Lupus pathobiology based on genomics

The Role of Genetic Risk Factors in Pathogenesis of Childhood-Onset Systemic Lupus Erythematosus

The pathogenesis of childhood-onset systemic lupus erythematosus (cSLE) is complex and not fully understood. It involves three key factors: genetic risk factors, epigenetic mechanisms, and environmental triggers. Genetic factors play a significant role in the development of the disease, particularly in younger individuals. While cSLE has traditionally been considered a polygenic disease, it is now recognized that in rare cases, a single gene mutation can lead to the disease. Although these cases are uncommon, they provide valuable insights into the disease mechanism, enhance our understanding of pathogenesis and immune tolerance, and facilitate the development of targeted treatment strategies. This review aims to provide a comprehensive overview of both monogenic and polygenic SLE, emphasizing the implications of specific genes in disease pathogenesis. By conducting a thorough analysis of the genetic factors involved in SLE, we can improve our understanding of the underlying mechanisms of the disease. Furthermore, this knowledge may contribute to the identification of effective biomarkers and the selection of appropriate therapies for individuals with SLE.

Panel sequencing links rare, likely damaging gene variants with distinct clinical phenotypes and outcomes in juvenile-onset SLE

OBJECTIVES

Juvenile-onset systemic lupus erythematosus (jSLE) affects 15-20% of lupus patients. Clinical heterogeneity between racial groups, age groups and individual patients suggests variable pathophysiology. This study aimed to identify highly penetrant damaging mutations in genes associated with SLE/SLE-like disease in a large national cohort (UK JSLE Cohort Study) and compare demographic, clinical and laboratory features in patient sub-cohorts with 'genetic' SLE vs remaining SLE patients.

METHODS

Based on a sequencing panel designed in 2018, target enrichment and next-generation sequencing were performed in 348 patients to identify damaging gene variants. Findings were integrated with demographic, clinical and treatment related datasets.

RESULTS

Damaging gene variants were identified in ∼3.5% of jSLE patients. When compared with the remaining cohort, 'genetic' SLE affected younger children and more Black African/Caribbean patients. 'Genetic' SLE patients exhibited less organ involvement and damage, and neuropsychiatric involvement developed over time. Less aggressive first line treatment was chosen in 'genetic' SLE patients, but more second and third line agents were used. 'Genetic' SLE associated with anti-dsDNA antibody positivity at diagnosis and reduced ANA, anti-LA and anti-Sm antibody positivity at last visit.

CONCLUSION

Approximately 3.5% of jSLE patients present damaging gene variants associated with younger age at onset, and distinct clinical features. As less commonly observed after treatment induction, in 'genetic' SLE, autoantibody positivity may be the result of tissue damage and explain reduced immune complex-mediated renal and haematological involvement. Routine sequencing could allow for patient stratification, risk assessment and target-directed treatment, thereby increasing efficacy and reducing toxicity.

Personalized Recommendation Algorithm for Movie Data Combining Rating Matrix and User Subjective Preference

The film industry has also caught the fast train of Internet development. Various movie resources have come into view. Users need to spend a lot of time searching for movies they are interested in. This method wastes time and is very bad. The article proposes an NMF personalized movie recommendation algorithm, which can recommend movies to users based on their historical behavior and preference. The research results of the article show the following: (1) the experiment counts movie reviews of different users in the same time span. The results show that 48.42% of users have only commented on a movie once, 79.76% of users have posted less than or equal to 5 comments, and 89.92% of user reviews have posted less than or equal to 10 times. (2) In the comparative experiments of the NMF algorithm in different dimensions, the effect of the NMF-E algorithm is much better than that of the NMF-A algorithm. The accuracy, recall, and F1 value of the NME-E algorithm are all 3 types. The experimental results show that the NME-E algorithm is the best among all algorithms. (3) In the experiment to test the effectiveness of the NMF personalized recommendation algorithm, comparing the experimental results, the MAE value of the improved NMF personalized recommendation algorithm is lower than that of the unimproved algorithm. When the number of neighbors is 10, the highest value of the improved MAE of the previous algorithm is 0.837. After the improved algorithm, the MAE value is the highest (0.83), and the MAE value has dropped by 0.007, indicating that the error is smaller after the improved algorithm, and the result of recommending movies is more accurate. The recall value of the four algorithms will increase as the number of neighbors increases. Among them, the recall value of the NMF algorithm proposed in the article is the highest among several algorithms. The highest value can reach 0.200, which is higher than the highest value of other algorithms. It shows that the recommendation effect of NMF algorithm is the best. (4) According to the results of the questionnaire, after using the NMF personalized recommendation algorithm, users' satisfaction increased from 20% to 50%, an increase of 30%, and their dissatisfaction decreased from 15% to 8%, a decrease of 7%. Relative satisfaction increased from 52% to 55%, an increase of 3%, satisfaction increased from 35% to 60%, an increase of 25%, and dissatisfaction decreased from 40% to 20%, a decrease of 20%, indicating that the algorithm can meet the requirements of most people.

Clinical Patterns and Morphology of COVID-19 Dermatology

Coronavirus disease 2019 (COVID-19), an emergent disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has rapidly spread throughout the globe since its discovery in December 2019. Although first appreciated to cause pneumonia, numerous organ systems are now known to be involved. The objective of this article is to review the broad spectrum of cutaneous manifestations reported in association with SARS-CoV-2 infection. The most commonly reported cutaneous manifestations associated with COVID-19 infection include pernio (chilblain)-like acral lesions, morbilliform (exanthematous) rash, urticaria, vesicular (varicella-like) eruptions, and vaso-occlusive lesions (livedo racemosa, retiform purpura). It is important to consider SARS-CoV-2 infection in the differential diagnosis of a patient presenting with these lesions in the appropriate clinical context, as cutaneous manifestations may be present in otherwise asymptomatic individuals, or present before developing other symptoms of infection. With increased access to diagnostic testing, we are beginning to understand the utility and limitations of currently available assays.

Impaired B Cell Apoptosis Results in Autoimmunity That Is Alleviated by Ablation of Btk

While apoptosis plays a role in B-cell self-tolerance, its significance in preventing autoimmunity remains unclear. Here, we report that dysregulated B cell apoptosis leads to delayed onset autoimmune phenotype in mice. Our longitudinal studies revealed that mice with B cell-specific deletion of pro-apoptotic Bim (BBimfl/fl ) have an expanded B cell compartment with a notable increase in transitional, antibody secreting and recently described double negative (DN) B cells. They develop greater hypergammaglobulinemia than mice lacking Bim in all cells and accumulate several autoantibodies characteristic of Systemic Lupus Erythematosus (SLE) and related Sjögren's Syndrome (SS) including anti-nuclear, anti-Ro/SSA and anti-La/SSB at a level comparable to NODH2h4 autoimmune mouse model. Furthermore, lymphocytes infiltrated the tissues including submandibular glands and formed follicle-like structures populated with B cells, plasma cells and T follicular helper cells indicative of ongoing immune reaction. This autoimmunity was ameliorated upon deletion of Bruton's tyrosine kinase (Btk) gene, which encodes a key B cell signaling protein. These studies suggest that Bim-mediated apoptosis suppresses and B cell tyrosine kinase signaling promotes B cell-mediated autoimmunity.

Expression of DDX11 and DNM1L at the 12p11 Locus Modulates Systemic Lupus Erythematosus Susceptibility

Objectives: This study employed genetic and functional analyses using OASIS meta-analysis of multiple existing GWAS and gene-expression datasets to identify novel SLE genes. Methods: Four hundred and ten genes were mapped using SNIPPER to 30 SLE GWAS loci and investigated for expression in three SLE GEO-datasets and the Cordoba GSE50395-dataset. Blood eQTL for significant SNPs in SLE loci and STRING for functional pathways of differentially expressed genes were used. Confirmatory qPCR on SLE monocytes was performed. The entire 12p11 locus was investigated for genetic association using two additional GWAS. Expression of 150 genes at this locus was assessed. Based on this significance, qPCRs for DNM1L and KRAS were performed. Results: Fifty genes were differentially expressed in at least two SLE GEO-datasets, with all probes directionally aligned. DDX11, an RNA helicase involved in genome stability, was downregulated in both GEO and Cordoba datasets. The most significant SNP, rs3741869 in OASIS locus 12p11.21, containing DDX11, was a cis-eQTL regulating DDX11 expression. DDX11 was found repressed. The entire 12p11 locus showed three association peaks. Gene expression in GEO datasets identified DNM1L and KRAS, besides DDX11. Confirmatory qPCR validated DNM1L as an SLE susceptibility gene. DDX11, DNM1L and KRAS interact with each other and multiple known SLE genes including STAT1/STAT4 and major components of IFN-dependent gene expression, and are responsible for signal transduction of cytokines, hormones, and growth-factors, deregulation of which is involved in SLE-development. Conclusion: A genomic convergence approach with OASIS analysis of multiple GWAS and expression datasets identified DDX11 and DNM1L as novel SLE-genes, the expression of which is altered in monocytes from SLE patients. This study lays the foundation for understanding the pathogenic involvement of DDX11 and DNM1L in SLE by identifying them using a systems-biology approach, while the 12p11 locus harboring these genes was previously missed by four independent GWAS.

COVID-19 Related Acro-Ischemic Neuropathic-like Painful Lesions in Pediatric Patients: A Case Series

BACKGROUND

A variety of skin manifestations have been associated with COVID-19 infection. Acral lesions on hands and feet, closely resembling chilblains, have been reported in association with COVID-19, which are nonspecific. These acro-ischemic painful lesions have been described mainly in asymptomatic and mildly symptomatic pediatric COVID-19 positive patients, without a precise pathogenetic mechanism. COVID-19-induced chilblains may portend an indolent course and a good outcome. In young patients, the IFN-1 response induces microangiopathic changes and produces a chilblain lupus erythematosus-like eruption with vasculitic neuropathic pain features.

OBJECTIVES

This paper presented a case series of pediatric patients with COVID-19-related skin lesions and neuropathic-like pain.

METHODS

Clinical outcomes were collected from 11 patients diagnosed with painful erythematous skin lesions with neuropathic-like pain and positive IgG for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

RESULTS

It is a mildly symptomatic condition not related to severe pain rates, and it is treated with paracetamol due to the transitory nature of the problem, which provides good results.

CONCLUSIONS

A particular point of interest is skin lesion manifestation as a further indirect sign of SARS-CoV-2 infection. Due to the initial manifestation of chilblains in pauci-symptomatic pediatric patients, they need to be immediately tested and isolated. Chilblains can be considered a clinical clue to suspect SARS-CoV-2 infection and help in early diagnosis, patient triage, and infection control.

IFN-γ Mediates the Development of Systemic Lupus Erythematosus

Objective

Systemic lupus erythematosus (SLE) is a chronic autoimmune disease that can affect all organs in the body. It is characterized by overexpression of antibodies against autoantigen. Although previous bioinformatics analyses have identified several genetic factors underlying SLE, they did not discriminate between naive and individuals exposed to anti-SLE drugs. Here, we evaluated specific genes and pathways in active and recently diagnosed SLE population.

Methods

GSE46907 matrix downloaded from Gene Expression Omnibus (GEO) was analyzed using R, Metascape, STRING, and Cytoscape to identify differentially expressed genes (DEGs), enrichment pathways, protein-protein interaction (PPI), and hub genes between naive SLE individuals and healthy controls.

Results

A total of 134 DEGs were identified, in which 29 were downregulated, whereas 105 were upregulated in active and newly diagnosed SLE cases. GO term analysis revealed that transcriptional induction of the DEGs was particularly enhanced in response to secretion of interferon-γ and interferon-α and regulation of cytokine production innate immune responses among others. KEGG pathway analysis showed that the expression of DEGs was particularly enhanced in interferon signaling, IFN antiviral responses by activated genes, class I major histocompatibility complex (MHC-I) mediated antigen processing and presentation, and amyloid fiber formation. STAT1, IRF7, MX1, OASL, ISG15, IFIT3, IFIH1, IFIT1, OAS2, and GBP1 were the top 10 DEGs.

Conclusions

Our findings suggest that interferon-related gene expression and pathways are common features for SLE pathogenesis, and IFN-γ and IFN-γ-inducible GBP1 gene in naive SLE were emphasized. Together, the identified genes and cellular pathways have expanded our understanding on the mechanism underlying development of SLE. They have also opened a new frontier on potential biomarkers for diagnosis, biotherapy, and prognosis for SLE.

Genome Variation and Precision Medicine in Systemic Lupus Erythematosus

Systemic lupus erythematosus (SLE) is a complex autoimmune disease which is facing the difficulties in treatment. Genetics play an important role in SLE. Several studies have shown that genetic factors not only affect the development of SLE, but also affect its clinical progress. In this review article, we focus on exploring the influence of genetics on different aspects of SLE pathogenesis, clinical course, and treatment and will provide some references in further precision medicine for SLE patients. The coming era of precision medicine, SLE patients will be stratified by genetic profiling. This will enable us to make more effective and precise choices of treatment plan.

Cross-Talk between Mitochondrial Dysfunction-Provoked Oxidative Stress and Aberrant Noncoding RNA Expression in the Pathogenesis and Pathophysiology of SLE

Systemic lupus erythematosus (SLE) is a prototype of systemic autoimmune disease involving almost every organ. Polygenic predisposition and complicated epigenetic regulations are the upstream factors to elicit its development. Mitochondrial dysfunction-provoked oxidative stress may also play a crucial role in it. Classical epigenetic regulations of gene expression may include DNA methylation/acetylation and histone modification. Recent investigations have revealed that intracellular and extracellular (exosomal) noncoding RNAs (ncRNAs), including microRNAs (miRs), and long noncoding RNAs (lncRNAs), are the key molecules for post-transcriptional regulation of messenger (m)RNA expression. Oxidative and nitrosative stresses originating from mitochondrial dysfunctions could become the pathological biosignatures for increased cell apoptosis/necrosis, nonhyperglycemic metabolic syndrome, multiple neoantigen formation, and immune dysregulation in patients with SLE. Recently, many authors noted that the cross-talk between oxidative stress and ncRNAs can trigger and perpetuate autoimmune reactions in patients with SLE. Intracellular interactions between miR and lncRNAs as well as extracellular exosomal ncRNA communication to and fro between remote cells/tissues via plasma or other body fluids also occur in the body. The urinary exosomal ncRNAs can now represent biosignatures for lupus nephritis. Herein, we’ll briefly review and discuss the cross-talk between excessive oxidative/nitrosative stress induced by mitochondrial dysfunction in tissues/cells and ncRNAs, as well as the prospect of antioxidant therapy in patients with SLE.

Expression of several long noncoding RNAs in peripheral blood mononuclear cells of patients with systemic lupus erythematosus

PURPOSE

Accumulating evidence has linked long noncoding RNAs (lncRNAs) to autoimmune and inflammatory disorders. This study aimed to detect the expression levels of five lncRNAs (lnc0640, lnc3643, lnc5150, lnc7514 and lncagf) in peripheral blood mononuclear cells (PBMCs) of patients with systemic lupus erythematosus (SLE), as well as their correlation with clinical and laboratory features.

MATERIALS/METHODS

We recruited 76 patients with SLE and 71 normal controls into the present study, and obtained PBMCs from the blood samples of all study subjects. Expression levels of lncRNAs were determined by quantitative real-time reverse transcription polymerase chain reaction and their associations with clinical and laboratory characteristics were analyzed.

RESULTS

Lnc5150 expression levels were statistically significantly decreased (Z=-6.016, P < 0.001) compared with normal controls. Lnc3643 levels were also statistically significantly decreased in SLE patients with proteinuria compared with those without (Z=-2.934, P = 0.003), and the lnc7514 levels were statistically significantly lower in anti-dsDNA(+) patients compared with anti-dsDNA(-) patients. The expression levels of lnc3643 were correlated with C-reactive protein and erythrocyte sedimentation rate (ESR), lnc7514 was correlated with disease activity and ESR (all P < 0.01).

CONCLUSIONS

The aberrant lncRNA expression levels and their associations with laboratory features in SLE suggest their important role in SLE pathogenesis.

Immune Profiling and Precision Medicine in Systemic Lupus Erythematosus

Systemic lupus erythematosus (SLE) is an autoimmune disorder with a wide range of clinical symptoms. Enormous progress has been made in the immunological and genetic understanding of SLE. However, the biology of disease heterogeneity in SLE has remained largely unexplored. Human immune profiling studies, helped by recent technological advances especially in single-cell and “omics” analyses, are now shedding light on the cellular and molecular basis of clinical symptoms and disease flares in individual patients. Peripheral blood immunophenotyping analysis with flow cytometry or mass cytometry are identifying responsible cell subsets and markers characteristic of disease heterogeneity. Transcriptome analysis is discovering molecular networks responsible for disease activity, disease subtype and future relapse. In this review, we summarize recent advances in the immune profiling analysis of SLE patients and discuss how they will be used for future precision medicine.

Cytosolic Genomic DNA functions as a Natural Antisense

Stress conditions such as UV irradiation, exposure to genotoxic agents, stalled DNA replication, and even tumors trigger the release of cytosolic genomic DNA (cgDNA). Classically, cgDNA induces interferon response via its binding to proteins such as STING. In this study, we found previously reported cgDNA (cg721) exists in the cytosol of the mouse cell lines, cultured under no stress conditions. The overexpression of cg721 suppressed the complementary RNA expression using strand selection and knockdown of DNA/RNA hybrid R-loop removing enzyme RNase H and three prime repair exonuclease 1 TREX1 increased the expression levels of cg721 and thus, inhibited the target Naa40 transcript, as well as protein expression, with a phenotypic effect. In addition, cgDNA was incorporated into extracellular vesicles (EVs), and the EV-derived cg721 inhibited gene expression of the acceptor cells. Thus, our findings suggest that cg721 functions as a natural antisense DNA and play a role in cell-to-cell gene regulation once it secreted outside the cell as EVs.

Lyn, Lupus, and (B) Lymphocytes, a Lesson on the Critical Balance of Kinase Signaling in Immunity

Systemic lupus erythematosus (SLE) is a progressive autoimmune disease characterized by increased sensitivity to self-antigens, auto-antibody production, and systemic inflammation. B cells have been implicated in disease progression and as such represent an attractive therapeutic target. Lyn is a Src family tyrosine kinase that plays a major role in regulating signaling pathways within B cells as well as other hematopoietic cells. Its role in initiating negative signaling cascades is especially critical as exemplified by Lyn-/- mice developing an SLE-like disease with plasma cell hyperplasia, underscoring the importance of tightly regulating signaling within B cells. This review highlights recent advances in our understanding of the function of the Src family tyrosine kinase Lyn in B lymphocytes and its contribution to positive and negative signaling pathways that are dysregulated in autoimmunity.

Novel linkage disequilibrium clustering algorithm identifies new lupus genes on meta-analysis of GWAS datasets

Systemic lupus erythematosus (SLE) is a complex disorder. Genetic association studies of complex disorders suffer from the following three major issues: phenotypic heterogeneity, false positive (type I error), and false negative (type II error) results. Hence, genes with low to moderate effects are missed in standard analyses, especially after statistical corrections. OASIS is a novel linkage disequilibrium clustering algorithm that can potentially address false positives and negatives in genome-wide association studies (GWAS) of complex disorders such as SLE. OASIS was applied to two SLE dbGAP GWAS datasets (6077 subjects; ∼0.75 million single-nucleotide polymorphisms). OASIS identified three known SLE genes viz. IFIH1, TNIP1, and CD44, not previously reported using these GWAS datasets. In addition, 22 novel loci for SLE were identified and the 5 SLE genes previously reported using these datasets were verified. OASIS methodology was validated using single-variant replication and gene-based analysis with GATES. This led to the verification of 60% of OASIS loci. New SLE genes that OASIS identified and were further verified include TNFAIP6, DNAJB3, TTF1, GRIN2B, MON2, LATS2, SNX6, RBFOX1, NCOA3, and CHAF1B. This study presents the OASIS algorithm, software, and the meta-analyses of two publicly available SLE GWAS datasets along with the novel SLE genes. Hence, OASIS is a novel linkage disequilibrium clustering method that can be universally applied to existing GWAS datasets for the identification of new genes.