Large-scale genome-wide association studies reveal the genetic causal etiology between air pollutants and autoimmune diseases

Autoimmune diseases (ADs) are an intricate group of chronic inflammatory disorders characterized by an aberrant response to normal host tissues and rank third in global morbidity statistics, with an unknown etiology [1]. This significantly strains public health systems, further intensified by the critical shortage of effective intervention strategies. The pathogenesis of inflammatory autoimmune diseases exhibits a distinctive pattern: a stable or sudden metamorphosis from the existence of minimal or no pathogenic autoantigen-specific T and B cells to a pathogenic state, which consequently results in the discharge of copious amounts of IgG antibodies [2]. Despite noteworthy advances in animal-modeled autoimmune disease treatment, a significant temporal gap persists before such strategies can yield clinical breakthroughs [3]. Thus, the present-day therapeutic approaches remain anchored in treating patients with nonspecific immunosuppression, unfortunately culminating in heightened morbidity and mortality rates [4]. Importantly, a diverse range of factors-environmental, behavioral, and genetic collectively contribute to the instigation and progression of autoimmune diseases. These encompass aspects such as dietary habits, infections, drug exposure, physical activity levels, smoking habits, microorganism interaction, and contact with various pollutants [5, 6]. It is essential to recognize and understand these influences in order to effectively combat the global autoimmune disease burden. Notably, with increased awareness of environmental protection, exposure to environmental pollutants, also known as particulate matter, is a key risk factor for susceptibility to autoimmune diseases, leading to growing concern. [7, 8].

Air contamination remains a cardinal health concern, encompassing a complex amalgamation of gases and particulate matter, inclusive but not exhaustive of carbon monoxide, nitrates, sulfur dioxide, ozone, lead, and tobacco-linked by-products [9]. Nitrogen oxide (NO_X), a molecule composed of nitrogen and oxygen, is particularly relevant to ambient air pollutants and is an environmental pollutant in the public health policies of many industrial countries. Respirable particulate matter (PM) itself can be classified into PM10, PM2.5, and ultrafine particulate matter (UFPM) based on particle size. In general, particles larger than 10 µm are mostly filtered by the nose and upper respiratory tract and are unlikely to reach the lower respiratory tract. In contrast, particles smaller than 10 µm will reach the lower airways, penetrate, and deposit in deeper airways such as the terminal bronchi and alveoli. Inhaling such pollutants has been associated with generating oxidative stress and subsequent inflammation, causing acute and extended systemic inflammation and autoimmunity [10]. Though the correlation between continuous exposure to atmospheric contaminants and autoimmune diseases has been under investigation, the evidence supporting this claim remains inconclusive. Limited studies have indicated that when air pollutant molecules enter the respiratory tract or skin mucosa, they can trigger the activation of macrophages, inflammatory neutrophils, dendritic cells, and lymphocytes, leading to an imbalance in the immune system [11]. This state of immune dysregulation may contribute to the development of autoimmune diseases.

A recent large observational study involving 12 million individuals showed that for every one-decile increase in industrial air pollutant emissions, including fine particulate matter (PM2.5), nitrogen dioxide (NO₂), and sulfur dioxide (SO₂), the adjusted hazard ratio was 1.018 [95% confidence interval (CI) = 1.013–1.022] [12]. The study found that industrial PM2.5 was the most significant contributor to systemic autoimmune rheumatic diseases (SARDs). Meanwhile, mice spontaneously susceptible to systemic lupus erythematosus (SLE) exhibited a number of negative health effects after daily exposure to 600 µg/m³ of inhaled concentrated PM2.5. The mice showed decreased survival, increased circulating neutrophil counts, early onset of proteinuria, increased kidney weight, and enlarged kidney cortex as compared to mice that were exposed to filtered air [13]. Chronic air pollution exposure can cause lung inflammation through mechanisms such as inducing oxidative stress, damaging airway mucosa, and inducing a localized inflammatory response, and maybe the point of initiation of inflammatory responses in autoimmune diseases. Air pollutants can not only affect T and B cells, producing large numbers of antibodies and auto-reactive T lymphocytes, but can also potentially cause epigenetic changes. Given the limitations of observational studies, this paper employs Mendelian randomization grounded in Mendel’s law to probe into the causative relationship between air pollutants and autoimmune diseases. This approach allows to establish new perspectives on the environmental determinants of these diseases, offering a broader understanding and potential interventions for autoimmune conditions.

Mendelian randomization (MR) is an instrumental approach employed in genetic epidemiology, utilizing genetic variants to analyze the causal associations between a particular exposure (here air pollutants) and an outcome (here ADs) [14]. Rooted firmly in Mendel’s principles of inheritance, MR posits that the allocation of genetic variants from parents to offspring is an arbitrary process [15]. Thus, by juxtaposing genetic variants related to exposure within a population against the prevalence of a disease, researchers can discern whether the exposure under investigation is causally linked to the concerned disease [16]. Mendelian randomization works by exploiting the random allocation of genetic variants that affect the exposure of interest (such as air pollutants) and using these as genetic instrumental variables in statistical analysis, which mimics the design of randomized controlled trials. This genetic variation is fixed at conception and thus not subject to the confounding factors that affect the exposure-disease relationship in traditional observational studies [17]. Therefore, Mendelian randomization can help to establish causality between exposure and disease outcome. Nevertheless, it is paramount to recognize the limitations of the Mendelian randomization approach, including the potential for pleiotropic effects scenarios in which one genetic variant influences multiple traits of population stratification, which could potentially integrate bias into the conducted analyses. Comprehensive and careful study design and the precise selection of genetic variants are vital to uphold the reliability of the deduced results [18]. Additionally, the execution of critical sensitivity analyses, including weighted median, MR-Egger, and leave-out-one analysis, can facilitate the identification of pleiotropic and heterogeneous effects, thus boosting the credibility of the results [19].

Importantly, transcriptome-wide association studies (TWAS) are a genetic approach to study the role of gene expression in the development of specific traits and diseases by prioritizing the identification of candidate causal genes in analyses following genome-wide association studies [20]. The UK Biobank database of air pollution data is one of the most commonly used and largest publicly available databases and contains data on PM10, PM2.5, NO_X, and NO₂ measured in 2010 [21, 22]. This paper has hence pinpointed genetic variants correlated with exposure to four air pollutants using summary statistics from expansive genetic studies on European populations. By incorporating these as instruments in a Mendelian randomization approach, we aim to estimate the causal impacts of air pollutants on various autoimmune diseases, including type 1 diabetes (T1D), Crohn’s disease (CD), celiac disease (CeD), asthma and allergy (AA), multiple sclerosis (MS), ulcerative colitis (UC), systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), psoriasis, primary sclerosing cholangitis (PSC), irritable bowel syndrome (IBS), sicca syndrome (SS), ankylosing spondylitis (AS), hypothyroidism, and hyperthyroidism. Moreover, TWAS was utilized to identify hub genes that play key roles in air pollution-genetic-autoimmune disease interactions to explore the possible pathological mechanisms of air pollution-induced autoimmune diseases.

To the best of our knowledge, this study performed a two-sample and multivariable MR for the first time to explore the causal relationship between air pollutants and multiple autoimmune diseases and investigate the potential mediators between them. Combining observational evidence from previous studies and genetic evidence from this MR analysis, we suggested that air pollutants were causally related to higher risks of hypothyroidism, SLE, RA, and UC and a lower risk of CeD.

The integrity of a dynamic, balanced immune system is pivotal for facilitating optimal health. Current findings depicting a putative association between airborne pollutants and autoimmune diseases generate a spectrum of perspectives, underscoring the necessity for more precise analyses, including the exploration of genetic susceptibility's pivotal role in moderating this relationship. Limited studies have shown that air pollutants contribute to the development of autoimmune diseases mainly by modulating the immune response of different cell types, such as macrophages, inflammatory neutrophils, dendritic cells, and lymphocytes, which produce pro-inflammatory factors [11]. Cellular experiments have confirmed that air pollutant components activate inflammatory cells through multiple mechanisms, including Toll-Like Receptors (TLRs), reactive oxygen species (ROS) pathways, and polyaromatic hydrocarbon (PAH) pathways. These pathways activate intracellular signaling cascades, such as the NF-kB and MAPK pathways, promoting the inflammatory cascade response [11].

Recent evidence from a prospective cohort analysis that incorporated 342,973 participants from the UK Biobank reveals associations of NO₂ (OR: 1.03, 95%CI: 0.98–1.09, p_Trend = 4.20 × 10⁻⁴) and NO_X (OR: 1.07, 95%CI: 1.02–1.12, p_Trend = 1.10 × 10⁻⁵) with heightened risks of RA [53]. Chau-Ren Jung et al. [54] found that long-term exposure to NO₂ (28–38 ppb) was related to the elevated risk of SLE (HR = 1.21, 95% CI: 1.08–1.36). Peng Chen et al. found that a 1 μg/m³ increment of NO₂ resulted in a 0.038-day increase in hospital stay (95% CI: 0.0159–0.0601, p = 0.0008) and a $38.4 increase in hospital costs (95% CI: 0.0017–0.0679, p = 0.0395) in SLE patients [55]. Studies corroborate NO_X's toxicity, underscored by its tendency to combine with high atmospheric concentrations of O₃ and VOC to generate heterogeneous oxidants, like hydroxyl radicals, peroxyl radicals, and singlet oxygen, causing severe oxidative stress [11]. In vitro experiments substantiate that NO_X suppresses reactive oxygen species levels and precipitates pro-inflammatory cytokines production via the NF-κB signaling pathway, leading to the polarization of macrophages from M1 to M2 phenotype [56].

The relationship between PM and autoimmune diseases remains elusive despite clear associations with autoimmune and inflammatory responses. In vivo and in vitro experiments have shown that PM induces substantial oxidative stress and reduction of endogenous antioxidants, induction of NF-κB and AP-1 signaling, and transcription of genes containing antioxidant response element (ARE) promoters [11]. Moreover, it has been suggested that PM activates a series of pro-inflammatory factors such as TNFα, RORγt, STAT1, Nrf2, and NF-κB via the aryl hydrocarbon receptor (AhR) pathway in inflammatory cells [57]. Quantile g-computational model of time confirms that industrial PM2.5 contributes more to the development of systemic autoimmune rheumatic diseases relative to other industrial air pollutants, such as NO₂ and SO₂ [12]. Long-term exposure to PM2.5 (18–46 μg/m³) was associated with an increased risk of SLE, and SLE was positively associated with a 10.2 μg/m³ increase in exposure to fine particles (PM2.5) (HR = 1.12, 95% CI: 1.02–1.23) [54]. A time-series study found that chronic exposure to particulate matter (PM2.5 and PM10) was significantly associated with readmission rates for rheumatoid arthritis and was more pronounced in women and older patients [58].

Interestingly, this paper identified a lot of key genes and enriched signaling pathways that are involved in air pollutants and autoimmune diseases that not been discovered out before. For example, the BEN structural domain-containing protein 3 (BEND3), localized in the cytoplasm, is involved in chromatin function and transcription. It has been shown that BEND3 is expressed in both CD4⁺ and CD8⁺ T cells in peripheral blood and can lead to the production of various cytokines via the TCR/CD3 complex [59]. Protein phosphatase 2A (PP2A) is a serine-threonine phosphatase that plays an important role in regulating the activation, differentiation, and function of T cells [60]. RNF20, encoding the E3 ubiquitin-protein ligase BRE1A, thereby mediates monoubiquitination of histone H2B at lysine 120 and has been shown to play a background-dependent role in the development of inflammatory bowel disease [61]. C–C chemokine receptor type 9 (CCR9) is a heptameric transmembrane protein that maps to the chemokine receptor gene cluster region. Studies have shown that CCR9 and its ligands can play important roles in a variety of inflammation-related diseases by targeting inflammatory cells and promoting inflammatory responses [62]. Recent studies have demonstrated the important role of AMP-dependent transcription factor 7 (ATF7) in innate immune memory. ATF7 enhances protection against re-infection by inhibiting the expression of a group of genes encoding factors involved in innate immunity in macrophages [63].

In addition, we found that most of these enrichment pathways are related to cellular metabolism, immune regulation, amino acid, and gene modification pathways. For example, ubiquitination is a highly specific and tightly regulated ATP-dependent biological process that proceeds through a complex enzymatic cascade. It has been shown that ubiquitin-related genes play an important role in a variety of autoimmune diseases [64]. Many lipid metabolism-related pathways have been found to be enriched in both NO₂ and autoimmune diseases. Studies have shown that many biologically active lipids are involved in various stages of the inflammatory process as well as in the pathophysiology of different chronic autoimmune diseases, such as RA, MS, T1D, and SLE [65]. Human metabolism is closely linked to ongoing inflammatory and immune responses, and alterations in the metabolic structure of immune cells can lead to dysregulation of immune responses and are characteristic of autoimmunity [66]. When faced with various dynamically changing and challenging environmental conditions, immune cells need to display dynamic metabolic adaptation processes. Inflammation-stimulated immune cells urgently need to produce more energy and biomolecules to support the growth, proliferation, and production of pro-inflammatory molecules. Metabolic reorganization affects the effector phase of inflammation and the resolution of inflammation by regulating the fate and function of immune cells. Increasing research suggests that exploring the immunometabolic pathways that control the fate of cells of the innate and adaptive immune system at all stages of activation, proliferation, differentiation, and effector response is critical to the development of new targets for the treatment of autoimmune diseases. Furthermore, intermediate analyses revealed that air pollutants increased the risk of autoimmune diseases by modulating the expression of POR, HSPA1B, SHANK3, and BRD2. Cytochrome P450 reductase (POR) is a membrane-bound enzyme that mediates electron transfer between NADPH, cytochrome P450, and heme proteins in the endoplasmic reticulum of eukaryotic cells [67]. Studies have shown that POR plays an important role in energy metabolism, inflammatory immunity, and tumor development [68]. P450 (CYP) regulates the conversion of fatty acids to pro- or anti-inflammatory mediators, including interleukin (IL)-1β, IL-6, and tumor necrosis factor-α (TNF-α) [69]. Bromodomain-containing protein 2 (BRD2), belongs to a novel protein kinase with a role in the transcription of cell cycle responses in autoimmune and cancer diseases [70]. BRD2 coordinates various extracellular or intracellular danger signals through PRRs expressed in immune and non-immune cells in a variety of diseases and has emerged as a promising therapeutic target [71].

However, there are still several unavoidable limitations in our study. First, the participants included in our data were all European populations and without other ethnic groups. The current observational studies of air pollutants and autoimmune diseases cover data from various populations and countries, leading to possible incompleteness and partial bias in our conclusions. Second, air pollutant intake changes over time as people's lifestyles and regional environmental protection measures change. In this paper, we used GWAS data on air pollution measured by participants in the UK in 2010. The causal relationship between air pollution and autoimmune disease may need to be reassessed in the future as sample size increases. Third, based on the paucity of current basic research on air pollutants in autoimmune diseases, we have not explored these possible molecular mechanisms in depth, although we have identified many key genes and pathways using TWAS and enrichment pathway analysis. Fourth, in the selection of covariates, we chose those modifiable lifestyles that were closely related to air pollution and autoimmune diseases based on previous studies. This leads us to inevitably overlook some other important variables. Fifth, in designing this study, we had to choose 5 × 10^–6 instead of 5 × 10^–8 in order to obtain sufficient instrumental variables. MR was based on three key assumptions: (1) IVs are strongly associated with the exposure; (2) no shared cause with the outcome; (3) IVs only affect the outcome through the exposure. Thus, compared with the threshold of 5 × 10^–8, 5 × 10^–6 might bring less strong IVs and potential pleiotropy, although we made several analyses to test these potential biases. Additionally, the validated GWAS of the SLE, CeD, and hypothyroidism we employed had partial sample overlapping with the exposure from the UK biobank, although the overlap might not bias the results as previously thought when IVs are strong enough [72]. The current study included only four air pollution molecules as exposures and did not include other molecules such as nitrous oxide and sulfide, most notably due to the lack of appropriate GWAS data. Last but not least, many other mediating factors, such as family/genetic background, physical/mental health status, and type of work, were not included in the study analysis.

In summary, using single nucleotide polymorphisms obtained from the latest large-scale GWAS in this paper, robust evidence suggests a causal relationship between air pollutants and autoimmune disease. Our findings might shed light on the development of air pollutants-based interventions for autoimmune diseases in the future.