Low copy numbers of FCGR3A and FCGR3B associated with Chinese patients with SLE and AASV

Deciphering the Genetic Code of Autoimmune Kidney Diseases

Autoimmune kidney diseases occur due to the loss of tolerance to self-antigens, resulting in inflammation and pathological damage to the kidneys. This review focuses on the known genetic associations of the major autoimmune kidney diseases that result in the development of glomerulonephritis: lupus nephritis (LN), anti-neutrophil cytoplasmic associated vasculitis (AAV), anti-glomerular basement disease (also known as Goodpasture's disease), IgA nephropathy (IgAN), and membranous nephritis (MN). Genetic associations with an increased risk of disease are not only associated with polymorphisms in the human leukocyte antigen (HLA) II region, which governs underlying processes in the development of autoimmunity, but are also associated with genes regulating inflammation, such as NFkB, IRF4, and FC γ receptors (FCGR). Critical genome-wide association studies are discussed both to reveal similarities in gene polymorphisms between autoimmune kidney diseases and to explicate differential risks in different ethnicities. Lastly, we review the role of neutrophil extracellular traps, critical inducers of inflammation in LN, AAV, and anti-GBM disease, where inefficient clearance due to polymorphisms in DNase I and genes that regulate neutrophil extracellular trap production are associated with autoimmune kidney diseases.

Developing a non-invasive diagnostic model for pediatric Crohn's disease using RNA-seq analysis

Introduction: Pediatric Crohn's disease is a chronic inflammatory condition that affects the digestive system in children and adolescents. It is characterized by symptoms such as abdominal pain, diarrhea, weight loss, and malnutrition, and can also cause complications like growth delays and delayed puberty. However, diagnosing pediatric Crohn's disease can be difficult, especially when it comes to non-invasive methods. Methods: In this study, we developed a diagnostic model using RNA-seq to analyze gene expression in ileal biopsy samples from children with Crohn's disease and non-pediatric Crohn's controls. Results: Our results showed that pediatric Crohn's disease is associated with altered expression of genes involved in immune response, inflammation, and tissue repair. We validated our findings using two independent datasets from the Gene Expression Omnibus (GEO) database, as well as through one prospective independent dataset, and found that our model had a high accuracy rate. Discussion: These findings suggest the possibility of non-invasive diagnosis for pediatric Crohn's disease and may inform the development of targeted therapies for this condition.

Identification of novel genes in Behcet's disease using integrated bioinformatic analysis

Behcet’s disease (BD) is a chronic vascular inflammatory disease. However, the etiology and molecular mechanisms underlying BD development have not been thoroughly understood. Gene expression data for BD were obtained from the Gene Expression Omnibus database. We used robust rank aggregation (RRA) to identify differentially expressed genes (DEGs) between patients with BD and healthy controls. Gene ontology functional enrichment was used to investigate the potential functions of the DEGs. Protein–protein interaction (PPI) network analysis was performed to identify the hub genes. Receiver operating characteristic analyses were performed to investigate the value of hub genes in the diagnosis of BD. GSE17114 and GSE61399 datasets were included, comprising 32 patients with BD and 26 controls. The RRA integrated analysis identified 44 significant DEGs among the GSE17114 and GSE61399 CD4 + T lymphocytes. Functional enrichment analysis revealed that protein tyrosine/threonine phosphatase activity and immunoglobulin binding were enriched in BD. PPI analysis identified FCGR3B as a hub gene in the CD4 + T lymphocytes of BD patients. Our bioinformatic analysis identified new genetic features, which will enable further understanding of the pathogenesis of BD.

Association of BCL2 polymorphisms and the IL19 single nucleotide polymorphism rs2243188 with systemic lupus erythematosus

Objective

Abnormal B cell lymphoma-2 (Bcl-2) and interleukin-19 (IL-19) expression is closely related to systemic lupus erythematosus (SLE) pathogenesis. We aimed to determine whether BCL2 polymorphisms and a single nucleotide polymorphism (SNP) of IL19 are significantly associated with SLE susceptibility and if this is affected by synergism between IL19 and BCL2 genotypes.

Methods

This observational cohort study randomly enrolled 150 patients with SLE and 150 healthy controls. Major BCL2 and IL19 allele and genotype distributions were examined in the two groups. The IL19 SNP rs2243188 was determined using the TaqMan-MGB probe method. The synergistic effect between BCL2 and IL19 and clinical symptoms of SLE was also analyzed.

Results

The distribution of major BCL2 genotypes and common BCL2 alleles, especially for genotypes 191, 193, and 197, differed significantly between patients and controls. A significant difference in the dominant genetic model was also observed between groups, but not in the recessive model. The risk of disease in individuals who carried both 195-bp BCL2 and 138-bp IL19 susceptibility alleles was higher than in those carrying either allele alone.

Conclusions

This preliminary study suggested that BCL2 polymorphisms and the IL19 SNP rs2243188 are closely related to the pathogenesis of SLE.

Advances in the genomics of ANCA-associated vasculitis-a view from East Asia

Recent genome-wide association studies (GWAS) in populations of European ancestry have identified several susceptibility genes to anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV). The most significant association was observed in HLA-DP variants in granulomatosis with polyangiitis and proteinase 3 (PR3)-ANCA positive vasculitis, while HLA-DQ variants were strongly associated with microscopic polyangiitis (MPA) and myeloperoxidase (MPO)-ANCA positive vasculitis (MPO-AAV). In non-HLA genes, SERPINA1, PRTN3 and PTPN22 were identified as susceptibility genes to AAV. The observations in GWAS suggested the presence of shared and non-shared susceptibility genes among AAV subsets. Epidemiological features of AAV are strikingly different in the East Asian populations; the proportions of MPO-AAV among total AAV, MPO-ANCA positive patients among GPA, and patients with interstitial lung disease among total AAV are considerably higher in Japan as compared with Europe. Such population differences suggest the critical role for genetic background behind these conditions. Although no GWAS has been reported in the Asian populations so far, the association of HLA-class II alleles with MPA and MPO-AAV was identified. Future genomics studies on AAV, especially from Asian populations, will provide valuable information to elucidate the molecular mechanisms and to identify molecular targets for AAV.

Antineutrophil Cytoplasmic Antibody-Associated Vasculitis Update: Genetic Pathogenesis

Antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) is characterized by the inflammation of small and medium vessels and presence of proteinase 3-ANCA or myeloperoxidase-ANCA in the circulation. AAV comprises three clinical subtypes: granulomatosis with polyangiitis (GPA), microscopic polyangiitis (MPA), and eosinophilic GPA (EGPA). Although the pathogenesis of AAV is still unclear, genetic and environmental factors and the immune system are thought to be involved. Genetic factors have been confirmed to play an important role in AAV. Genome-wide association studies have identified numerous genetic variants in MHC and non-MHC regions associated with AAV. The strongest evidence of MHC association in AAV is human leukocyte antigen (HLA)-DP. A significant association between AAV and genetic variations in non-MHC regions, such as CTLA-4, FCGR2A, PTPN22, SERPINA1, and TLR9 has also been found. Moreover, different clinical subtypes of AAV have distinct genetic backgrounds. GPA is associated with HLA-DP1, MPA with HLA-DQ, and EGPA with HLA-DRB4. These findings could help elucidate the etiology of AAV and develop new biomarkers for diagnosis and targeted therapy. Herein, we briefly summarize the updates on the genetic pathogenesis and biomarkers of AAV.

Polymorphisms in Fc Gamma Receptors and Susceptibility to Malaria in an Endemic Population

Repeated infections by Plasmodium falciparum result in a humoral response that could reduce disease symptoms and prevent the development of clinical malaria. The principal mechanism underlying this humoral response is that immunoglobulin G (IgG) binds directly to the parasites, thus causing their neutralization. However, the action of antibodies alone is not always sufficient to eliminate pathogens from an organism. One key element involved in the recognition of IgG that plays a crucial role in the destruction of the parasites responsible for spreading malaria is the family of Fc gamma receptors. These receptors are expressed on the surface of immune cells. Several polymorphisms have been detected in the genes encoding these receptors, associated with susceptibility or resistance to malaria in different populations. In this review, we describe identified polymorphisms within the family of Fc gamma receptors and the impact of these variations on the response of a host to infection as well as provide new perspectives for the design of an effective vaccine for malaria.

Contributions of de novo variants to systemic lupus erythematosus

By performing whole-genome sequencing in a Swedish cohort of 71 parent-offspring trios, in which the child in each family is affected by systemic lupus erythematosus (SLE, OMIM 152700), we investigated the contribution of de novo variants to risk of SLE. We found de novo single nucleotide variants (SNVs) to be significantly enriched in gene promoters in SLE patients compared with healthy controls at a level corresponding to 26 de novo promoter SNVs more in each patient than expected. We identified 12 de novo SNVs in promoter regions of genes that have been previously implicated in SLE, or that have functions that could be of relevance to SLE. Furthermore, we detected three missense de novo SNVs, five de novo insertion-deletions, and three de novo structural variants with potential to affect the expression of genes that are relevant for SLE. Based on enrichment analysis, disease-affecting de novo SNVs are expected to occur in one-third of SLE patients. This study shows that de novo variants in promoters commonly contribute to the genetic risk of SLE. The fact that de novo SNVs in SLE were enriched to promoter regions highlights the importance of using whole-genome sequencing for identification of de novo variants.

Identification of differentially expressed circulating exosomal lncRNAs in IgA nephropathy patients

Background

Although immunoglobulin A nephropathy (IgAN) is one of the foremost primary glomerular disease, treatment of IgAN is still in infancy. Non-invasive biomarkers are urgently needed for IgAN diagnosis. We investigate the difference in expression profiles of exosomal long non-coding-RNAs (lncRNAs) in plasma from IgAN patients compared with their healthy first-degree relatives, which may reveal novel non-invasive IgAN biomarkers.

Methods

We isolated exosomes from the plasma of both IgAN patients and their healthy first-degree relatives. High-throughput RNA sequencing and real-time quantitative polymerase chain reaction (qRT-PCR) was used to validate lncRNA expression profiles. Pathway enrichment analysis was used to predict their nearest protein-coding genes.

Results

lncRNA-G21551 was significantly down-regulated in IgAN patients. Interestingly, the nearest protein-coding gene of lncRNA-G21551 was found to be encoding the low affinity receptor of the Fc segment of immunoglobulin G (FCGR3B).

Conclusions

Exosomal lncRNA-G21551, with FCGR3B as the nearest protein-coding gene, was down-regulated in IgAN patients, indicating its potential to serve as a non-invasive biomarker for IgAN.

Current State of Precision Medicine in Primary Systemic Vasculitides

Precision medicine (PM) is an emerging data-driven health care approach that integrates phenotypic, genomic, epigenetic, and environmental factors unique to an individual. The goal of PM is to facilitate diagnosis, predict effective therapy, and avoid adverse reactions specific for each patient. The forefront of PM is in oncology; nonetheless, it is developing in other fields of medicine, including rheumatology. Recent studies on elucidating the genetic architecture of polygenic and monogenic rheumatological diseases have made PM possible by enabling physicians to customize medical treatment through the incorporation of clinical features and genetic data. For complex inflammatory disorders, the prevailing paradigm is that disease susceptibility is due to additive effects of common reduced-penetrance gene variants and environmental factors. Efforts have been made to calculate cumulative genetic risk score (GRS) and to relate specific susceptibility alleles for use of target therapies. The discovery of rare patients with single-gene high-penetrance mutations informed our understanding of pathways driving systemic inflammation. Here, we review the advances in practicing PM in patients with primary systemic vasculitides (PSVs). We summarize recent genetic studies and discuss current knowledge on the contribution of epigenetic factors and extracellular vesicles (EVs) in disease progression and treatment response. Implementation of PM in PSVs is a developing field that will require analysis of a large cohort of patients to validate data from genomics, transcriptomics, metabolomics, proteomics, and epigenomics studies for accurate disease profiling. This multi-omics approach to study disease pathogeneses should ultimately provide a powerful tool for stratification of patients to receive tailored optimal therapies and for monitoring their disease activity.