnicity, including 65 female patients with PAPS and 45 matched healthy controls, using polymerase chain reaction-restriction fragment length polymorphism. Results were verified using automated sequencing.

Results

The homozygous wild-type (AA, aspartic acid) rs4986790 variant and (CC, threonine) rs4986791 variant were the predominant genotypes in the control and PAPS groups.

Conclusion

The results of this preliminary study of TLR4 gene variants among patients with PAPS in an Egyptian population found no association between the rs4986790 and rs4986791 variants and susceptibility to PAPS.

HLA class II immunopeptidomics reveals that co-inherited HLA-allotypes within an extended haplotype can improve proteome coverage for immunosurveillance

Human leucocyte antigen (HLA) class II molecules in humans are encoded by three different loci, HLA-DR, -DQ, and -DP. These molecules share approximately 70% sequence similarity and all present peptide ligands to circulating T cells. While the peptide repertoires of numerous HLA-DR, -DQ, and -DP allotypes have been examined, there have been few reports on the combined repertoire of these co-inherited molecules expressed in a single cell as an extended HLA haplotype. Here we describe the endogenous peptide repertoire of a human B lymphoblastoid cell line (C1R) expressing the class II haplotype HLA-DR12/DQ7/DP4. We have identified 71350 unique naturally processed peptides presented collectively by HLA-DR12, HLA-DQ7, or HLA-DP4. The resulting "haplodome" is complemented by the cellular proteome defined by standard LC-MS/MS approaches. This large dataset has shed light on properties of these class II ligands especially the preference for membrane and extracellular source proteins. Our data also provides insights into the co-evolution of these conserved haplotypes of closely linked and co-inherited HLA molecules; which together increase sequence coverage of cellular proteins for immune surveillance with minimal overlap between each co-inherited HLA-class II allomorph.

Risk of Systemic Lupus Erythematosus in Patients With Anti-phospholipid Syndrome: A Population-Based Study

Objective: To investigate the association between anti-phospholipid syndrome (APS) and the risk of newly diagnosed systemic lupus erythematosus (SLE). Methods: We used 2003-2013 data derived from Taiwan's National Health Insurance Research Database to conduct this nationwide, population-based. We identified AS patients newly diagnosed between 2005 to 2013 as the study group and applied age-sex matched (1:20) and propensity score-matched (PSM) (1:2) non-SLE individuals as controls. The association between APS and risk of incident SLE was determined by calculating hazard ratios (HRs) with 95% confidence intervals (CIs) using Cox proportional hazard regression analysis. Results: We identified 1,245 patients with APS as well as 24,900 age- and sex-matched non-APS controls and 727 APS patients as well as 1,454 PSM non-APS controls. We found that the risk for incident SLE in the APS group was 80.70 times higher than the non-APS group, and the association remained robust after PSM (HR, 28.55; 95% CI, 11.49-70.91). The increased risk for SLE in patients with APS mainly existed within 5 years after the diagnosis of APS. The sensitivity analyses found that the risk for SLE in patients with APS was consistent excluding patients with ITP/AIHA and using distinct definitions of SLE. Conclusion: The present population-based study revealed a robust association between SLE risk and recent APS and highlights the need for vigilance of SLE-associated symptoms in patients who had been diagnosed with APS.

Thrombotic antiphospholipid syndrome: A practical guide to diagnosis and management

Thrombotic antiphospholipid syndrome (APS) is characterised by venous, arterial and/or small vessel thrombosis in the context of persistently positive antiphospholipid antibodies (aPL). The diagnosis and management of thrombotic APS continues to prove challenging for clinicians. We provide a practical guide to the diagnosis of APS including who to test for aPL and which tests to do. We also consider clinical practice points on the management of venous, arterial and small vessel thrombosis, in the context of first and recurrent thrombotic events. Non-criteria manifestations of APS are reviewed. An approach to recurrent thrombosis and anticoagulant-refractory APS is discussed, with options including increasing the anticoagulation intensity of vitamin K antagonists, switching to low-molecular-weight-heparin, the use of fondaparinux and/or the addition of antiplatelet treatment. Adjunctive options such as vitamin D, hydroxychloroquine and statins are also addressed.

Genetic Factors in Antiphospholipid Syndrome: Preliminary Experience with Whole Exome Sequencing

As in many autoimmune diseases, the pathogenesis of the antiphospholipid syndrome (APS) is the result of a complex interplay between predisposing genes and triggering environmental factors, leading to a loss of self-tolerance and immune-mediated tissue damage. While the first genetic studies in APS focused primarily on the human leukocytes antigen system (HLA) region, more recent data highlighted the role of other genes in APS susceptibility, including those involved in the immune response and in the hemostatic process. In order to join this intriguing debate, we analyzed the single-nucleotide polymorphisms (SNPs) derived from the whole exome sequencing (WES) of two siblings affected by APS and compared our findings with the available literature. We identified genes encoding proteins involved in the hemostatic process, the immune response, and the phospholipid metabolism (PLA2G6, HSPG2, BCL3, ZFAT, ATP2B2, CRTC3, and ADCY3) of potential interest when debating the pathogenesis of the syndrome. The study of the selected SNPs in a larger cohort of APS patients and the integration of WES results with the network-based approaches will help decipher the genetic risk factors involved in the diverse clinical features of APS.

Management of anticoagulant-refractory thrombotic antiphospholipid syndrome

Lifelong anticoagulation with warfarin or alternative vitamin K antagonist is the standard anticoagulant treatment for thrombotic antiphospholipid syndrome. Anticoagulant-refractory thrombotic antiphospholipid syndrome can be broadly defined as breakthrough thrombosis while on standard oral anticoagulation treatment and its management is a major challenge given the serious nature of the thrombotic disease observed, which has become refractory to oral anticoagulation. The factors (genetic and cellular) that cause anticoagulant-refractory thrombotic antiphospholipid syndrome are now better understood. However, efforts to use this greater understanding have not yet transformed the capacity to treat it successfully in many patients. In this Viewpoint, we review the factors that are likely to be contributing to the cause of this syndrome and consider how they might be modified or inhibited. We also discuss management, including general strategies to minimise thrombotic risk, intensification of anticoagulation, addition of an antiplatelet agent, adjunctive treatment for thrombosis, immunomodulatory therapy, complement inhibition, vascular options, and future potential therapeutic targets.