Interferon subverts an AHR-JUN axis to promote CXCL13+ T cells in lupus

T cell-B cell interactions in human autoimmune diseases

Activation of autoreactive B cells and production of specific autoantibodies are hallmark features of many autoimmune diseases. B cell differentiation into antibody-secreting cells typically requires help from cognate T cells, which provide both cytokines and cell surface signals in an intricate intercellular interaction. A range of T cells can provide this help to B cells, including T follicular helper cells in follicles of secondary lymphoid organs, as well as T peripheral helper cells, which accumulate within inflamed target tissues in autoimmune diseases. Here, we discuss recent observations about the phenotypes of B cell-helper T cells that accumulate in inflamed tissues and in circulation of patients with autoimmune diseases, the correlations between B cell-helper T cells and B cells in these tissues, and key mediators of productive T cell-B cell interactions, with a focus on mediators that are being targeted therapeutically. Understanding the scope of B cell-helper T cells and their functions will improve our ability to quantify and track pathologic T cell-B cell interactions in human autoimmune diseases and may highlight critical mediators that can be targeted to suppress these interactions therapeutically.

Recent Advances of Type I Interferon on the Regulation of Immune Cells and the Treatment of Systemic Lupus Erythematosus

Systemic lupus erythematosus (SLE) is a chronic autoimmune disease with multiple organ damage. Several studies have found that, in addition to significant production of autoantibodies, the majority of SLE patients exhibit increased expression of type I interferon (IFN-I) regulated genes (also known as IFN-I traits), and that IFN-I plays a crucial role in the pathogenesis of SLE. In SLE, virtually all immune cells are dysregulated, and most of these aberrant dysregulations are directly or indirectly affected by IFN-I. The mechanism of action of IFN-I in these immune cells is multifaceted. In this review, we focus on the immune cell types that produce IFN-I and are affected by IFN-I in SLE. Importantly, we explore the research progress of related drugs in terms of IFN-I production, itself, and downstream. Here we provide the most up-to-date information on the mechanisms that lead to the pathogenesis of SLE, providing the basis for the development of innovative future therapies and future research directions.

RNA modification: a promising code to unravel the puzzle of autoimmune diseases and CD4+ T cell differentiation

Dynamic changes in various forms of RNA modification are critical to the functional homeostasis of the immune system and the pathophysiology of autoimmune diseases. RNA modification-related proteins play an essential role in these processes. At present, the research methods of RNA modification in autoimmune diseases are mainly to detect the expression changes of RNA modification-related proteins in tissues or cells, but there is a lack of explorations of target RNAs and in-depth mechanisms. Considering the important role of CD4+ T cell dysfunction in the pathogenesis and progression of autoimmune diseases, the regulatory effect of abnormal RNA modification on CD4+ T cells deserves attention, which will provide a perspective for further exploring the mechanism of RNA modification in autoimmune diseases. In this Review, we discuss the abnormal RNA modification changes in patients with autoimmune diseases and highlight the effects of these abnormal changes on CD4+ T cells.

Systemic lupus erythematosus: updated insights on the pathogenesis, diagnosis, prevention and therapeutics

Systemic lupus erythematosus (SLE) is a chronic inflammatory illness with heterogeneous clinical manifestations covering multiple organs. Diversified types of medications have been shown effective for alleviating SLE syndromes, ranging from cytokines, antibodies, hormones, molecular inhibitors or antagonists, to cell transfusion. Drugs developed for treating other diseases may benefit SLE patients, and agents established as SLE therapeutics may be SLE-inductive. Complexities regarding SLE therapeutics render it essential and urgent to identify the mechanisms-of-action and pivotal signaling axis driving SLE pathogenesis, and to establish innovative SLE-targeting approaches with desirable therapeutic outcome and safety. After introducing the research history of SLE and its epidemiology, we categorized primary determinants driving SLE pathogenesis by their mechanisms; combed through current knowledge on SLE diagnosis and grouped them by disease onset, activity and comorbidity; introduced the genetic, epigenetic, hormonal and environmental factors predisposing SLE; and comprehensively categorized preventive strategies and available SLE therapeutics according to their functioning mechanisms. In summary, we proposed three mechanisms with determinant roles on SLE initiation and progression, i.e., attenuating the immune system, restoring the cytokine microenvironment homeostasis, and rescuing the impaired debris clearance machinery; and provided updated insights on current understandings of SLE regarding its pathogenesis, diagnosis, prevention and therapeutics, which may open an innovative avenue in the fields of SLE management.

Altered X-chromosome inactivation of the TLR7/8 locus and heterogeneity of pDCs in systemic sclerosis

Systemic sclerosis (SSc) is an autoimmune disease that has a strong female predominance. Both the X-linked TLR7 and TLR8 can induce type I IFN (IFN-I) by plasmacytoid DCs (pDCs), which can promote fibrosis. We identified five subclusters of pDCs, including ISGhigh clusters that were over-represented in SSc patients. We observed that both TLR7 and TLR8 genes escape from X chromosome inactivation (XCI) at higher frequency in pDCs of SSc patients, which was associated with changes in TLR7 protein profile. Combined DNA/RNA FISH analysis revealed that the TLR7/8 locus is preferentially located outside of the inactive X (Xi) territory when TLR7 is expressed, suggesting that higher-order loop formation is linked to TLR7/8 expression from the Xi. Furthermore, the expression levels of XIST and the transcriptional repressor SPEN were reduced in SSc pDCs. Hence, our data revealed the heterogeneity of pDCs in SSc and suggested that altered XCI at the TLR7/8 locus may contribute to the chronic IFN-I activity of pDCs in female SSc patients.

Treg fitness signatures as a biomarker for disease activity in Juvenile Idiopathic Arthritis

Juvenile Idiopathic Arthritis (JIA) is an autoimmune condition characterised by flares of joint inflammation. However, no reliable biomarker exists to predict the erratic disease course. Normally, regulatory T cells (Tregs) maintain tolerance, with altered Tregs associated with autoimmunity. Treg signatures have shown promise in monitoring other conditions, therefore a Treg gene/protein signature could offer novel biomarker potential for predicting disease activity in JIA. Machine learning on our nanoString Treg 48-gene signature on peripheral blood (PB) Tregs generated a model to distinguish active JIA (active joint count, AJC≥1) Tregs from healthy controls (HC, AUC = 0.9875 on test data). Biomarker scores from this model successfully differentiated inactive (AJC = 0) from active JIA PB Tregs. Moreover, scores correlated with clinical activity scores (cJADAS), and discriminated subclinical disease (AJC = 0, cJADAS≥0.5) from remission (cJADAS<0.5). To investigate altered protein expression as a surrogate measure for Treg fitness in JIA, we utilised spectral flow cytometry and unbiased clustering analysis. Three Treg clusters were of interest in active JIA PB, including TIGIThighCD226highCD25low Teff-like Tregs, CD39-TNFR2-Helioshigh, and a 4-1BBlowTIGITlowID2intermediate Treg cluster predominated in inactive JIA PB (AJC = 0). The ratio of these Treg clusters correlated to cJADAS, and higher ratios could potentially predict inactive individuals that flared by 9-month follow-up. Thus, we demonstrate altered Treg signatures and subsets as an important factor, and useful biomarker, for disease progression versus remission in JIA, revealing genes and proteins contributing to Treg fitness. Ultimately, PB Treg fitness measures could serve as routine biomarkers to guide disease and treatment management to sustain remission in JIA.

Dysregulated Intestinal Host-Microbe Interactions in Systemic Lupus Erythematosus: Insights from Patients and Mouse Models

Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by chronic inflammation that affects multiple organs, with its prevalence varying by ethnicity. Intestinal dysbiosis has been observed in both SLE patients and murine models. Additionally, intestinal barrier impairment is thought to contribute to the ability of pathobionts to evade and breach immune defenses, resulting in antigen cross-reactivity, microbial translocation, subsequent immune activation, and, ultimately, multiple organ failure. Since the detailed mechanisms underlying these processes are difficult to examine using human samples, murine models are crucial. Various SLE murine models, including genetically modified spontaneous and inducible murine models, offer insights into pathobionts and how they dysregulate systemic immune systems. Furthermore, since microbial metabolites modulate systemic immune responses, bacteria and their metabolites can be targeted for treatment. Based on human and mouse research insights, this review examines how lupus pathobionts trigger intestinal and systemic immune dysregulation. Therapeutic approaches, such as fecal microbiota transplantation and dietary adjustments, show potential as cost-effective and safe methods for preventing and treating SLE. Understanding the complex interactions between the microbiota, host factors, and immune dysregulation is essential for developing novel, personalized therapies to tackle this multifaceted disease.

Multi-centered clinical validation demonstrating superior precision in lupus diagnosis: T cell autoantibodies and TC4d outperform conventional lupus erythematosus biomarkers

Introduction

T Cell autoantibodies, TIgG and TIgM, as well as the T Cell-bound complement protein fragment C4d (TC4d) are novel diagnostic biomarkers that have demonstrated high specificity and sensitivity for SLE. The present study aims to characterize the clinical performance characteristics of the emergent T Cell biomarkers in a multi-center clinical validation cohort.

Methods

A cohort of 400 adult patients enrolled across 3 academic and 2 community-based autoimmune rheumatic centers, comprised of 105 SLE patients, 173 patients with autoimmune rheumatic diseases (ARD), 83 apparently healthy volunteers (AHV) and 39 other (non-autoimmune) disease (OD) controls were tested for TC4d, TIgG, TIgM and an extensive autoantibody profile. Diagnostic specificity was assessed against the ARD, AHV and OD groups, individually. Semi-quantitative flow cytometry analysis included TIgG and TIgM autoantibodies, cell-bound complement activation products (CB-CAPs), TC4d, erythrocyte-bound C4d (EC4d) and B lymphocyte-bound C4d (BC4d). Conventional autoantibodies and soluble complement proteins, C3 and C4, were assessed by ELISA and immunoturbidimetry, respectively.

Results

ROC analysis distinguishing ANA-positive (ANA+) SLE (N = 91) from ARD, TIgG, BC4d and TC4d demonstrated AUC values 0.81, 0.80 and 0.79, respectively, outperforming anti-dsDNA (0.72), C3 (0.69), TIgM (0.67), C4 (0.66) and anti-Smith (0.61). A similar ranking of discriminatory power was observed in ROC analysis distinguishing ANA+ SLE vs. OD as well as ANA+ SLE vs. AHV. At 95% diagnostic specificity for SLE vs. AHV, the sensitivity (95% CI) of TC4d, TIgG and TIgM for SLE was 58.1% (48.1 - 67.7%), 31.4% (22.7 - 41.2%) and 29.5% (21.0 - 39.2%), respectively. The T Cell SLE biomarkers uniquely identified 19% (20/105) of SLE patients who were otherwise negative (serologically inactive) for conventional SLE autoantibodies and had normal serum complement levels. Among the serologically inactive SLE subset, the T Cell SLE biomarkers collectively identified 53% of subjects.

Conclusions

The novel SLE biomarkers TC4d, TIgG and TIgM consistently outperform conventional markers across multiple cohorts. Their integration enhances diagnostic sensitivity, especially in SLE-specific autoantibody negative patients with normal complement levels. When coupled with conventional biomarkers, these novel tests may enable earlier and more accurate SLE detection, leading to more timely diagnosis and treatment.

Cellular and molecular determinants mediating the dysregulated germinal center immune dynamics in systemic lupus erythematosus

Introduction

Systemic lupus erythematosus (SLE) is characterized by dysregulated humoral immunity, leading to the generation of autoreactive B cells that can differentiate both within and outside of lymph node (LN) follicles.

Methods

Here, we employed spatial transcriptomics and multiplex imaging to investigate the follicular immune landscaping and the in situ transcriptomic profile in LNs from SLE individuals.

Results

Our spatial transcriptomic analysis revealed robust type I IFN and plasma cell signatures in SLE compared to reactive, control follicles. Cell deconvolution revealed that follicular T cell subsets are mainly affected by the type I IFN fingerprint of SLE follicles. Dysregulation of TFH differentiation was documented by i) the significant reduction of Bcl6hi TFH cells, ii) the reduced cell density of potential IL-4 producing TFH cell subsets associated with the impaired transcriptomic signature of follicular IL-4 signaling and iii) the loss of their correlation with GC-B cells. This profile was accompanied by a marked reduction of Bcl6hi B cells and an enrichment of extrafollicular CD19hiCD11chiTbethi, age-associated B cells (ABCs), known for their autoreactive potential. The increased prevalence of follicular IL-21hi cells further reveals a hyperactive microenvironment in SLE compared to control.

Discussion

Taken together, our findings highlight the altered immunological landscape of SLE follicles, likely fueled by potent inflammatory signals such as sustained type I IFN and/or IL-21 signaling. Our work provides novel insights into the spatial molecular and cellular signatures of SLE follicular B and TFH cell dynamics, and points to druggable targets to restore immune tolerance and enhance vaccine responses in SLE patients.

Inflammatory Gene Signature Identified by Machine Algorithms Reveals Novel Biomarkers of Coronary Artery Disease

Purpose

Inflammatory activation of immune cells plays a pivotal role in the development of coronary artery diseases (CAD). This study aims to investigate the immune responses of peripheral blood mononuclear cells (PBMCs) in CAD and to identify novel signature genes and biomarkers using machine learning algorithms.

Methods

The GSE113079 dataset was analyzed and differentially expressed genes (DEGs) were identified between CAD and normal samples. The intersection of DEGs with inflammation-related genes was used to identify the differentially expressed inflammation-related genes (DIRGs). Then, the receiver operating characteristic (ROC) curves were plotted for each DIRG, and those with an area under the curve (AUC) greater than 0.9 were selected for subsequent analysis. Furthermore, machine learning algorithms were employed to identify biomarkers. A nomogram was developed based on these biomarkers. The CIBERSORT algorithm and Wilcoxon test method were used to analyze the differences in immune cells between the CAD and normal samples. The identified biomarkers were validated in PBMCs from patients with CAD and in atherosclerotic aortas from ApoE-/- mice.

Results

A total of 574 DEGs were identified between CAD and normal samples. From this intersection, 29 DIRGs were identified, of which 14 DIRGs (PTGER1, IL17RC, KLKB1, GPR32, ADM, NUPR1, SCN9A, IL17B, CX3CL1, FFAR3, PYDC2, SYT11, RORA, and GPR31) exhibited high diagnostic efficacy. Four biomarkers (ADM, NUPR1, PTGER1, and PYDC2) were identified using Support Vector Machine (SVM). Ten types of immune cells, including CD8+ T cells, regulatory T cells (Tregs), and resting NK cells, showed significant differences between the CAD and normal groups. Furthermore, increased levels of ADM, NUPR1, PTGER1, and PYDC2 were validated in PBMCs isolated from CAD patients. In addition, ADM, NUPR1, and PTGER1 were upregulated in the mouse atherosclerotic aorta.

Conclusion

Our findings revealed novel inflammatory gene signatures of CAD that could be potential biomarkers for the early diagnosis of CAD.

Single cell profiling of circulating autoreactive CD4 T cells from patients with autoimmune liver diseases suggests tissue imprinting

Autoimmune liver diseases (AILD) involve dysregulated CD4 T cell responses against liver self-antigens, but how these autoreactive T cells relate to liver tissue pathology remains unclear. Here we perform single-cell transcriptomic and T cell receptor analyses of circulating, self-antigen-specific CD4 T cells from patients with AILD and identify a subset of liver-autoreactive CD4 T cells with a distinct B-helper transcriptional profile characterized by PD-1, TIGIT and HLA-DR expression. These cells share clonal relationships with expanded intrahepatic T cells and exhibit transcriptional signatures overlapping with tissue-resident T cells in chronically inflamed environments. Using a mouse model, we demonstrate that, following antigen recognition in the liver, CD4 T cells acquire an exhausted phenotype, play a crucial role in liver damage, and are controlled by immune checkpoint pathways. Our findings thus suggest that circulating autoreactive CD4 T cells in AILD are imprinted by chronic antigen exposure to promote liver inflammation, thereby serving as a potential target for developing biomarkers and therapies for AILD.

Clonal relationships between Tph and Tfh cells in patients with SLE and in murine lupus

Pathologic T cell-B cell interactions drive disease in systemic lupus erythematosus (SLE). The T cells that activate B cell responses include T peripheral helper (Tph) and T follicular helper (Tfh) cells, yet the developmental and clonal relationships between these B cell-helper T cell populations are unclear. Here we use T cell receptor (TCR) profiling to demonstrate clonal overlap between Tph and Tfh cells in the circulation of patients with SLE. Expanded Tph and Tfh cell clones persist over the course of 1 year in patients with a new diagnosis of SLE, and clones are observed to shift both from Tfh to Tph cells and from Tph to Tfh cells over time. High resolution analysis of cells sorted as Tph cells (CXCR5- PD-1hi) and Tfh cells (CXCR5+ PD-1hi) from SLE patients revealed considerable heterogeneity among cells sorted as Tph cells and highlighted a specific cluster of cells that expressed transcriptomic features of activated B cell-helper T cells. This cell population, marked by expression of TOX and CXCL13, was found in both sorted Tph and Tfh cells, and was clonally linked in these two populations. Analysis of B cell-helper T cells in murine pristane-induced lupus demonstrated similar populations of Tph and Tfh cells in both lung and spleen with strong clonal overlap. T cell-specific loss of Bcl6 prevented accumulation of Tfh cells and reduced accumulation of Tph cells in pristane-treated mice, indicating a role for Bcl6 in the survival and expansion of both populations. Together, these observations demonstrate a shared developmental path among pathologically expanded Tph and Tfh cells in lupus. The persistence of expanded Tph and Tfh cells clones over time may impose barriers to induction of stable tolerance by immunosuppressive medications or by B cell depletion.

Disease-associated B cells and immune endotypes shape adaptive immune responses to SARS-CoV-2 mRNA vaccination in human SLE

Severe acute respiratory syndrome coronavirus 2 mRNA vaccination has reduced effectiveness in certain immunocompromised individuals. However, the cellular mechanisms underlying these defects, as well as the contribution of disease-induced cellular abnormalities, remain largely unexplored. In this study, we conducted a comprehensive serological and cellular analysis of patients with autoimmune systemic lupus erythematosus (SLE) who received the Wuhan-Hu-1 monovalent mRNA coronavirus disease 2019 vaccine. Our findings revealed that patients with SLE exhibited reduced avidity of anti-receptor-binding domain antibodies, leading to decreased neutralization potency and breadth. We also observed a sustained anti-spike response in IgD-CD27- 'double-negative (DN)' DN2/DN3 B cell populations persisting during memory responses and with greater representation in the SLE cohort. Additionally, patients with SLE displayed compromised anti-spike T cell immunity. Notably, low vaccine efficacy strongly correlated with higher values of a newly developed extrafollicular B and T cell score, supporting the importance of distinct B cell endotypes. Finally, we found that anti-BAFF blockade through belimumab treatment was associated with poor vaccine immunogenicity due to inhibition of naive B cell priming and an unexpected impact on circulating T follicular helper cells.

The essential roles of memory B cells in the pathogenesis of systemic lupus erythematosus

Emerging evidence indicates that memory B cells are dysfunctional in systemic lupus erythematosus (SLE). They are hyporesponsive to signalling through the B cell receptor (BCR) but retain responsiveness to Toll-like receptor (TLR) and type I interferon signalling, as well as to T cell-mediated activation via CD40-CD154. Chronic exposure to immune complexes of ribonucleoprotein (RNP)-specific autoantibodies and TLR-engaging or BCR-engaging cargo is likely to contribute to this partially anergic phenotype. TLR7 or TLR8 signalling and the resulting production of type I interferon, as well as the sustained activation by bystander T cells, fuel a positive feedforward loop in memory B cells that can evade negative selection and permit preferential expansion of anti-RNP autoantibodies. Clinical trials of autologous stem cell transplantation or of B cell-targeted monoclonal antibodies and chimeric antigen receptor (CAR) T cells have correlated replenishment of the memory B cell population with relapse of SLE. Moreover, the BCR hyporesponsiveness of memory B cells might explain the failure of non-depleting B cell-targeting approaches in SLE, including BTK inhibitors and anti-CD22 monoclonal antibodies. Thus, targeting of dysfunctional memory B cells might prove effective in SLE, while also avoiding the adverse events of broad-spectrum targeting of B cell and plasma cell subsets that are not directly involved in disease pathogenesis.

Unraveling the origins of pathogenic CXCL13+ helper T cells in systemic lupus erythematosus

This Research Highlight discusses a recent publication, where the authors identified an increase in CXCL13+ peripheral helper T/follicular helper T cells, which was concomitant with a decrease in CD96+ T helper 22 (TH22) cells in patients with systemic lupus erythematosus. The genetic and epigenetic cues that reciprocally regulate this pathogenic imbalance of T-cell subsets were also identified, thus providing targets for therapeutic intervention.

Environment and systemic autoimmune rheumatic diseases: an overview and future directions

Introduction

Despite progress in our understanding of disease pathogenesis for systemic autoimmune rheumatic diseases (SARD), these diseases are still associated with high morbidity, disability, and mortality. Much of the strongest evidence to date implicating environmental factors in the development of autoimmunity has been based on well-established, large, longitudinal prospective cohort studies.

Methods

Herein, we review the current state of knowledge on known environmental factors associated with the development of SARD and potential areas for future research.

Results

The risk attributable to any particular environmental factor ranges from 10-200%, but exposures are likely synergistic in altering the immune system in a complex interplay of epigenetics, hormonal factors, and the microbiome leading to systemic inflammation and eventual organ damage. To reduce or forestall the progression of autoimmunity, a better understanding of disease pathogenesis is still needed.

Conclusion

Owing to the complexity and multifactorial nature of autoimmune disease, machine learning, a type of artificial intelligence, is increasingly utilized as an approach to analyzing large datasets. Future studies that identify patients who are at high risk of developing autoimmune diseases for prevention trials are needed.

Lymphocyte antigen 6 family member E suppresses apoptosis and promotes pancreatic cancer growth and migration via Wnt/β-catenin pathway activation

Pancreatic cancer (PC) is the primary cause of cancer-related mortality. Due to the absence of reliable biomarkers for predicting prognosis or guiding treatment, there is an urgent need for molecular studies on PC. Lymphocyte antigen 6 family member E (LY6E) is implicated in uncontrolled cell growth across various cancers. However, the precise mechanism of LY6E in PC remains unclear. Here, we conducted comprehensive bioinformatic analyses using online tools and R- × 64-4.1.1, complemented by experimental validation through Western blotting, immunohistochemistry, immunosorbent assays, flow cytometry, cell assays, and animal models. Our findings reveal significantly elevated expression of LY6E in PC, correlating with poor prognosis. LY6E knockdown inhibited proliferation, invasion, and migration of PC cells, while enhancing apoptosis evidenced by increased cleaved caspase 3 levels and alterations in the Bcl-2/Bax ratio. Conversely, LY6E overexpression promoted PC cell proliferation and migration, and inhibited apoptosis. Mechanistically, LY6E downregulation suppressed the Wnt/β-catenin signaling pathway. In vivo studies demonstrated that LY6E suppression attenuated tumor growth in murine models. Additionally, LY6E suppression resulted in reduced tumor growth in mice. In conclusion, our study confirms the significant role of LY6E in the progression of PC. LY6E, serving as an independent prognostic indicator, has the potential to serve as a valuable biomarker for PC to inform treatment strategies.