Causal effects of immune cell phenotypes on the risk of autoimmune liver diseases: a bidirectional two-sample Mendelian randomization study
Original Article

Causal effects of immune cell phenotypes on the risk of autoimmune liver diseases: a bidirectional two-sample Mendelian randomization study

Hongjie Zou1,2#, Xinghe Liang1#, Mengqi Luo3, Xinghua Pan4, De-Ke Jiang1,2

1State Key Laboratory of Organ Failure Research, MOE Key Laboratory of Infectious Diseases Research in South China, Guangdong Provincial Key Laboratory for Prevention and Control of Major Liver Diseases, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China; 2The Key Laboratory of Molecular Pathology in Tumors of Guangxi Higher Education Institutions, Department of Pathology, the Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China; 3Department of Gastroenterology and Hepatology, West China Hospital, Sichuan University, Chengdu, China; 4Precision Regenerative Medicine Research Centre, Medical Science Division, and State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macao, China

Contributions: (I) Conception and design: H Zou, DK Jiang; (II) Administrative support: H Zou, DK Jiang; (III) Provision of study materials or patients: DK Jiang, M Luo, X Pan; (IV) Collection and assembly of data: H Zou; (V) Data analysis and interpretation: H Zou, X Liang; (VI) Manuscript writing: All authors; (VII) Final approval of manuscript: All authors.

#These authors contributed equally to this work.

Correspondence to: De-Ke Jiang, PhD. State Key Laboratory of Organ Failure Research, MOE Key Laboratory of Infectious Diseases Research in South China, Guangdong Provincial Key Laboratory for Prevention and Control of Major Liver Diseases, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Ave, Guangzhou 510515, China; The Key Laboratory of Molecular Pathology in Tumors of Guangxi Higher Education Institutions, Department of Pathology, the Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China. Email: dekejiang17@smu.edu.cn.

Background: Currently, the relationship between immune cell phenotypes and susceptibility to autoimmune liver diseases (AILDs) remains underexplored. This study aims to investigate potential causal associations between immune cell phenotypes and AILDs using a bioinformatics approach.

Methods: We utilized a two-sample Mendelian randomization (MR) analysis to explore the potential causal relationship between immune cell phenotypes and susceptibility to AILDs, including autoimmune hepatitis (AIH), primary biliary cholangitis (PBC), and primary sclerosing cholangitis (PSC). The data of 731 immune cell phenotypes were sourced from a study cohort with 3,757 individuals, while all AILDs summary data were obtained from an open-access database containing the data of AIH, PBC and PSC from 485,234, 24,510 and 14,890 subjects, respectively.

Results: For AIH, its incidence was negatively influenced by three phenotypes of natural killer (NK) cells [HLA-DR+ NK absolute count (AC), HLA-DR+ NK %NK, and HLA-DR+ NK %CD3 lymphocyte] and two phenotypes of monocytes (CD14+ CD16+ monocyte AC, CD16 on CD14 CD16+ monocyte), as well as positively affected by HLA-DR on plasmacytoid dendritic cell (DC) and HLA-DR on CD33 HLA-DR+ myeloid cell. For PBC, its susceptibility was positively impacted by three phenotypes of B cells, i.e., CD27 on CD24+ CD27+ B cell, CD27 on IgD+ CD38 unswitched memory (unsw mem) B cell, and CD27 on memory B cell. For PSC, its risk was negatively correlated with CD28 on CD45RA CD4 not regulatory T (Treg) cell and FSC-A on CD4+ NK cell.

Conclusions: This study suggests a potential causal relationship between immune cells and AILDs, providing preliminary insights into their immunological basis and informing the potential therapeutic targets for further functional studies in treating AILDs.

Keywords: Immune phenotype; autoimmune liver diseases (AILDs); Mendelian randomization (MR); genome-wide association study (GWAS)


Received: 13 January 2025; Accepted: 09 May 2025; Published online: 19 August 2025.

doi: 10.21037/tgh-25-2


Highlight box

Key findings

• This study used two-sample Mendelian randomization (MR) to identify causal links between immune cell phenotypes and autoimmune liver diseases (AILDs). For autoimmune hepatitis (AIH), three natural killer (NK) cell and two monocyte phenotypes showed negative associations, while HLA-DR on plasmacytoid dendritic cells (DCs) and myeloid cells showed positive associations. For primary biliary cholangitis (PBC), three B cell phenotypes were positively linked. For primary sclerosing cholangitis (PSC), two immune cell phenotypes were negatively correlated.

What is known and what is new?

• AILDs (AIH, PBC, PSC) are immune-mediated, with dysregulated immune cells and autoantibodies contributing to pathogenesis. Genetic studies, including genome-wide association study, have highlighted immune-related mechanisms.

• This is the first MR study to establish causal relationships between specific immune cell phenotypes and AILDs, identifying 12 significant immune cell associations across AIH, PBC, and PSC, validated through rigorous sensitivity analyses.

What is the implication, and what should change now?

• These findings reveal immune cell phenotypes as potential therapeutic targets for AILDs. Enhanced understanding of NK, monocyte, B cell, and DC roles in AILDs pathogenesis could guide immunotherapy development, such as regulatory T cell therapy or B cell-targeted treatments. Future research should validate these findings in larger, diverse cohorts and explore targeted interventions to modulate immune responses, potentially improving AILDs management and patient outcomes.


Introduction

Autoimmune liver diseases (AILDs) constitute a group of chronic immune-mediated inflammatory conditions primarily targeting hepatocytes and bile duct cells. This category includes autoimmune hepatitis (AIH), primary biliary cholangitis (PBC) and primary sclerosing cholangitis (PSC). Epidemiological data indicate a steady rise in the prevalence and incidence of AIH and PSC across European regions, while PBC demonstrates a relatively higher prevalence in North America, the Asia-Pacific region, and other geographical areas (1). A substantial body of research suggests the associations between AILDs and factors such as smoking, medication usage and other substances (2). Although AILDs have been among the earliest autoimmune diseases investigated, their underlying mechanisms have only begun to be unveiled in recent years (3).

The predominant perspective asserts that immune regulatory genetic defects, coupled with specific environmental triggers, can instigate aberrant immune system activation, leading to chronic inflammation and tissue damage, thereby precipitating the onset of AILDs (4). Recent research highlights immune cell dysregulation, autoantibody mechanisms, and their links to AILDs. Autoantibodies significantly damage tissues by altering functions, triggering complement damage, forming immune complexes, and indirectly inducing cytokine release. Notably, antinuclear antibodies, antimitochondrial antibodies, and anti-neutrophil cytoplasmic antibodies are key contributors to AIH, PBC, and PSC progression, respectively. Studies highlight dysregulations in innate immune system activation and immune tolerance breakdown, resulting in abnormal activation of cells like Th17 and natural killer (NK) cells, as well as reduced regulatory T (Treg) cells. This complexity impedes full understanding of AILDs, hindering stage-specific therapeutic development. Encouragingly, research teams have conclusively shown the immunologically mediated aetiology of these three diseases using genetic investigations. This highlights the potential for further immune-related investigations into AILDs using genome-wide association study (GWAS) and related methods.

Currently, the lack of effective curative measures for AILDs leaves these conditions without definitive therapeutic solutions. Consequently, patients are frequently required to undergo lifelong administration of immunosuppressive drugs or bile acids to manage hepatic or biliary inflammation (5). Promising research, such as Treg cell therapy, offers hope by suggesting that enhancing Treg cells in the liver could mitigate disease severity (6). Therefore, further investigation is crucial to understand the intricate relationship between AILDs and immunity. We need a deeper understanding of the immune system’s role in AILDs pathogenesis.

Mendelian randomization (MR) is a statistical tool that boldly investigates whether a specific factor has a causal impact on a particular health outcome, like disease risk (7). This method harnesses genetic variants as instrumental variables (IVs), capitalizing on the fact that genetic variants are biologically linked to certain factors but remain unaffected by environmental influences. Consequently, MR has the capacity to mimic the effect of a randomized trial on disease risk without being confounded by extraneous factors (8). In recent years, GWAS advancements have provided researchers with extensive genetic variation data, enhancing the comprehensiveness and precision of MR studies. Our investigation aims to shed light on the causal relationship between immune cell characteristics and AILDs through a thorough MR analysis. We present this article in accordance with the STROBE-MR reporting checklist (available at https://tgh.amegroups.com/article/view/10.21037/tgh-25-2/rc).


Methods

Study design

This study employed a bold approach: the two-sample MR analysis, a robust causal inference method. By using genetic variants as IVs, this analysis establishes causal relationships between exposure and outcome, effectively mitigating biases arising from confounding and reverse causation issues. The selection of IVs adheres to three fundamental principles in MR analysis: (I) direct association of genetic variants with the exposure (relevance assumption); (II) independence of genetic variants from potential confounders between exposure and outcome (independence assumption); and (III) exclusion of genetic variants’ influence on the outcome through pathways other than the exposure (exclusion-restriction assumption) (8). We conducted a daring two-sample MR analysis, utilizing summary-level data from extensive GWAS, to evaluate the causal links between 731 immune cell phenotypes and AIH, PBC and PSC, respectively (Figure 1). Ethical approval was diligently obtained from the respective institutions for all GWAS studies included in this research. This study was conducted in accordance with the Declaration of Helsinki and its subsequent amendments.

Figure 1 The design of MR analysis on the relationship between immune cell phenotypes and AILDs. AIH, autoimmune hepatitis; AILD, autoimmune liver disease; GWAS, genome-wide association study; MR, Mendelian randomization; PBC, primary biliary cholangitis; PSC, primary sclerosing cholangitis; SNP, single nucleotide polymorphism.

GWAS resource

We harnessed publicly available GWAS datasets as our primary data source. The exposure data, comprising immune cell phenotypes, were derived from a study conducted in 2020 involving 3,757 Sardinian individuals. This study delved into 731 immune cell phenotypes, exploring their natural genetic variations. The dataset encompassed 118 absolute counts (ACs), 389 mean fluorescence intensities (MFIs), 32 morphological parameters (MPs), and 192 relative cell counts (RCs). After analyzing over 20 million single nucleotide polymorphisms (SNPs), the research team identified 763 trait-variant associations and 53 novel loci (9).

Similarly, outcome data were sourced from publicly available GWAS analysis summaries. Data for AIH were obtained from a comprehensive analysis of 485,234 Europeans conducted in 2021, encompassing over twenty-four million SNPs (10). Data for PBC were obtained from a meta-analysis of a similar scale conducted in the same year. This meta-analysis utilized data from 24,510 European subjects and represented the most extensive GWAS analysis of PBC to date (11). Data for PSC were obtained from a comprehensive GWAS analysis conducted in 2017, which included 14,890 cases of European ethnicity. It’s important to note that all original studies obtained ethical approval and informed consent from all participants (12). Hence, all anonymized patient data utilized in this study strictly adhered to standard ethical guidelines. To address potential population stratification, we confirmed that exposure and outcome GWAS datasets were derived from independent cohorts, minimizing sample overlap.

IVs selection

In this study, the abundance of immune phenotype sample data provided ample opportunity to extract significantly independent SNPs. To ensure robustness, the significance threshold was boldly adjusted to 5e−8, setting stringent criteria for SNP selection. Additionally, within a 10,000 kb distance, linkage disequilibrium (LD) analysis was conducted with an r2 threshold <0.001 in PLINK 2.0, based on the 1000 Genomes European reference panel, further fortifying the independence of each SNP and mitigating the influence of genetic pleiotropy on the results (13). Furthermore, to mitigate analytical errors stemming from weak IVs, the F-statistic for each IV was calculated. IVs with an F-statistic surpassing 10 were considered robust and thus incorporated into the study. The F-statistic formula utilized for this computation, F = R2 × (N − 2)/(1 − R2), R2 = 2EAF (1 − EAF) β2, where R2 represents the cumulative explained variance of the selected IV, EAF denotes the effect allele frequency, β signifies the SNP’s estimated effect, and N denotes the sample size of the GWAS, was employed for this purpose (14). SNPs identified with such factors were subsequently excluded from the study. Importantly, since the GWAS data of exposure and outcomes originated from different studies, concerns regarding population overlap were effectively nullified.

Reverse MR analysis

We conducted a reverse MR analysis utilizing SNPs that have been established to be associated with AILDs, with the objective of elucidating the potential causal influence of AILDs on the previously identified significant associations with immune cells. SNPs significantly associated with AILDs (P value <5e−8) were selected as IVs, following the same LD clumping (r2<0.001, 10,000 kb distance) and F-statistic criteria (F>10) as the primary MR analysis. The criteria for selecting the IVs in this reverse MR analysis adhered strictly to those applied in the primary MR analysis, ensuring consistency and rigor in our methodology.

Statistical analysis

In our MR analysis of the relationship between immune cell phenotypes and ALDs, we utilized five common analytical methods, including the inverse variance weighted (IVW) method, the MR Egger method, the weighted median method, the simple mode method, and the weighted mode method. The IVW method is simple and powerful but may be biased by genetic heterogeneity (15). To enhance the significance of our MR analysis results, we adjusted the significance threshold to 0.001, surpassing the conventional threshold of 0.05. Furthermore, we ensured consistency by selecting exposure SNPs that produced consistent odds ratios (ORs) across all five analytical methods, thereby enhancing the credibility of our analysis results. Sensitivity analyses were then conducted to scrutinize horizontal pleiotropy and heterogeneity, examining additional impacts of IVs bypassing exposure pathways or significant differences in variable effects among different subgroups (16). For a positive outcome, the P values of both sensitivity analysis and Cochran’s Q test exceeding 0.05 indicated the absence of pleiotropy or heterogeneity. Conversely, P values below 0.05 signaled the presence of pleiotropy or heterogeneity (17), mandating individual analyses to determine inclusion in the study scope. Moreover, the MR-Pleiotropy Residual Sum and Outlier (MR-PRESSO) method was also utilized to evaluate the potential pleiotropic effects by comparing the actual residual sum of squares to the anticipated residual sum of squares. Additionally, we utilized various visual analyses to reinforce the reliability of our study. These comprised leave-one-out analysis to scrutinize the influence of individual SNPs on overall results, scatter plots to confirm the absence of anomalous impacts on outcomes, and funnel plots to evaluate correlation robustness and heterogeneity presence. For this analysis, we utilized the R statistical software, specifically version 4.1.2. All analyses were performed using the TwoSampleMR package in R. Data preprocessing and visualization were conducted with R packages dplyr, ggplot2, and forestplot.


Results

Selection of IVs

After conducting significance and LD screening of SNPs on 731 immune cell phenotypes, a total of 2,803 influential SNPs were filtered, involving 607 immune cell phenotypes. These phenotypes were categorized based on their typical characteristics and cell types, yielding proportions for each cell category (Figure 2). Notably, the MP category encompasses a relatively minor array of cell types, comprising solely conventional dendritic cells (cDCs) as well as T, B and natural killer (TBNK) cells, while the remaining feature classifications encompass seven distinct cell categories. Remarkably, all IVs boasted F-statistics surpassing 10, underscoring the robustness of their selection.

Figure 2 The summary of SNPs across different cell types after selection. AC, absolute count; cDC, conventional dendritic cell; MFI, mean fluorescence intensity; MP, morphological parameters; RC, relative cell count; SNP, single nucleotide polymorphism; TBNK, T, B and natural killer cells; Treg, regulatory T cells.

Causal effects of immunophenotypes on AILDs

In the current investigation, IVs culled from exposure data underwent MR scrutiny against outcome data about AIH, PBC and PSC. In general, the standard error of the IVW method tends to be lower than that of other methods. As a result, in cases where heterogeneity and horizontal pleiotropy are absent, priority will be given to utilizing the results obtained from the IVW analysis, which is considered the gold standard of MR analysis. Therefore, we first screened the results of IVW analysis based on a P value of 0.05, obtaining 40, 24, and 61 SNPs in AIH, PBC, and PSC. To enhance significance, we further narrowed the threshold to 0.001, reducing the significant SNPs in AIH, PBC, and PSC to 15, 16, and 9. We presented these preliminary screening results in Figure 3 in the form of three volcano plots, with results generated by different thresholds displayed in different colors, and also provided an initial description of the positive or negative orientations of each SNP with OR (Figure 3).

Figure 3 Volcano plot of MR results in immune cell phenotypes on the risk of AILDs. AIH, autoimmune hepatitis; AILD, autoimmune liver disease; cDC, conventional dendritic cell; MR, Mendelian randomization; OR, odds ratio; PBC, primary biliary cholangitis; PSC, primary sclerosing cholangitis; TBNK, T, B and natural killer cells.

After further confirmation that each SNP had five different analysis methods, all of which pointed in the same direction, a collective total of seven significant associations were sustained for AIH, three for PBC, and two for PSC (Figure 4). Among the 12 immune cell phenotypes scrutinized, there were representatives of Treg, TBNK cells, myeloid cells, monocytes, cDC, and B cells (Figure 2).

Figure 4 The MR results of five methods for positive SNPs obtained after sensitivity analysis screening. (A) Characteristic phenotypes and their analysis results in AIH. (B) Characteristic phenotypes and their analysis results in PBC. (C) Characteristic phenotypes and their analysis results in PSC. AC, absolute count; AIH, autoimmune hepatitis; CI, confidence interval; DC, dendritic cell; MR, Mendelian randomization; NK, natural killer; OR, odds ratio; PBC, primary biliary cholangitis; PSC, primary sclerosing cholangitis; SNP, single nucleotide polymorphism; unsw mem, unswitched memory.

In the AIH group, our research has identified seven immune cell types that may have causal links with AIH (Figure 4). Among these, HLA-DR on plasmacytoid DC and HLA-DR on CD33 HLA-DR+ myeloid cell demonstrated a positive association with AIH, suggesting that these immune cell phenotypes could heighten the risk of AIH. Conversely, the remaining immune cell phenotypes, including three phenotypes of NK cells (HLA-DR+ NK AC, HLA-DR+ NK %NK, and HLA-DR+ NK %CD3 lymphocyte) and two phenotypes of monocytes (CD14+ CD16+ monocyte AC, CD16 on CD14 CD16+ monocyte), exhibited a negative correlation.

Within the PBC enclave, our study indicated that three phenotypes of B cells, such as CD27 on CD24+ CD27+ B cell, CD27 on IgD+ CD38 unswitched memory (unsw mem) B cell, and CD27 on memory B cell, might have causal connections with PBC (Figure 4). All of the three B cell phenotypes considered in our investigation showed a positive correlation with PBC, suggesting that heightened levels of surface markers expressed by these cells could elevate the likelihood of developing PBC.

Similarly, amidst the PSC cohort, our study results indicated that two immune cell phenotypes, i.e., CD28 on CD45RA CD4 not Treg cell and FSC-A on CD4+ NK cell, might be associated with potential causality in PSC (Figure 4). Both of the two immune cell phenotypes examined in our analysis exhibited inverse correlations with PSC, suggesting that an augmentation in the abundance of surface markers expressed by these immune cells could reduce the risk of PSC development.

Reverse MR analysis

After conducting a reverse MR analysis between AILDs and the previous 12 significant immune cells, we found no evidence of reverse causal relationships among them across all applied MR methods. Notably, Cochran’s Q test and the MR-Egger intercept test indicated partial heterogeneity and horizontal pleiotropy in the reverse MR analysis, indicating variability in the effects of individual SNPs (Table 1).

Table 1

The results of Cochran’s Q and MR Egger analysis for positive SNPs without sensitivity analysis screening

Outcome Exposure Method Cochran’s Q MR Egger, P value
Q P value
AIH CD14+ CD16+ monocyte AC MR Egger 3.177 0.20 >0.99
IVW 3.177 0.37
HLA-DR+ NK AC MR Egger 2.866 0.24 0.77
IVW 3.023 0.39
HLA-DR+ NK %NK MR Egger 2.350 0.50 0.70
IVW 2.527 0.64
HLA-DR+ NK %CD3 lymphocyte MR Egger 2.949 0.23 0.73
IVW 3.173 0.37
CD28 CD8br AC MR Egger 0.136 0.71 0.94
IVW 0.145 0.93
CD16 on CD14 CD16+ monocyte MR Egger 3.963 0.41 0.47
IVW 4.591 0.47
HLA-DR on plasmacytoid DC MR Egger 3.320 0.77 0.09
IVW 7.319 0.40
HLA-DR on CD33 HLA-DR+ MR Egger 1.381 0.50 0.76
IVW 1.503 0.68
PBC CD27 on CD24+ CD27+ MR Egger 1.330 0.51 0.70
IVW 1.527 0.68
CD27 on IgD+ CD38 unsw mem MR Egger 1.307 0.25 0.61
IVW 1.939 0.38
CD27 on memory B cell MR Egger 1.403 0.71 0.56
IVW 1.831 0.77
PSC CD28 on CD45RA CD4 not Treg MR Egger 0.027 0.87 0.51
IVW 0.956 0.62
FSC-A on CD4+ MR Egger 1.386 0.24 0.96
IVW 1.393 0.50
HLA-DR on CD14 CD16 MR Egger 1.484 0.48 0.09
IVW 11.445 0.01
HLA-DR on monocyte MR Egger 2.293 0.13 0.31
IVW 10.366 0.006
HLA-DR on CD33 HLA-DR+ MR Egger 7.553 0.006 0.68
IVW 9.924 0.007

AC, absolute count; AIH, autoimmune hepatitis; DC, dendritic cell; IVW, inverse variance weighted; MR, Mendelian randomization; NK, natural killer; PBC, primary biliary cholangitis; PSC, primary sclerosing cholangitis; unsw mem, unswitched memory.

Sensitivity analysis

The P values obtained from the level of pleiotropy and heterogeneity analyses in each group are illustrated in Table 1. Although the P values for pleiotropy and heterogeneity of CD28 CD8br AC of Treg cell in the AIH group meet the screening criteria, the 95% CI in its MR Egger method ranges from 0.002 to 1,846, indicating an extreme outlier. To ensure data reliability, this analysis opts to exclude this SNP. Additionally, as depicted in Table 1, in the PSC group, some SNPs fail to meet the requirements of the pleiotropy analysis’s Cochran’s Q value, where P value is less than 0.05, namely: HLA-DR on CD14 CD16 monocyte, HLA-DR on monocyte, HLA-DR on CD33 HLA-DR+ myeloid cell. Therefore, according to the screening rules, the results from MR Egger and IVW methods cannot be explained due to the level of pleiotropy, violating the assumptions of MR. Consequently, these three SNPs were excluded from the results. As depicted in Table 1, the MR-PRESSO global test revealed no evidence of horizontal pleiotropy effects, with all P values greater than 0.05, for all exposures except for three exposures (CD27 on CD24+ CD27+ B cell, CD28 on CD45RA CD4 not Treg cell, FSC-A on CD4+ TBNK cell) where testing was not feasible due to insufficient SNPs (less than 4 SNPs).

In the end, we created a heatmap to illustrate the potential associations between the MR analysis results and sensitivity analysis outcomes for each significant SNP. In Figure 5, this heatmap incorporates the results of IVW analysis, as well as pleiotropy and heterogeneity analyses, with the shade of each color block representing the significance of each SNP (Figure 5). Scatter plots and leave-one-out analyses conducted on the filtered data consistently demonstrate stability, further affirming the robustness of the results (Figures S1-S3).

Figure 5 The heatmap of heterogeneity statistics results based on the IVW method for positive SNPs (P value ≤0.05). AIH, autoimmune hepatitis; IVW, inverse variance weighted; PBC, primary biliary cholangitis; PSC, primary sclerosing cholangitis; SNP, single nucleotide polymorphism.

Discussion

To our knowledge, this study is the first to explore the causal link between immune cell phenotypes and AILDs by using the MR method. Our findings, validated through rigorous checks for horizontal pleiotropy, reveal significant and independent associations. These results provide new insights into potential immunotherapy targets for addressing AILDs.

In the AIH cohort, HLA-DR on plasmacytoid DC and HLA-DR on CD33 HLA-DR+ myeloid cell has robustly demonstrated a positive correlation with AIH incidence, emphasizing the pivotal role of HLA-DR in immune cell function. In Europeans and North American Caucasians, AIH shows a correlation with various HLA-DR alleles, while in Japan and Argentina, the presence of different HLA-DR alleles highlights the diversity in AIH susceptibility among populations (18). The exact pathogenic mechanisms of HLA-DR in AIH remain elusive. Current research indicates that HLA-DRB1 might facilitate antigen recognition by CD4+ cells and the formation of effector cells, thus contributing to immune response processes within liver tissue. These processes may entail the outbreak of interferon-gamma (IFN-γ) by effector Th1 cells, ultimately resulting in liver tissue damage (19). Also, other research reveals that interleukin (IL)-17 from HLA-DR-activated Th17 cells worsens AIH by inducing hepatocyte pyroptosis via the STAT3-IFI16 pathway, boosting IL-1β production (20). Blocking IL-17 in animal models reduces liver damage, suggesting anti-IL-17 therapies may benefit AIH patients upon clinical validation (21).

The CD33+ HLA-DR phenotype represents a highly distinctive characteristic according to current classifications of myeloid-derived suppressor cells (MDSCs). It is trustworthy that MDSCs can be significant in immunosuppression, immune evasion, and tumor progression through both immunomodulatory and non-immunomodulatory mechanisms. In this context, we propose the intriguing notion that cells exhibiting surface antigen expression contrary to that of MDSCs may potentially lead to immune hyperactivity or even autoimmunity (22). Salivary proteomics revealed elevated levels of cystatin A, statherin, and histatins in AIH, suggesting a heightened antimicrobial defence mechanism that may contribute to this immune hyperactivity (23). We hope this concept will inspire further exploration among researchers in the field.

However, the analysis results for three other immune cell phenotypes seem to “challenge” our understanding of HLA-DR. With HLA-DR, three distinct phenotypes of NK cells all correlate negatively with AIH, implying a specific protective association with the disease. Current research shows that HLA-DR+ NK cells possess the distinctive features of both NK cells and dendritic cells (DCs), fulfilling a pivotal function within the innate immune system. Liver-resident NK cells, a unique subset, demonstrate enhanced secretion of cytokines and chemokines, potentially fostering liver immune tolerance (24). High tetraantennary sialylation in plasma N-glycans emerged as a unique marker for AIH, potentially aiding non-invasive diagnosis and reflecting altered immune regulation by liver-resident NK cells (25). Although direct associations with AIH have not been reported, liver-resident NK cells have been linked to other autoimmune diseases, suggesting a potentially similar relationship with AIH.

In human monocyte classification, CD14+ CD16+ and CD14 CD16+ belong to intermediate and non-classical monocyte subsets, respectively. Non-classical monocytes and CD16+ monocytes are recognized for their anti-inflammatory effects (26). They contribute to wound healing and enhance neutrophil adhesion by secreting tumor necrosis factor-alpha (TNF-α). These monocytes migrate and participate in immunosurveillance, exhibiting dual anti-inflammatory and pro-inflammatory functions (27). Studies on similar autoimmune diseases suggest their role in attenuating inflammation progression through pathways involving Treg recruitment and immune suppression via CXCL12 and transforming growth factor beta (TGF-β). Moreover, CD16+ monocytes express higher levels of CX3CR1, indicating the induction of more fractalkine (CX3CL1) into endothelial cells. CX3CL1 facilitates leukocyte migration and adhesion, potentially preventing liver fibrosis in animal models. Therefore, understanding the impact of the axis on liver function, especially in AIH patients, may lead to new therapeutic strategies.

The analysis reveals that CD27 expression on B cells indicates a substantial connection with the progression of PBC. CD27+ B cells are generally defined as memory B cells (28). Autoreactive B cells, among them, can generate autoantibodies upon interaction with self-antigens. In humans, CD27+ B cells have been identified as marginal zone (MZ) B cells with autoreactivity, which are prevalent in patients with autoimmune diseases and mouse models. These cells may exert harmful effects due to their rapid response to antigens (29). Additionally, CD24hiCD27+ B cells, known for their robust TNF-α synthesis, influence the progression of PBC and the transition from Th1 to Th17 cells, which may be crucial for inflammation in PBC (30,31).

Mass spectrometry (MS) studies have significantly deepened our understanding of PBC, revealing multiple biomarkers that reflect immunological and metabolic disturbances. These studies have found that certain metabolic molecules, such as acylcarnitines and free fatty acids, are associated with the severity of fibrosis and inflammation, indicating the role of lipid metabolism disorders in disease progression (32). Additionally, MS analysis has detected new autoantigens in patients who are negative for traditional anti-mitochondrial antibodies (AMA), suggesting broader autoimmune targets (33). These metabolic and immune biomarkers, in combination with immune features such as CD27+ B cells, highlight the complex interplay between immune activation and metabolic dysfunction in PBC, providing new directions for non-invasive disease monitoring and potential therapeutic targets.

Within the PSC cohort, two immune phenotypes, CD28 on CD45RA CD4 not Treg cell and FSC-A on CD4+ NK cell, seem to correlate with a diminished risk of PSC onset. The CD45RA CD4 not Treg subset, characterized by the expression of CD4, CD25, and CD127, falls under the category of CD4+ memory T cells. Recent research suggests that CD25+CD127hi cells may play a role in regulating inflammatory responses by favoring a Th2-type bias and dampening pro-inflammatory reactions. CD28, a crucial co-stimulatory molecule, is found to be depleted in CD28-deficient T cells observed in various autoimmune disorders, possibly due to prolonged antigen stimulation and exposure to TNF-α (34). A liquid chromatography-tandem MS assays confirm CD28 dysregulation in autoimmunity, with elevated glutamine and tryptophan derivatives like kynurenine linked to altered T-cell metabolism in PSC (35). This depletion may weaken the regulatory effects on CD4+CD25+ Treg cells, leading to chronic activation of CD28 T cells. These activated T cells can migrate to liver tissues, accumulate around bile ducts, and release high levels of TNF-α and IFN-γ, promoting inflammatory progression in PSC by inducing the expression of inflammatory molecules in nearby bile epithelial cells Also, recent bile proteome studies in PSC confirm heightened inflammation through elevated IL-8 and ANXA1 (36), which correlate with T cell and NK cell activities, thus reinforcing the significance of CD28 and FSC-A phenotypes in PSC risk (23,37).

Our study possesses several strengths. Firstly, we used multiple MR methods to confirm our findings’ accuracy. Moreover, the potential bias stemming from weak IVs was mitigated, as all our F values exceeded 10. Reverse MR analysis demonstrated that genetically predicted AILDs had no causal effect on significant immune cells. Furthermore, by exclusively focusing on European populations, we minimized any potential bias arising from ethnic disparities. Therefore, these measures were taken to reduce the risk of plagiarism.

However, our study has certain limitations. Despite considering numerous immune cell phenotypes, some remained unexamined due to data limitations. Furthermore, the limited statistical data on such diseases in major global disease databases might compromise the universality of the analytical results. For robustness, future validation in larger, diverse patient cohorts is essential. This study initiates exploration into the connection between immune cell phenotypes and AILDs. Subsequent research can delve deeper into this association and explore potential immunotherapeutic targets, thus paving the way for innovative approaches to treating AILDs.


Conclusions

This study highlights the potentially causal correlation between immune cell phenotypes and AILDs, providing us with further clues to explore the pathogenesis of AILDs. Through an in-depth investigation of immune cell phenotypes, we may better understand the pathophysiological processes underlying AILDs, offering valuable insights for future functional studies to validate these associations and advance understanding of AILDs mechanisms.


Acknowledgments

We acknowledge the funding and the investigators who contributed to the research in this study.


Footnote

Reporting Checklist: The authors have completed the STROBE-MR reporting checklist. Available at https://tgh.amegroups.com/article/view/10.21037/tgh-25-2/rc

Peer Review File: Available at https://tgh.amegroups.com/article/view/10.21037/tgh-25-2/prf

Funding: This study was supported by the National Key Research and Development Program of China (No. 2022YFC2303600 to D.K.J.), the General Programs from the National Natural Science Foundation of China (No. 82272765 to D.K.J.), the Guangdong Basic and Applied Basic Research Foundation (No. 2022A1515220090 to D.K.J.), the Local Innovative and Research Teams Project of Guangdong Pearl River Talents Program (No. 2017BT01S131 to D.K.J.), the Innovative Research Team Project of Guangxi Province (No. 2017GXNSFGA198002 to D.K.J.), the Grant for Recruited Talents to Start Scientific Research from Nanfang Hospital, and the Outstanding Youth Development Scheme of Nanfang Hospital, Southern Medical University (No. 2017J001 to D.K.J.).

Conflicts of Interest: All authors have completed the ICMJE uniform disclosure form (available at https://tgh.amegroups.com/article/view/10.21037/tgh-25-2/coif). The authors have no conflicts of interest to declare.

Ethical Statement: The authors are accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved. This study was conducted in accordance with the Declaration of Helsinki and its subsequent amendments.

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doi: 10.21037/tgh-25-2
Cite this article as: Zou H, Liang X, Luo M, Pan X, Jiang DK. Causal effects of immune cell phenotypes on the risk of autoimmune liver diseases: a bidirectional two-sample Mendelian randomization study. Transl Gastroenterol Hepatol 2025;10:68.

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