Abstract
Introduction:
Immune cells are dynamic in the inflammatory environment and play a key role in eradicating periodontal pathogens, modulating immune responses, and instigating tissue destruction. Identifying specific immune cell phenotypes associated with periodontitis risk is essential for targeted immunotherapeutic interventions. However, the role of certain specific immune cell phenotypes in the development of periodontitis is unknown. Mendelian randomization offers a novel approach to reveal causality and address potential confounding factors through genetic instruments.
Methods:
This two-sample Mendelian randomization study assessed the causal relationship between 731 immune cell phenotypes and periodontitis using the inverse variance weighting method with the GWAS catalog genetic database. Methodological robustness was ensured through Cochran’s Q test, MR-Egger regression, MR-PRESSO, and Leave-One-Out analysis.
Results:
14 immune cell phenotypes showed potential positive causal associations with periodontitis risk (p < 0.05), suggesting an increased risk, while 11 immune cell phenotypes exhibited potential negative causal associations (p < 0.05), indicating a reduced risk. No significant heterogeneity or pleiotropy was observed.
Conclusion:
This study underscores certain immune cell types as potential periodontitis risk biomarkers, laying a theoretical foundation for future individualized treatment and precision medicine development.
1 Introduction
Periodontitis (PD) is an inflammatory disease caused by the imbalance of local microbial communities, which can lead to the destruction of tooth-supporting tissues (Slots, 2000). In addition, it is associated with systemic diseases and can exacerbate or trigger other systemic diseases such as rheumatoid arthritis and diabetes (; ). Emerging evidence suggests that PD is also related to the composition and function of the gut microbiota. The gut flora may interact with the oral flora and participate in the development of PD (; ). It is now widely believed that the pathogenesis of periodontal disease is not only caused by infecting microorganisms, but also by over-activation of the host immune response (; ).
Immune cells are a key component of the body’s natural defense against foreign invaders. They are made up of different subpopulations with a large number of special functions, mainly including T cells, B cells, dendritic cells, macrophages, and monocytes (). The differentiation of immune cell subsets and their complex interactions in the internal biological environment constitute a ‘pathophysiological network’ that plays a dual role in the development of inflammation (; ; ; ). Immunophenotype, as a critical indicator of immune system activity, refers to the expression pattern of surface molecules and receptor molecules of immune cells, which can regulate processes such as cell growth, differentiation and activity. During the diagnosis of diseases such as inflammation and infection, doctors can identify different receptors and molecules on the surface of immune cells to determine the type of disease and severity of the condition for better treatment. Therefore, understanding the phenotype of immune cells is crucial for the study of various immune-related diseases, as well as for advancing therapeutic strategies.
While previous observational studies have characterized immune cell profiles in periodontal tissues, they often lack the ability to establish causal associations or identify protective versus pathogenic immune responses. In contrast, Mendelian Randomization (MR) offers a novel approach to address several gaps and limitations in existing literature on the immune response in PD. In recent years, a large number of studies have utilized MR to identify the association between immune cell phenotype and disease, providing new insights into the development of more effective treatment strategies (; ).
MR, leveraging genetic variants as instrumental variables, allows for the exploration of causal relationships between exposures and outcomes, overcoming confounding and reverse causality biases inherent in observational studies, and saves human and material resources for subsequent studies by precise target screening (). By utilizing MR, this study aims to elucidate the causal links between 731 immune cell phenotypes and PD. This approach represents a paradigm shift in periodontal research, offering a robust framework to discern causal associations and identify potential therapeutic targets.
2 Materials and methods
2.1 Data sources
The schematic diagram of the MR study investigating the causal effects of immune cells phenotypes on PD is shown in Figure 1. The dataset for PD in this study was obtained from the OpenGWAS database, focusing on European samples (https://gwas.mrcieu.ac.uk). The study encompassed 3,046 European adults diagnosed with PD and a control sample of 195,395 European adults, retrieved from GWAS data. Summary statistics for 731 immune traits were obtained from the GWAS catalog database, accessible through accession numbers GCST09001391 to GCST90002121 (). These immunophenotypes covered various parameters, including absolute cell (AC) counts (n = 118), median fluorescence intensity (MFI) reflecting surface antigen levels (n = 389), morphological parameters (MP) (n = 32), and relative cell (RC) counts (n = 192). Specifically, MFI, AC, and RC features included panels such as B-cells, conventional dendritic cells (cDCs), T-cell maturation stages, monocytes, myeloid cells, TBNK (T-cells, B-cells, natural killer cells), and regulatory T cells (Tregs). The MP feature included cDC and TBNK panels.
FIGURE 1
2.2 Instrumental variable selection
In the MR analysis, single nucleotide polymorphisms (SNPs) served as instrumental variables (IVs) to assess the causal relationship between immune cell traits and PD. Selection of IVs adhered to three hypotheses: (1) the correlation hypothesis, indicating a strong correlation between IVs and immune cell traits; (2) the exclusivity hypothesis, affirming no direct relationship between IVs and PD traits; and (3) the independence hypothesis, ensuring no correlation between IVs and confounding factors (). IVs, chosen based on genome-wide significance (p = 1 × 10−5) and conditions of chain imbalance threshold (r2 = 0.001, kb = 10,000), underwent further refinement. To exclude the effect of bias of weak IVs, the F statistic of each IV was calculated, with IVs having F < 10 being excluded, and only those with F > 10 included for MR analysis. In this study, a reverse MR analysis of PD and immune cells was performed to screen eligible IVs at a threshold of p = 5 × 10−6.
2.3 Statistical analysis
The evaluation of the causal relationship between immune cells and PD was primarily conducted using R software (version 4.3.2), MRPRESSO (1.0), and Two Sample MR (0.5.8). MR analysis utilized inverse variance weighting (), weighted median () and MR-Egger methods (). A significant causal relationship between exposure and outcome was considered when p < 0.05. Heterogeneity, which refers to the variability in causal estimates across different genetic variants used as instrumental variables (IVs), was assessed using Cochran’s Q test and corresponding p-values. A significant p-value from Cochran’s Q test indicates heterogeneity in the causal estimates, suggesting that the IVs may not be valid due to underlying differences in their effects on the exposure of interest. To address potential pleiotropy or other biases that might affect the MR analysis results, we employed several sensitivity analyses: 1). MR-Egger Regression: The method can assess the presence of directional pleiotropy by testing for non-zero intercepts in the regression model. A significant intercept suggests the presence of pleiotropy, indicating that the MR estimates may be biased. 2). MR-PRESSO: It detects outlier SNPs that exhibit significant differences in the causal estimates compared to the overall trend, allowing for the correction of pleiotropy-induced bias. 3). Leave-One-Out Analysis: We conducted leave-one-out sensitivity analyses to assess the influence of individual SNPs on the MR estimates, thereby evaluating the robustness of the overall findings. 4). Funnel Plots: We generated funnel plots to visually inspect for asymmetry, which may indicate the presence of pleiotropy or other biases in the MR analysis.
3 Results
3.1 Instrumental variable result
In this study, the exposure factors included 731 immune cell phenotypes. A total of 559 SNPS were included in the two-sample MR analysis based on the SNPS screening criteria.
3.2 Causal relationship between immune cells and PD
The specific SNPs for each immune cell phenotype are listed in Supplementary Table S1. The results of the preliminary MR analysis of the 731 immune cell phenotypes and the risk of PD are presented in Figure 2 and Supplementary Table S2. A total of 25 immune profiles were directly and significantly associated with PD at a significance threshold of p < 0.05. The sketch of immune cell phenotypes associated with PD risk is shown in Figure 3. The statistical results and visualized forest plots are shown in Supplementary Table S3 and Figure 4. These include 3 cases in the B cell group, 5 cases in the cDC group, 5 cases in the mature T-cell group, 3 cases in the TBNK group, 5 cases in the monocyte group, and 7 cases in the Treg group. The results of MR analysis using a random effects model with the IVW method identified 14 immune cell characteristics as having a potential positive causal relationship with an increased risk of PD (Figure 5). These included CD127 on CD28− CD8br, Treg (OR = 0.928, 95% CI = 0.869-0.991, p = 0.027), CD28 on CD39+ secreting Treg, Treg (OR = 0.938, 95% CI = 0.890 to 0.987, p = 0.015), CD3 on TD CD4+, Maturation stages of T cell (OR = 0.945, 95% CI = 0.895 to 0.998, p = 0.044), CD4 on CD39+ resting Treg, Treg (OR = 0.921, 95% CI = 0.861 to 0.985, p = 0.016), CD45RA on TD CD8br, Maturation stages of T cell (OR = 0.901, 95% CI = 0.817 to 0.994, p = 0.038), CD86 on granulocyte, Treg (OR = 0.893, 95% CI = 0.825 to 0.967, p = 0.005), CX3CR1 on CD14+ CD16− monocyte, Monocyte (OR = 0.933, 95% CI = 0.882 to 0.987, p = 0.016), CX3CR1 on CD14+ CD16+ monocyte, Monocyte (OR = 0.946, 95% CI = 0.904 to 0.990, p = 0.016), HVEM on EM CD8br, Maturation stages of T cell (OR = 0.942, 95% CI = 0.895 to 0.991, p = 0.022), IgD on IgD+, B cell (OR = 0.940, 95% CI = 0.884 to 0.998, p = 0.044), IgD + CD38dim %lymphocyte, B cell (OR = 0.960, 95% CI = 0.930 to 0.991, p = 0.011).
FIGURE 2
FIGURE 3
FIGURE 4
FIGURE 5
In addition, 11 types of immune cells are negatively associated with an increased risk of PD (Figure 6), including CCR2 on CD62L + plasmacytoid DC, cDC (OR = 1.062, 95% CI = 1.001 to 1.127, p = 0.045), CCR2 on plasmacytoid DC, cDC (OR = 1.064, 95% CI = 1.003 to 1.128, p = 0.039), CD25 on IgD + CD38−, B cell (OR = 1.038, 95% CI = 1.012 to 1.066, p = 0.005), CD25 on secreting Treg, Treg (OR = 1.042, 95% CI = 1.004 to 1.082, p = 0.032), CD25hi CD45RA + CD4 not Treg %T cell, Treg (OR = 1.035, 95% CI = 1.003 to 1.067, p = 0.031), CD3 on CD39+ resting Treg, Treg (OR = 1.070, 95% CI = 1.010 to 1.134, p = 0.022), CD3 on HLA DR+ CD4+, TBNK (OR = 1.070, 95% CI = 1.009 to 1.134, p = 0.024), CD62L on granulocyte, cDC (OR = 1.135, 95% CI = 1.034 to 1.247, p = 0.008), CD8br %leukocyte, TBNK (OR = 1.113, 95% CI = 1.009 to 1.228, p = 0.032), FSC−A on HLA DR + CD8br, TBNK (OR = 1.058, 95% CI = 1.004 to 1.114, p = 0.033), HLA DR on DC, cDC (OR = 1.057, 95% CI = 1.001 to 1.115, p = 0.045), HLA DR on plasmacytoid DC, cDC (OR = 1.046, 95% CI = 1.002 to 1.093, p = 0.041), NKT AC, TBNK (OR = 1.066, 95% CI = 1.005 to 1.130, p = 0.033), SSC−A on NKT, TBNK (OR = 1.038, 95% CI = 1.002 to 1.075, p = 0.038).
FIGURE 6
4 Sensitivity analysis
To verify the reliability and robustness of the results, we performed inverse MR analysis to screen for 25 immune cell phenotypes causally associated with PD, which showed that there was no significant correlation (p > 0.05) between the two (Supplementary Table S4). In sensitivity analysis, we found no significant heterogeneity across the selected IVs, indicating consistency in the causal estimates and supporting the validity of the IVs used in the MR analysis (Supplementary Table S5). In addition, the intercept from MR-Egger regression was not statistically significant (p > 0.05), suggesting no evidence of directional pleiotropy (Supplementary Table S6). MR-PRESSO analyses showed no significant outliers were detected, further supporting the robustness of the causal inferences (Supplementary Table S7). The funnel plot showed that the SNP distribution was more symmetrical, and the causality was unlikely to be affected by potential bias, indicating the stability of the results (Supplementary Figure S1 and S2). Leave-one-out analysis showed that the significant causality had no change or reversal of the combined effect after removing SNPs one by one (Supplementary Figures S3 and S4), indicating that the results were plausible. In summary, there was a consistent positive correlation between 14 immune cells and PD and a consistent negative correlation between another 11 immune cells and PD.
5 Discussion
The immune system plays a pivotal role in oral health, particularly in the pathogenesis of PD, and its involvement is increasingly gaining attention in both basic science and clinical research. By regulating inflammatory and immune responses, the immune system combats pathogens in the oral cavity and maintains the healthy state of oral tissues. However, the current understanding of the genetic-level relationship between the immune system and PD remains insufficient. To our knowledge, this is the first study to explore the causal relationship between immune cell phenotypes and PD. The study identified 25 immune cells correlated with the risk of PD, with further screening revealing 14 that were positively associated and 11 negatively associated with PD risk. The findings offer crucial insights for future research in this domain.
The mechanism by which immune cells regulate PD in the host immune microenvironment is shown in Figure 7. Dendritic cells play a crucial role in the development of PD, acting as the “conductors” of T-cell differentiation. These cells possess a remarkable ability to stimulate and regulate effector responses of T cells, thereby enhancing the inflammatory response in periodontal tissues by upregulating the activation of Th1 and Th17 cells (; ). In cases of periodontal tissue infection and inflammation, Porphyromonas gingivalis can stimulate mature dendritic cells to secrete IL-12 and IFN-γ, promoting a Th1 cell response and exacerbating inflammation (Su et al., 2015; ). The results of our study indicate that dendritic cell immunophenotypes contribute to the risk of PD, including CCR2 on CD62L + plasmacytoid DC, CCR2 on plasmacytoid DC, CD62L on granulocyte, HLA DR on DC, HLA DR on plasmacytoid DC. CCR2, or C-C chemokine receptor type 2, plays a crucial role in inflammation and bone metabolic diseases. Our findings align with previous studies indicating that CCR2 has a significant inflammatory effect in periodontal tissues. Previous experiments demonstrated high expression of CCR2 in human and mouse periodontal tissues. When CCR2 was reduced, there was a decrease in inflammatory monocyte and macrophage infiltration in periodontal tissues, along with reduced levels of inflammatory mediators and osteoclasts (). Additionally, in periodontal tissues affected by peri-implantitis, the elimination of CCR2 resulted in reduced production of pro-inflammatory cytokines and impaired osteoclast activity, suppressing peri-implant inflammation and bone loss (Yuan et al., 2023).
FIGURE 7
T cells, also known as thymus-dependent lymphocytes, constitute the primary component of lymphocytes and serve various biological functions, including the direct killing of target cells and assisting or inhibiting antibody production by B cells (
Tregs are a subset of lymphocytes responsible for negatively regulating the body’s immune response, playing a crucial role in maintaining self-tolerance and preventing excessive damage from immune responses. During inflammation resulting from periodontal tissue infection, there is often an accumulation of Treg cells in the body (
Mononuclear macrophages play a pivotal role in activating the host’s defense mechanisms against bacterial infections, helping maintain the delicate balance between the host and microbes (Sima et al., 2019). Bacteria and their byproducts, such as endotoxins, can activate the monocyte/macrophage system, leading to the production of numerous pro-inflammatory factors that can trigger inflammation or immune responses (
B cells exhibit diverse immune functions, encompassing antibody secretion, antigen presentation, cytokine production, and the regulation of T effector cell differentiation (
It is necessary to acknowledge that there are several limitations to this study. Firstly, given that this study relies on data from a European-origin population, it is important to consider the potential impact of population stratification on the observed associations. European populations are genetically diverse, and differences in allele frequencies can exist between subpopulations, such as those from different regions or with different ancestries. Considering the genetic heterogeneity among different ethnic groups, the results may vary from population to population. Therefore, whether our findings can be generalized to other ethnic groups needs to be further verified by prospective studies. In addition, GWAS provide summary statistics for the association between genetic variants and traits, rather than individual-level genotype data. While summary data offer the advantage of large sample sizes and cost-effectiveness, the limitation is the inability to directly assess and control for confounding factors or perform individual-level analyses and to capture important covariates or environmental factors that could confound genetic associations.
Furthermore, the interaction between genetic predispositions and environmental or lifestyle factors is a critical aspect of the pathogenesis of PD. While this study focuses on elucidating the genetic basis of PD through MR analyses, incorporating environmental and lifestyle factors into future analyses is essential for constructing a comprehensive risk model for the disease. By leveraging large-scale genetic datasets and comprehensive phenotypic information, future MR studies can explore gene-environment interactions and identify causal pathways underlying periodontal disease risk. Finally, variations in the definition of PD across different studies and differences in the selected GWAS datasets for PD may also impact the consistency of the conclusions.
6 Clinical implications and future directions
In a clinical setting, understanding the implications of immune cell phenotypes on PD is essential for developing targeted interventions and precision medicine. For instance, the identification of immune cell phenotypes associated with PD risk can facilitate patient stratification in clinical trials. Stratifying patients based on their immune cell profiles may help identify subgroups that are more likely to benefit from targeted interventions, thereby enhancing treatment efficacy and patient outcomes. Moreover, immune cell phenotypes identified in the study could serve as potential biomarkers for monitoring disease progression and treatment response in clinical trials. Incorporating these biomarkers into trial protocols can provide valuable mechanistic insights and facilitate the assessment of treatment effects on immune dysregulation in PD. Finally, the study’s findings support the development of precision medicine approaches in PD, wherein treatment strategies are tailored to individual patients based on their immune profiles. Leveraging advances in omics technologies and computational modeling can further refine patient stratification and enable personalized treatment regimens.
However, the immune response in PD is complex and involves interactions between multiple cell types and signaling pathways. Targeting specific immune cell phenotypes may not fully capture the intricacies of the immune dysregulation in PD. Therefore, translating research findings into effective clinical interventions may require a comprehensive understanding of the underlying mechanisms. 1). Individual variability: There is significant variability in immune cell phenotypes and responses among individuals, influenced by factors such as genetics, environmental exposures, and host-microbiome interactions. Developing personalized immunotherapies based on immune cell phenotypes may require tailored approaches to account for this variability. 2). Therapeutic target identification: While the study identifies immune cell phenotypes associated with PD risk, further research is needed to elucidate the specific molecular targets and pathways underlying these associations. Identifying druggable targets and developing targeted therapies may require extensive preclinical validation and translational research efforts. 3). Clinical trial design challenges: These include selecting appropriate patient populations, defining clinically relevant endpoints, and ensuring the safety and efficacy of experimental interventions. Additionally, optimizing trial designs to account for potential confounders and heterogeneity in treatment responses is essential for generating robust and generalizable results.
In conclusion, this study marks the inaugural application of two-sample MR study to unravel the causal relationship between immune cells and PD. It unveils the impact of particular immune cell phenotypes on the risk of PD, offering novel insights for targeted immunotherapeutic strategies.
Statements
Data availability statement
Publicly available datasets were analyzed in this study. This data can be found here: https://gwas.mrcieu.ac.uk. https://www.nature.com/articles/s41588-020-0684-4.
Author contributions
YB: Conceptualization, Data curation, Investigation, Methodology, Software, Writing–original draft. PX: Conceptualization, Data curation, Writing–original draft. ZJ: Investigation, Software, Writing–original draft. SQ: Supervision, Writing–review and editing. GM: Funding acquisition, Supervision, Writing–review and editing.
Funding
The author(s) declare that financial support was received for the research, authorship, and/or publication of this article. This research was funded by the National Natural Science Foundation of China (grant number 62171077).
Conflict of interest
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Publisher’s note
All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.
Supplementary material
The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fgene.2024.1382270/full#supplementary-material
Abbreviations
PD, Periodontitis; MR, Mendelian randomization; IV, Instrumental variable; AC, Absolute cell; MFI, Median fluorescence intensity; MP, Morphological parameters; RC, Relative cell; cDC, Conventional dendritic cell; TBNK, T-cells, B-cells, natural killer cells; Tregs, Regulatory T cells; SNPs, Single nucleotide polymorphisms; IVW, Inverse variance weighting; TCR, T cell receptor.
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Summary
Keywords
Mendelian randomization, risk factor, immune system, immune cells, periodontitis
Citation
Bai Y, Xie P, Jin Z, Qin S and Ma G (2024) Leveraging genetics to investigate causal effects of immune cell phenotypes in periodontitis: a mendelian randomization study. Front. Genet. 15:1382270. doi: 10.3389/fgene.2024.1382270
Received
05 February 2024
Accepted
04 June 2024
Published
21 June 2024
Volume
15 - 2024
Edited by
Michelle Lacey, Tulane University, United States
Reviewed by
Xiaonan Zhang, Chongqing Medical University, China
Marcos Edgar Herkenhoff, University of São Paulo, Brazil
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Copyright
© 2024 Bai, Xie, Jin, Qin and Ma.
This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Shengao Qin, shengaoqin123@163.com; Guowu Ma, mgw640242000@aliyun.com
† These authors have contributed equally to this work
Disclaimer
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