Common genetic factors among autoimmune diseases

Enhanced TLR7-dependent production of type I interferon by pDCs underlies pandemic chilblains

Outbreaks of chilblains were reported during the COVID-19 pandemic. Given the essential role of type I interferon (I-IFN) in protective immunity against SARS-CoV-2 and the association of chilblains with inherited type I interferonopathies, we hypothesized that excessive I-IFN responses to SARS-CoV-2 might underlie the occurrence of chilblains in this context. We identified a transient I-IFN signature in chilblain lesions, accompanied by an acral infiltration of activated plasmacytoid dendritic cells (pDCs). Patients with chilblains were otherwise asymptomatic or had mild disease without seroconversion. Their leukocytes produced abnormally high levels of I-IFN upon TLR7 stimulation with agonists or ssRNA viruses-particularly SARS-CoV-2-but not with DNA agonists of TLR9 or the dsDNA virus HSV-1. Moreover, the patients' pDCs displayed cell-intrinsic hyperresponsiveness to TLR7 stimulation regardless of TLR7 levels. Inherited TLR7 or I-IFN deficiency confers a predisposition to life-threatening COVID-19. Conversely, our findings suggest that enhanced TLR7 activity in predisposed individuals could confer innate, pDC-mediated, sterilizing immunity to SARS-CoV-2 infection, with I-IFN-driven chilblains as a trade-off.

Molecular mimicry in the pathogenesis of autoimmune rheumatic diseases

Autoimmune rheumatic diseases (ARDs) are a heterogeneous group of conditions characterized by excessive and misdirected immune responses against the body's own musculoskeletal tissues. Their exact aetiology remains unclear, with genetic, demographic, behavioural and environmental factors implicated in disease onset. One prominent hypothesis for the initial breach of immune tolerance (leading to autoimmunity) is molecular mimicry, which describes structural or sequence similarities between human and microbial proteins (mimotopes). This similarity can lead to cross-reactive antibodies and T-cell receptors, resulting in an immune response against autoantigens. Both commensal microbes in the human microbiome and pathogens can trigger molecular mimicry, thereby potentially contributing to the onset of ARDs. In this review, we focus on the role of molecular mimicry in the onset of rheumatoid arthritis and systemic lupus erythematosus. Moreover, implications of molecular mimicry are also briefly discussed for ankylosing spondylitis, systemic sclerosis and myositis.

Cardiovascular Health, Genetic Susceptibility, and the Risk of Incident Autoimmune Disorders in the UK Biobank: A Prospective Cohort Study

BACKGROUND

Autoimmune diseases are closely linked to cardiovascular diseases. This study aimed to assess the relationship between cardiovascular health (CVH) defined by Life's Essential 8 (LE8), genetic predisposition, and the risk of 19 autoimmune disorders.

METHODS AND RESULTS

A total of 247 660 participants without prior autoimmune diseases from the UK Biobank were included. CVH was assessed using LE8 scores, categorized into low, moderate, and high. Cox proportional hazards models estimated the association between CVH, genetic susceptibility, and autoimmune disorder risk. Over 13.2 years of follow-up, 11 422 incident autoimmune disorders occurred. Higher CVH levels were associated with reduced risks of overall autoimmune disorders (hazard ratio, 0.68 [95% CI, 0.62-0.74]) and specific conditions, including Graves disease, inflammatory bowel disease, polymyalgia rheumatica, psoriasis, rheumatoid arthritis, and type 1 diabetes. Dose-response analyses revealed a linear negative relationship between continuous LE8 scores and the risks of Graves disease, inflammatory bowel disease, polymyalgia rheumatica, psoriasis, rheumatoid arthritis, and type 1 diabetes (Pnonlinear>0.05). Genetic predisposition to autoimmune disorders (including ankylosing spondylitis, celiac disease, Graves disease, inflammatory bowel disease, polymyalgia rheumatica, psoriasis, rheumatoid arthritis, Sjögren syndrome, systemic lupus erythematosus, systemic sclerosis, and type 1 diabetes) significantly modified these associations (Pinteraction<0.05), with protective effects more pronounced in women, participants aged <65 years, and those with low genetic risk.

CONCLUSIONS

LE8 scores inversely and linearly predicted autoimmune disease incidence. Prioritizing CVH optimization through LE8 adherence may reduce the global autoimmune disease burden.

Target-specific high-throughput screening of anti-inflammatory phytosteroids for autoimmune diseases: A molecular docking-dynamics simulation approach

Without proper pathophysiology and recommended therapy, synthetic steroids are widely used as a first-line option for the management of autoimmune diseases. However, their prolonged use often leads to severe side effects such as osteoporosis, hypertension, cardiovascular, gastrointestinal complications, etc. To search for potential and safer therapeutic options, the present study aims to explore the potency and drug-ability profiles of anti-inflammatory phytosteroids (PSs). In a target-specific approach, we have selected three key molecular targets: glucocorticoid receptor/GR (PDB ID: 4P6W), cyclooxygenase-2/COX2 (PDB ID: 5F1A), and inducible nitric oxide synthase/iNOS (PDB ID: 4NOS) for a docking study of 167) selected PSs. The drug-chemistry profiles (physicochemical, toxicity, pharmacokinetic, drug-ability, etc.) of PSs were also assessed using various bioinformatics and chemoinformatics tools. The above assessment suggested that withaminilide B (PS46) is a lead candidate with higher drug-ability properties. Further, the drug stability and kinetic behaviour of the lead with the GR target 'GR-withaminilide B' in comparison with the control drug, 'GR-triamcinolone acetonide' docking complex, were studied through molecular dynamics (MD) simulation at 200 nanosecond with free energy calculation (MM/PBSA). Overall findings suggested that PSs exhibit distinct drug-ability profiles based on their functional attachments with a steroidal core moiety, where withaminilide B is a lead PSs among all to be used as alternative/ complementary candidates expected with limited adverse effects. Further experimentation is essential before mainstream application, but the study provided a platform to select drug-able candidates with a higher chance of experimental success and accelerate the drug discovery process within limited resources.

Coevolutionary interplay: Helminths-trained immunity and its impact on the rise of inflammatory diseases

The gut biome, a complex ecosystem of micro- and macro-organisms, plays a crucial role in human health. A disruption in this evolutive balance, particularly during early life, can lead to immune dysregulation and inflammatory disorders. 'Biome repletion' has emerged as a potential therapeutic approach, introducing live microbes or helminth-derived products to restore immune balance. While helminth therapy has shown some promise, significant challenges remain in optimizing clinical trials. Factors such as patient genetics, disease status, helminth species, and the optimal timing and dosage of their products or metabolites must be carefully considered to train the immune system effectively. We aim to discuss how helminths and their products induce trained immunity as prospective to treat inflammatory and autoimmune diseases. The molecular repertoire of helminth excretory/secretory products (ESPs), which includes proteins, peptides, lipids, and RNA-carrying extracellular vesicles (EVs), underscores their potential to modulate innate immune cells and hematopoietic stem cell precursors. Mimicking natural delivery mechanisms like synthetic exosomes could revolutionize EV-based therapies and optimizing production and delivery of ESP will be crucial for their translation into clinical applications. By deciphering and harnessing helminth-derived products' diverse modes of action, we can unleash their full therapeutic potential and pave the way for innovative treatments.

Pharmacotherapeutic strategies to promote regulatory T cell function in autoimmunity

Autoimmune diseases arise when self-antigen-specific T and B cells escape central and peripheral mechanisms of tolerance. One such mechanism is control of autoreactivity by regulatory T cells (Tregs), which have an essential role in suppressing autoimmunity. Consequently, there is significant interest in developing ways to boost or restore the function of Tregs in order to prevent or treat autoimmunity, induce tolerance, and thus reduce the reliance on broadly immunosuppressive agents. Strategies include enhancing the numbers and/or function of Tregs directly in vivo or via adoptive cell therapy. Here, we review recent advances in our understanding of how pharmacologic approaches can be applied to enhance Treg function in vivo through repurposing of established drug therapies or application of new therapies. Specifically, we discuss the potential of Treg-promoting drugs, including interleukin-2 and its derivatives, and tumor necrosis factor receptor 2 agonists, as well as Treg-preserving tyrosine kinase 2 inhibitors. We discuss how co-stimulatory blockade with CTLA-4 immunoglobulin affects tolerogenic environments and consider whether lymphodepleting therapies, such as antithymocyte globulin and teplizumab, might be needed to condition the environment for better Treg-promoting effects. We focus on the potential application of Treg-promoting drugs in type 1 diabetes and draw on evidence from transplantation. With multiple pharmacotherapeutic strategies to optimize Tregs in vivo, there is significant promise for new approaches to effectively and durably induce autoimmune disease remission.

Environmental factors and rheumatic diseases

The pathogenesis and pathophysiology of rheumatic diseases is complex and relies on the interaction of different factors. The common view is that the pathological autoimmunity develops in genetically predisposed individuals upon exposure to an environmental trigger. This highlights the importance of recognizing and deconstructing the effects of environmental agents in rheumatic diseases. Several factors have been identified in the last decades, with detrimental or protective effects, impacting not only on disease onset, but also on its natural history. Cigarette smoking has been identified as one of the strongest environmental risk factors, being associated with disease development and severity for several rheumatic diseases, including rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), and spondyloarthropathies. Moreover, other airborne pollutants, such as silica, solvents, asbestos and metals are recognized risk factors for rheumatic diseases. The effect of some other agents is however not straightforward, of which a remarkable example is alcohol consumption. Alcohol has been associated with both pro- and anti-inflammatory effects, exerting a variable effect on rheumatic diseases depending on quantity and frequency of consumption, as well as sex and ethnicity. Similarly, ultraviolet light exposure has been associated with a higher risk of SLE but lower risk of RA. The relationship between microbial exposure and autoimmunity is also complex: while some infectious agents increase the risk of rheumatic diseases, it is widely accepted that less exposure to microbial agents, particularly during immune system development, increases the risk of autoimmunity. Furthermore, in recent years the spotlight has switched to the human microbiome, as alterations in organ-specific microbiome composition are anticipated to be early participants in the onset of immune-mediated illnesses. The aim of this review is to highlight the most relevant environmental factors and their role in Rheumatology, with a specific focus on proposed pathophysiological effect and correlation with clinical outcomes.

Exploring bidirectional causal relationships between antibody-mediated immune responses to infectious agents and systemic lupus erythematosus through Mendelian randomization and meta-analyses

BACKGROUND

Previous investigations into the causal relationship between infections and systemic lupus erythematosus (SLE) have yielded controversial results. This study delves into the bidirectional causal relationships between various infectious agents and SLE, employing two-sample Mendelian randomization (MR) from an immunological perspective.

METHODS

Utilizing genome-wide association study (GWAS) data for 46 antibody-mediated immune responses (AMIRs) to 13 pathogens and three distinct SLE datasets, we employed Bayesian Weighted MR (BWMR) and inverse variance weighted (IVW) methods to ascertain causal links, supplemented by meta-analysis to resolve inconsistencies. Sensitivity was evaluated using complementary methodologies. Genes mapped by instrumental variables (IVs) of each significant phenotype were further analyzed using summary-data-based MR (SMR).

RESULTS

Meta-analysis of forward MR results suggested a protective role of elevated antibody levels against Epstein-Barr virus (EBV) antigens EBNA-1 (IVW: OR = 0.70, 95 % CI = 0.60-0.83, p < 0.001) and ZEBRA (IVW: OR = 0.72, 95 % CI = 0.53-0.97, p < 0.05) in SLE. Conversely, reverse MR indicated positive correlations between SLE and antibodies to Chlamydia trachomatis pGP3 (IVW: OR = 1.03, 95 % CI = 1.01-1.06, p < 0.01) and human herpesvirus 7 (HHV-7) U14 (IVW: OR = 1.03, 95 % CI = 1.01-1.06, p < 0.05), along with negative correlations with antibodies to Helicobacter pylori GroEL (IVW: OR = 0.96, 95 % CI = 0.92-0.99, p < 0.05), varicella-zoster virus (VZV) glycoproteins E and I (IVW: OR = 0.98, 95 % CI = 0.98-0.99, p < 0.001), and polyomavirus BKV IgG (IVW: OR = 0.92, 95 % CI = 0.88-0.95, p < 0.001). Additionally, SLE-associated genes were enriched in pathways such as the response to muramyl dipeptide (MDP), with seven genes showing significant causal relationships with AMIRs according to SMR analysis.

CONCLUSIONS

Our findings do not support that antibody response to infections increase the risk of SLE. Rather, SLE itself influences antibody response to infections. These insights provide a deeper understanding of the interplay between infectious pathogens and SLE and may guide future preventive and therapeutic strategies.

Mesenchymal Stromal Cell-Based Therapy: A Promising Approach for Autoimmune Diseases

Autoimmune diseases are characterized by immune dysregulation, resulting in aberrant reactivity of T cells and antibodies to self-antigens, leading to various patterns of inflammation and organ dysfunction. However, current therapeutic agents exhibit broad-spectrum activity and lack disease-specific selectivity, leading to enduring adverse effects, notably severe infections, and malignancies, and patients often fail to achieve the intended clinical goals. Mesenchymal stromal cells (MSCs) are multipotent stromal cells that can be easily derived from various tissues, such as adipose tissue, umbilical cords, Wharton's jelly, placenta, and dental tissues. MSCs offer advantages due to their immunomodulatory and anti-inflammatory abilities, low immunogenicity, and a high capacity for proliferation and multipotent differentiation, making them excellent candidates for cell-based treatment in autoimmune disorders. This review will cover preclinical studies and clinical trials involving MSCs in autoimmune diseases, as well as the primary challenges associated with the clinical application of MSC therapies and strategies for maximizing their therapeutic potential.

The cryptic immunopeptidome in health and disease

Peptides presented by MHC proteins regulate all aspects of T cell biology. These MHC-associated peptides (MAPs) form what is known as the immunopeptidome and their comprehensive analysis has catalyzed the burgeoning field of immunopeptidomics. Advances in mass spectrometry (MS) and next-generation sequencing have facilitated significant breakthroughs in this area, some of which are highlighted in this article on the cryptic immunopeptidome. Here, 'cryptic' refers to peptides and proteins encoded by noncanonical open reading frames (ORFs). Cryptic MAPs derive mainly from short unstable proteins found in normal, infected, and neoplastic cells. Cryptic MAPs show minimal overlap with cryptic proteins found in whole-cell extracts. In many cancer types, most cancer-specific MAPs are cryptic.

Causal relationships between air pollution and common autoimmune diseases: a two-sample Mendelian randomization study

Air pollution is strongly associated with autoimmune diseases (ADs), however, the genetic causality between them remains poorly understood. Therefore, the aim of this study is to determine the relationship between common air pollutants and ADs through Mendelian randomization (MR) analysis. We conducted a MR study using aggregated data from publicly available genome-wide association studies (GWAS). Single nucleotide polymorphisms (SNPs) associated with 5 common air pollutants are used as instrumental variables. Random-effects inverse variance weighted (IVW) is used as the primary method to assess causal relationships, with results reported in terms of odds ratios (OR). In addition, we used a two-step MR to assess the mediating role of common risk factors for ADs in the effects of air pollution on ADs. Our analysis revealed causal associations between selected air pollutants and specific ADs. Exposure to nitrogen oxides was positively associated with the risk of rheumatoid arthritis (RA) (OR = 1.47,95% CI 1.01-2.14, P = 0.043), Sjogren's syndrome (SS) (OR = 2.29,95% CI 1.08-4.89, P = 0.032), and systemic lupus erythematosus (OR = 7.26,95% CI 2.25-23.40, P = 9.10E-04). Genetically predicted PM2.5 and PM10 were risk factors for ulcerative colitis (OR = 1.68,95% CI 1.05-2.68, P = 0.032) and psoriasis (OR = 1.34,95% CI 1.02-1.76, P = 0.037), respectively. Our results also suggest a negative causal relationship between PM2.5-10 and SS (OR = 0.29, 95% CI 0.10-0.90, P = 0.032). In risk factor-related mediation analyses, BMI and smoking mediated 6% (95% CI 1-10%) and 9% (95% CI 2-17%) of the effect of nitrogen oxides on RA, respectively. This study provides evidence of a causal relationship between air pollutants and specific ADs risks, suggesting that improving air pollution may be important in preventing ADs.

Advances and applications in single-cell and spatial genomics

The applications of single-cell and spatial technologies in recent times have revolutionized the present understanding of cellular states and the cellular heterogeneity inherent in complex biological systems. These advancements offer unprecedented resolution in the examination of the functional genomics of individual cells and their spatial context within tissues. In this review, we have comprehensively discussed the historical development and recent progress in the field of single-cell and spatial genomics. We have reviewed the breakthroughs in single-cell multi-omics technologies, spatial genomics methods, and the computational strategies employed toward the analyses of single-cell atlas data. Furthermore, we have highlighted the advances made in constructing cellular atlases and their clinical applications, particularly in the context of disease. Finally, we have discussed the emerging trends, challenges, and opportunities in this rapidly evolving field.

Rapid prediction of acute thrombosis via nanoengineered immunosensors with unsupervised clustering for multiple circulating biomarkers

The recent SARS-CoV-2 pandemic underscores the need for rapid and accurate prediction of clinical thrombotic events. Here, we developed nanoengineered multichannel immunosensors for rapid detection of circulating biomarkers associated with thrombosis, including C-reactive protein (CRP), calprotectin, soluble platelet selectin (sP-selectin), and D-dimer. We fabricated the immunosensors using fiber laser engraving of carbon nanotubes and CO2 laser cutting of microfluidic channels, along with the electrochemical deposition of gold nanoparticles to conjugate with biomarker-specific aptamers and antibody. Using unsupervised clustering based on four biomarker concentrations, we predicted thrombotic events in 49 of 53 patients. The four-biomarker combination yielded an area under the receiver operating characteristic curve (AUC) of 0.95, demonstrating high sensitivity and specificity for acute thrombosis prediction compared to the AUC values for individual biomarkers: CRP (0.773), calprotectin (0.711), sP-selectin (0.683), and D-dimer (0.739). Thus, a nanoengineered multichannel platform with unsupervised clustering provides accurate and efficient methods for predicting thrombosis, guiding personalized medicine.

Genetically predicted metabolite mediates the causal relationship between immune cells and autoimmune diseases

BACKGROUND

This study investigates the causal role of metabolites mediating immune cells in rheumatoid arthritis (RA) and ankylosing spondylitis (AS) through a Mendelian randomization (MR) study.

METHODS

The two-sample and two-step MR methods were used for the current analysis: (1) causal effects of immune cells on RA and AS; (2) mediation effects of metabolites. Inverse variance weighted (IVW) is the main method to analyze causality, and MR results are verified by several sensitive analyses.

RESULTS

This study first identified the immune cells and metabolites that are causally associated with RA and AS, respectively. Subsequent mediation analyses revealed that of the 61 metabolic factors that were causally associated with RA, 6 were identified as mediators of the relationship between immune cells and RA, including 4-cholesten-3-one levels (mediation ratio: 8.91%), N-lactoyl isoleucine levels (13%), 3- phosphoglycerate to glycerate ratio (12.9%, 2.31%, respectively), Gamma-glutamyl histidine levels (9.54%), and Citrulline to phosphate ratio (15.6%). Among the 52 metabolic factors that were causally associated with AS, 2 were identified as mediators of the relationship between immune cells and AS, including salicylate levels (10.4%) and Glucose to N-palmitoyl-sphingosine (d18:1 to 16:0) ratio (8.72%). These results performed well in sensitivity analysis.

CONCLUSIONS

Genetic predictions show causal relationships between immune cells and autoimmune diseases, and that these causal relationships can be mediated by certain metabolites as mediators.

miR-147-3p in pathogenic CD4 T cells controls chemokine receptor expression for the development of experimental autoimmune diseases

Incomplete Freund's adjuvant (IFA) has long been used to trigger autoimmune diseases in animal models, such as experimental autoimmune encephalitis and collagen-induced arthritis. However, the molecular mechanisms that control CD4 T cell effector functions and lead to the development of autoimmune diseases are not well understood. A self-antigen and heat-killed Mycobacterium tuberculosis emulsified in IFA augmented the activation of CD4 T cells, leading to the differentiation of pathogenic CD4 T cells in the draining lymph nodes. In contrast, IFA emulsification did not elicit Foxp3+ regulatory T cell expansion. We found that pathogenic Th1 cells expressed miR-147-3p, which targets multiple genes to affect T cell function. Finally, miR-147-3p expressed in CXCR6+SLAMF6- Th1 cells was required for the onset of neurological symptoms through the control of CXCR3 expression. Our findings demonstrate that miR-147-3p expressed in pathogenic CD4 T cells regulates the migratory potential in peripheral tissues and impacts the development of autoimmune diseases.

Autoimmune Disease is Increased in Women with Primary Ovarian Insufficiency

CONTEXT

Autoimmune disease is common in women with primary ovarian insufficiency (POI) and the genetic etiology of autoimmune disease suggests that it could be hereditary in families of women with POI.

OBJECTIVE

We hypothesized that a subset of women with POI and their family members would have increased risk for autoimmune disorders.

DESIGN

Population-based study using electronic health records from 1995-2022.

SETTING

Two major Utah healthcare systems serving 85% of the state.

SUBJECTS

Women with POI (n=610) were identified using ICD codes and chart reviewed for accuracy. First-, second-, and third-degree relatives were identified using genealogy data in the Utah Population Database.

INTERVENTION

Autoimmune diagnoses were identified using ICD codes.

MAIN OUTCOME MEASURES

The relative risk of autoimmune disease in women with POI and relatives was estimated by comparison to population rates.

RESULTS

At least one autoimmune disease was identified in 25% of women with POI. The relative risk of autoimmune hypothyroidism (OR [95%CI] 6.88 [5.71, 8.22]; p<0.001), adrenal insufficiency (4.72 [1.73, 10.28]; p=0.0020), type 1 diabetes (4.13 [2.14, 7.22]; p=5.25X10-5), rheumatoid arthritis (5.66 [3.10, 9.50]; p=3.70X10-7), vitiligo (15.33 [6.16, 31.58]; p=5.25X10-7), celiac disease (7.58 [3.47, 14.39]; p=4.47X10-6), psoriasis (3.90 [2.01, 6.81]; p=9.04X10-5) and systemic lupus erythematosus (4.43 [1.63, 9.64]; p=0.0027) were increased in women with POI compared to population rates. There was no increased risk of autoimmune disease in family members.

CONCLUSIONS

Data confirm increased autoimmune disease in women with POI. The increased risk is largely related to autoimmune polyglandular syndrome types 1 through 4 and autoimmune hypothyroidism. The absence of risk in family members may result from differences in environmental influences or hormone milieu.

Leveraging pleiotropy identifies common-variant associations with selective IgA deficiency

Selective IgA deficiency (SIgAD) is the most common inborn error of immunity (IEI). Unlike many IEIs, evidence of a role for highly penetrant rare variants in SIgAD is lacking. Previous SIgAD studies have had limited power to identify common variants due to their small sample size. We overcame this problem first through meta-analysis of two existing GWAS. This identified four novel common-variant associations and enrichment of SIgAD-associated variants in genes linked to Mendelian IEIs. SIgAD showed evidence of shared genetic architecture with serum IgA and a number of immune-mediated diseases. We leveraged this pleiotropy through the conditional false discovery rate procedure, conditioning our SIgAD meta-analysis on large GWAS of asthma and rheumatoid arthritis, and our own meta-analysis of serum IgA. This identified an additional 18 variants, increasing the number of known SIgAD-associated variants to 27 and strengthening the evidence for a polygenic, common-variant aetiology for SIgAD.

Two-Sample Mendelian Randomization Study Identifies Tissue-Dependent Risk Genes in Autoimmune Diseases

Autoimmune diseases are among the most prevalent diseases across the world with genetic and environmental factors that contribute to their etiology. Because the exact causes of autoimmune diseases are largely unknown, a Mendelian randomization (MR) approach is used here to examine the potential causal association between gene expression levels and disease risk across various tissues. Specifically, this study focuses on six autoimmune diseases including Crohn's disease, ulcerative colitis, rheumatoid arthritis, multiple sclerosis, type 1 diabetes mellitus, and systemic lupus erythematosus. Several of these diseases are currently treatable with immunosuppressants that target specific genes, such as TNF-alpha, IL-23, CD20, and more. In this study, a two-sample MR analysis is performed with multitissue expression quantitative trait loci (eQTLs) and large-scale genome-wide association studies to investigate how gene expression can influence the risk of developing these diseases. Our results show that genes HLA-DQA1/2, HLA-DRB1/6, HLA-DQB2, C4A, CYP21A2, and HLA-DQB1-AS1 have a high causal effect across several diseases and tissues, and almost all of these findings originate from the major histocompatibility complex (MHC) region on Chromosome 6. Our findings support the current knowledge of genes associated with these diseases while also revealing novel genes that can be used for drug therapies in the future. Although several drug therapies currently exist to treat this selection of autoimmune diseases, we provide further insights into the main, common pathways responsible for autoimmune disease pathogenesis and discuss novel genes that lack research focus.

Special Issue "Advances in Molecular Research on Autoimmune Diseases"

Autoimmune diseases represent a diverse array of disorders in which the immune system mistakenly attacks the body's own cells and tissues [...].

Advances in the study of artemisinin and its derivatives for the treatment of rheumatic skeletal disorders, autoimmune inflammatory diseases, and autoimmune disorders: a comprehensive review

Artemisinin and its derivatives are widely recognized as first-line treatments for malaria worldwide. Recent studies have demonstrated that artemisinin-based antimalarial drugs, such as artesunate, dihydroartemisinin, and artemether, not only possess excellent antimalarial properties but also exhibit antitumor, antifungal, and immunomodulatory effects. Researchers globally have synthesized artemisinin derivatives like SM735, SM905, and SM934, which offer advantages such as low toxicity, high bioavailability, and potential immunosuppressive properties. These compounds induce immunosuppression by inhibiting the activation of pathogenic T cells, suppressing B cell activation and antibody production, and enhancing the differentiation of regulatory T cells. This review summarized the mechanisms by which artemisinin and its analogs modulate excessive inflammation and immune responses in rheumatic and skeletal diseases, autoimmune inflammatory diseases, and autoimmune disorders, through pathways including TNF, Toll-like receptors, IL-6, RANKL, MAPK, PI3K/AKT/mTOR, JAK/STAT, and NRF2/GPX4. Notably, in the context of the NF-κB pathway, artemisinin not only inhibits NF-κB expression by disrupting upstream cascades and/or directly binding to NF-κB but also downregulates multiple downstream genes controlled by NF-κB, including inflammatory chemokines and their receptors. These downstream targets regulate various immune cell functions, apoptosis, proliferation, signal transduction, and antioxidant responses, ultimately intervening in systemic autoimmune diseases and autoimmune responses in organs such as the kidneys, nervous system, skin, liver, and biliary system by modulating immune dysregulation and inflammatory responses. Ongoing multicenter randomized clinical trials are investigating the effects of these compounds on rheumatic, inflammatory, and autoimmune diseases, with the aim of translating promising preclinical data into clinical applications.

Pioneering discovery and therapeutics at the brain-vascular-immune interface

The brain-vascular-immune interface has emerged as a dynamic player in brain physiology and disease. We propose integrating vascular risk factors with genetic susceptibility as the nexus for the discovery of mechanisms and therapies for neuroinflammation, neurodegeneration, and neurorepair across polygenic neurologic diseases.

Periodontal disease: A systemic condition

For decades, periodontitis has been considered to be a local inflammatory disease of the periodontal tissues in the oral cavity. Initially, associations of periodontitis with a multitude of noncommunicable diseases were each studied separately, and relationships were shown. The associations of periodontitis with morbidities, such as cardiovascular diseases, rheumatoid arthritis, diabetes mellitus, respiratory diseases, have been demonstrated. As most such studies were cross-sectional in nature, questions about causality cannot be univocally answered. And periodontitis as an independent risk factor for one systemic disease, becomes even more difficult to assess since recently periodontitis has also been associated with multimorbidity. Periodontitis and many systemic diseases share environmental, lifestyle and genetic risk factors, and share immunopathology. Moreover, suffering from one common noncommunicable disease may increase the susceptibility for another such chronic disease; the systemic effects of one condition may be one of various risk factors for another such disease. The overarching effect of any systemic disease is it causing a pro-inflammatory state in the individual; this has also been shown for periodontitis. Moreover, in periodontitis a prothrombotic state and elevated immunological activity have been shown. As such, when we consider periodontal disease as another systemic disease, it can affect the susceptibility and progression of other systemic diseases, and importantly, vice versa. And with this, it is not surprising that periodontitis is associated with a variety of other noncommunicable diseases. The medical definition of a systemic disease includes diseases that affect different organs and systems. Thus, the aim of this opinion paper is to propose that periodontitis should be considered a systemic disease in its own right and that it affects the individual's systemic condition and wellbeing. The dental and medical profession and researchers alike, should adapt this paradigm shift, advancing periodontal disease out of its isolated anatomical location into the total of chronic noncommunicable diseases, being for some conditions a comorbid disease and, vice versa, comorbidities can affect initiation and progression of periodontal disease.

Tridecylcyclohexane in incomplete Freund's adjuvant is a critical component in inducing experimental autoimmune diseases

Incomplete Freund's adjuvant (IFA) has been used for many years to induce autoimmune diseases in animal models, including experimental autoimmune encephalitis and collagen-induced arthritis. However, it remains unclear why it is necessary to emulsify autoantigen and heat-killed Mycobacterium tuberculosis (HKMtb) with IFA to induce experimental autoimmune diseases. Here, we found that immunization with self-antigen and HKMtb was insufficient to induce autoimmune diseases in mice. Furthermore, IFA or one of its components, mineral oil, but not mannide monooleate, was required for the development of experimental autoimmune disease. Immunization with autoantigen and HKMtb emulsified in mineral oil facilitated innate immune activation and promoted the differentiation of pathogenic CD4+ T cells, followed by their accumulation in neuronal tissues. Several water-soluble hydrocarbon compounds were identified in mineral oil. Of these, immunization with HKMtb and autoantigen emulsified with the same amount of hexadecane or tridecylcyclohexane as mineral oil induced the development of experimental autoimmune encephalitis. In contrast, immunization with HKMtb and autoantigen emulsified with tridecylcyclohexane, but not hexadecane, at doses equivalent to those found in mineral oil, resulted in neuronal dysfunction. These data indicate that tridecylcyclohexane in mineral oil is a critical component in the induction of experimental autoimmune disease.

Epidemiologic and genetic associations between primary biliary cholangitis and extrahepatic rheumatic diseases

Patients with primary biliary cholangitis (PBC) commonly experience extrahepatic rheumatic diseases. However, the epidemiologic and genetic associations as well as causal relationship between PBC and these extrahepatic conditions remain undetermined. In this study, we first conducted systematic review and meta-analyses by analyzing 73 studies comprising 334,963 participants across 17 countries and found strong phenotypic associations between PBC and rheumatic diseases. Next, we utilized large-scale genome-wide association study summary data to define the shared genetic architecture between PBC and rheumatic diseases, including rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), systemic sclerosis (SSc) and Sjögren's syndrome (SS). We observed significant genetic correlations between PBC and each of the four rheumatic diseases. Pleiotropy and heritability enrichment analysis suggested the involvement of humoral immunity and interferon-associated processes for the comorbidity. Of note, we identified four variants shared between PBC and RA (rs80200208), SLE (rs9843053), and SSc (rs27524, rs3873182) using cross-trait meta-analysis. Additionally, several pleotropic loci for PBC and rheumatic diseases were found to share causal variants with gut microbes possessing immunoregulatory functions. Finally, Mendelian randomization revealed consistent evidence for a causal effect of PBC on RA, SLE, SSc, and SS, but no or inconsistent evidence for a causal effect of extrahepatic rheumatic diseases on PBC. Our study reveals a profound genetic overlap and causal relationships between PBC and extrahepatic rheumatic diseases, thus providing insights into shared biological mechanisms and novel therapeutic interventions.

Exploring the HLA complex in autoimmunity: From the risk haplotypes to the modulation of expression

The genes mapping at the HLA region show high density, strong linkage disequilibrium and high polymorphism, which affect the association of HLA class I and class II genes with autoimmunity. We focused on the HLA haplotypes, genomic structures consisting of an array of specific alleles showing some degrees of genetic association with different autoimmune disorders. GWASs in many pathologies have identified variants in either the coding loci or the flanking regulatory regions, both in linkage disequilibrium in haplotypes, that are frequently associated with increased risk and may influence gene expression. We discuss the relevance of the HLA gene expression because the level of surface heterodimers determines the number of complexes presenting self-antigen and, thus, the strength of pathogenic autoreactive T cells immune response.

Identification of common genetic factors and immune-related pathways associating more than two autoimmune disorders: implications on risk, diagnosis, and treatment

Autoimmune disorders (ADs) are chronic conditions resulting from failure or breakdown of immunological tolerance, resulting in the host immune system attacking its cells or tissues. Recent studies report shared effects, mechanisms, and evolutionary origins among ADs; however, the possible factors connecting them are unknown. This study attempts to identify gene signatures commonly shared between different autoimmune disorders and elucidate their molecular pathways linking the pathogenesis of these ADs using an integrated gene expression approach. We employed differential gene expression analysis across 19 datasets of whole blood/peripheral blood cell samples with five different autoimmune disorders (rheumatoid arthritis, multiple sclerosis, systemic lupus erythematosus, Crohn's disease, and type 1 diabetes) to get nine key genes-EGR1, RUNX3, SMAD7, NAMPT, S100A9, S100A8, CYBB, GATA2, and MCEMP1 that were primarily involved in cell and leukocyte activation, leukocyte mediated immunity, IL-17, AGE-RAGE signaling in diabetic complications, prion disease, and NOD-like receptor signaling confirming its role in immune-related pathways. Combined with biological interpretations such as gene ontology (GO), pathway enrichment, and protein-protein interaction (PPI) network, our current study sheds light on the in-depth research on early detection, diagnosis, and prognosis of different ADs.

Transposable elements regulate thymus development and function

Transposable elements (TEs) are repetitive sequences representing ~45% of the human and mouse genomes and are highly expressed by medullary thymic epithelial cells (mTECs). In this study, we investigated the role of TEs on T-cell development in the thymus. We performed multiomic analyses of TEs in human and mouse thymic cells to elucidate their role in T-cell development. We report that TE expression in the human thymus is high and shows extensive age- and cell lineage-related variations. TE expression correlates with multiple transcription factors in all cell types of the human thymus. Two cell types express particularly broad TE repertoires: mTECs and plasmacytoid dendritic cells (pDCs). In mTECs, transcriptomic data suggest that TEs interact with transcription factors essential for mTEC development and function (e.g., PAX1 and REL), and immunopeptidomic data showed that TEs generate MHC-I-associated peptides implicated in thymocyte education. Notably, AIRE, FEZF2, and CHD4 regulate small yet non-redundant sets of TEs in murine mTECs. Human thymic pDCs homogenously express large numbers of TEs that likely form dsRNA, which can activate innate immune receptors, potentially explaining why thymic pDCs constitutively secrete IFN ɑ/β. This study highlights the diversity of interactions between TEs and the adaptive immune system. TEs are genetic parasites, and the two thymic cell types most affected by TEs (mTEcs and pDCs) are essential to establishing central T-cell tolerance. Therefore, we propose that orchestrating TE expression in thymic cells is critical to prevent autoimmunity in vertebrates.

The impact of genetic variants related to vitamin D and autoimmunity: A systematic review

Over the past few years, there has been a notable increment in scientific literature aimed at unraveling the genetic foundations of vitamin D signaling and its implications for susceptibility to autoimmunity, however, most of them address isolated diseases. Here, we conducted a systematic review of genetic variants related to vitamin D and autoimmune diseases and we discussed the current landscape of susceptibility and outcomes. Of 65 studies analyzed, most variants cited are in vitamin D binding protein (VDBP; rs2282679 GC gene), 25-hydroxylase (rs10751657 CYP2R1), 1α-hydroxylase (rs10877012, CYP27B1) and the nuclear hormone receptor superfamily [FokI (rs2228570), BsmI (rs1544410), ApaI (rs7975232), and TaqI (rs731236) in VDR gene]. Therefore, our findings confirmed the associations of several genetic variants of vitamin D signaling with a broad spectrum of autoimmune diseases/traits. In addition, given the low number of papers found with functional analysis, further studies to elucidate the real effect that the variants exert on Vitamin D signaling are recommended.

Shared genomic segments analysis identifies MHC class I and class III molecules as genetic risk factors for juvenile idiopathic arthritis

Juvenile idiopathic arthritis (JIA) is a complex rheumatic disease encompassing several clinically defined subtypes of varying severity. The etiology of JIA remains largely unknown, but genome-wide association studies (GWASs) have identified up to 22 genes associated with JIA susceptibility, including a well-established association with HLA-DRB1. Continued investigation of heritable risk factors has been hindered by disease heterogeneity and low disease prevalence. In this study, we utilized shared genomic segments (SGS) analysis on whole-genome sequencing of 40 cases from 12 multi-generational pedigrees significantly enriched for JIA. Subsets of cases are connected by a common ancestor in large extended pedigrees, increasing the power to identify disease-associated loci. SGS analysis identifies genomic segments shared among disease cases that are likely identical by descent and anchored by a disease locus. This approach revealed statistically significant signals for major histocompatibility complex (MHC) class I and class III alleles, particularly HLA-A∗02:01, which was observed at a high frequency among cases. Furthermore, we identified an additional risk locus at 12q23.2-23.3, containing genes primarily expressed by naive B cells, natural killer cells, and monocytes. The recognition of additional risk beyond HLA-DRB1 provides a new perspective on immune cell dynamics in JIA. These findings contribute to our understanding of JIA and may guide future research and therapeutic strategies.

Expression levels of GSDMB and ORMDL3 are associated with relapsing-remitting multiple sclerosis and IKZF3 rs12946510 variant

Multiple sclerosis (MS), a noncurable autoimmune neurodegenerative disease, requires constant research that could improve understanding of both environmental and genetic factors that lead to its occurrence and/or progression. Recognition of the genetic basis of MS further leads to an investigation of the regulatory role of genetic variants on gene expression. Among risk variants for MS, Ikaros zinc finger 3 (IKZF3) gene variant rs12946510 was identified as one of the top-ranked and the expression quantitative trait loci (eQTL) for genes residing in chromosomal locus 17q12-21. The study aimed to investigate the association of gene expression of the immunologically relevant genes, which map to indicated locus, ORMDL3, GSDMB, and IKZF3, with MS and rs12946510 genotype, taking into account disease phase, clinical parameters of disease progression, and severity and immunomodulatory therapy. We used TaqMan® technology for both allelic discrimination and gene expression determination in 67 relapsing MS patients and 50 healthy controls. Decreased ORMDL3 and GSDMB mRNA levels had significant associations with MS and rs12946510 TT rare homozygote among patients. Significant positive correlations between ORMDL3 and GSDMB mRNA expression were observed in both patients and controls. We detected the significant between-effect of sex and rs12946510 on the expression of ORMDL3 in the patient group and interferon β therapy and rs12946510 on GSDMB expression. Our results show the association of ORMDL3 and GSDMB mRNA expression with the clinical manifestation of MS and confirm that IKZF3 rs12946510 exerts the eQTL effect on both genes in multiple sclerosis. Besides providing novel insight related to MS phases and interferon β therapy, the study results confirm previous studies on regulatory genetic variants, autoimmunity, and MS.

Is immunology doing well? A look at 100 immune-mediated inflammatory diseases for 100 years of the Journal

It is now 60 years since Ian Mackay and Macfarlane Burnet published their seminal text "The Autoimmune Diseases" in which they examined the full scope of human inflammatory pathology as a manifestation of the underlying structure and function of the immune system. Here I revisit this approach to ask to what extent has the promise of Mackay and Burnet's work been exploited in clinical medicine as currently practiced. In other words, is immunology doing well? Despite spectacular headline contributions of immunology in clinical medicine, I present evidence suggesting a performance ceiling in our capacity to answer the relatively straightforward questions that patients frequently ask about their own diseases and find that this ceiling exists across almost all of the 100 immune-mediated inflammatory diseases examined. I propose that these questions are difficult, not so much because the immune system is overwhelmingly complex but rather that we have more to learn about the relatively simple agents and rules that may underpin self-organizing complex interacting systems as revealed in studies from other disciplines. The way that the immune system has evolved to exploit the ancient machinery determining three independent cell fate timers as described in this Journal would be a great place to start to decode the self-organizing principles that underpin the emergent pathology that we observe in the clinic.

Revisiting Coley's Toxins: Immunogenic Cardiolipins from Streptococcus pyogenes

Coley's toxins, an early and enigmatic form of cancer (immuno)therapy, were based on preparations of Streptococcus pyogenes. As part of a program to explore bacterial metabolites with immunomodulatory potential, S. pyogenes metabolites were assayed in a cell-based immune assay, and a single membrane lipid, 18:1/18:0/18:1/18:0 cardiolipin, was identified. Its activity was profiled in additional cellular assays, which showed it to be an agonist of a TLR2-TLR1 signaling pathway with a 6 μM EC50 and robust TNF-α induction. A synthetic analog with switched acyl chains had no measurable activity in immune assays. The identification of a single immunogenic cardiolipin with a restricted structure-activity profile has implications for immune regulation, cancer immunotherapy, and poststreptococcal autoimmune diseases.