Myasthenia gravis-specific aberrant neuromuscular gene expression by medullary thymic epithelial cells in thymoma

The characteristics of new-onset myasthenia gravis after COVID-19 outbreak: a cross-sectional study

BACKGROUND

Little research has been conducted on new-onset myasthenia gravis (MG) patients following the coronavirus disease 2019 (COVID-19) pandemic. COVID-19 surged in China on December 7th, 2022. This study aimed to explore the clinical characteristics of new-onset MG patients after COVID-19 and analyze factors affecting their disease improvement.

METHODS

All new-onset MG patients before (December 1st, 2021 to December 7th, 2022) and after COVID-19 outbreak (December 8th, 2022 to November 30th, 2023) were included in this study. Data was collected through the electronic medical record system and follow-up. Multivariate logistic regression was used to identify independent predictors of clinical improvement in patients with new-onset MG.

RESULTS

359 new-onset MG patients (165 before COVID-19 outbreak and 194 after COVID-19 outbreak) were enrolled in this study. After COVID-19 outbreak, there was an increase in new-onset MG patients, with more cases occurring within the first three months. The rates of pulmonary inflammation (40.28%), COVID-19 vaccination (88.14%), and treatment with tacrolimus (15.98%) and MG duration (15 weeks, IQR: 5.75, 32) were higher, while rates of thymectomy (13.92%), baseline MG-ADL (3, IQR: 3, 6), and QMGS (7, IQR: 5,8) were lower compared to new-onset MG patients before COVID-19 outbreak. Multivariate logistic regression analysis showed that age at onset (OR 0.964, p < 0.001), baseline MG-ADL (OR 1.611, p < 0.001), and ocular MG (OR 0.401, p = 0.041) were independent predictors of clinical improvement in new-onset MG after the COVID-19 outbreak.

CONCLUSION

In this single-center cross-sectional study, new-onset MG patients following the COVID-19 outbreak showed altered seasonal onset patterns, milder disease severity, and higher OMG onset age. Age at onset is an independently negative predictor of improvement in new-onset MG patients after the COVID-19 outbreak. Whereas baseline MG-ADL is an independently positive predictor.

Mechanisms of autoimmune-mediated paraneoplastic syndromes: immune tolerance and disease pathogenesis

Paraneoplastic syndromes represent a clinically heterogeneous group of disorders that arise in cancer patients. Although their underlying mechanisms are only partly understood, immune or endocrine mechanisms are believed to play key roles. Autoimmune-mediated paraneoplastic syndromes (AMPS) are typically characterized by the presence of autoantibodies, making their identification important for both AMPS diagnosis and early cancer detection. This review synthesizes emerging insights into the pathogenesis of AMPS, with a particular focus on how genomic instability in cancer cells promotes immune recognition of altered self-proteins. Mechanisms such as ectopic expression, protein modifications (such as isoaspartylation), and gene amplifications can disrupt immune tolerance, leading to autoimmunity. Additionally, chronic inflammation and the formation of tertiary lymphoid structures within the tumor microenvironment contribute to both antitumor immunity and autoimmunity. Immune checkpoint inhibitors (ICIs), have revolutionized cancer treatment by enhancing antitumor immunity, but they can also induce immune-related adverse events (irAEs), some of which mimic AMPS. These irAEs highlight the critical roles of both humoral and cellular immunity in AMPS development. By exploring the relationships between ICI treatment, immune tolerance, and tumor-specific antigens, this review aims to clarify the mechanisms driving AMPS and their dual role in cancer control and immune-mediated disease. Bridging these knowledge gaps may inform the development of novel therapeutic strategies for managing AMPS and in optimizing the use of ICIs in cancer care.

Clinical Application of 68 Ga-Pentixafor PET/CT for the Detection of Thymoma: A Pilot Study

PURPOSE

This study was designed to evaluate 68 Ga-pentixafor, which targets C-X-C chemokine receptor 4 (CXCR4), in the noninvasive diagnosis of thymomas.

PATIENTS AND METHODS

With institutional review board approval and signed informed consent, 32 patients with thymic masses were enrolled in this study, and all patients underwent 68 Ga-pentixafor PET/CT scans.

RESULTS

Among the 28 patients included in the analysis, 13 patients were diagnosed with thymomas, 9 patients with cysts, and 6 patients with other anterior mediastinal masses. 68 Ga-pentixafor identified all patients with thymomas (13/13, 100%), and the mean SUV max in all 13 thymomas lesions was 13.96±8.20, which was significantly higher than that in patients with cysts (1.54±0.88) and other anterior mediastinal masses (2.59±1.68), respectively ( P <0.001).

CONCLUSIONS

The preliminary study indicates the diagnostic utility of 68 Ga-pentixafor in thymomas and the differential diagnostic ability of 68 Ga-pentixafor in thymomas, thymic cysts and other benign anterior mediastinal masses.

Thymic Mimetic Cells: Evolutionarily Ancient Mirrors of the Periphery

Thymic mimetic cells are hybrids of medullary thymic epithelial cells and diverse peripheral cell types. They are important for imposition of self-tolerance and perform other functions similar to those of their peripheral counterparts. Following early histological observations of “misplaced” stromal cells in thymi from multiple species, mimetic cells were first molecularly investigated in mice. Recent studies have characterized mimetic cells in humans and zebrafish with high-resolution. Many mimetic cell types are conserved across species, although specialized subtypes as well as variable frequencies and levels of specialization are also apparent. Features of the human mimetic cell repertoire, such as the expanded nature of muscle mimetic cells with potential implications in myasthenia gravis and the similarity of tuft mimetic cells and thymic carcinomas, hint at their relevance in human disease. Here we review what is known about mimetic cells across diverse organisms. We discuss potential pressures shaping the composition of the mimetic cell repertoire within and across species, and highlight potential therapeutic applications in human disease.

UniMap: Type-Level Integration Enhances Biological Preservation and Interpretability in Single-Cell Annotation

Integrating single-cell datasets from multiple studies provides a cost-effective way to build comprehensive cell atlases, granting deeper insights into cellular characteristics across diverse biological systems. However, current data integration methods struggle with interference in partially overlapping datasets and varying annotation granularities. Here, a multiselective adversarial network is introduced for the first time and present UniMap, which functions as a "discerner" to identify and exclude interfering cells from various data sources during dataset integration. Compared to other state-of-the-art methods, UniMap emphasizes type-level integration and proves to be the best model for preserving biological variability, achieving noticeably higher accuracy in single-cell automated annotation under various circumstances. Additionally, it enhances interpretability by revealing shared and domain-specific cell types and providing prediction confidence. The efficacy of UniMap is demonstrated in terms of identifying new cell types, creating high-resolution cell atlases, annotating cells along developmental trajectories, and performing cross-species analysis, underscoring its potential as a robust tool for single-cell research.

Phenotypic and functional dysregulations of CD8 + T Cells in myasthenia gravis

Myasthenia Gravis (MG) is a heterogeneous autoimmune disorder characterized by fluctuating muscle weakness caused by autoantibodies targeting neuromuscular junction components. While the role of CD4 + T cells in MG is well established, the contribution of CD8 + T cells remains poorly understood. In this study, we analyze CD8 + T cells in 36 MG patients and 38 age- and gender-matched controls using flow cytometry to evaluate subset distribution, granzyme expression, and cytokine production. MG patients exhibit an altered CD4 + /CD8 + T cell ratio and significant changes in CD8 + T cell subsets, including increased central memory CD8 + T cell (Tcm) proportions and decreased effector memory CD8 + T cell (Tem) proportions. Granzyme B expression in Tcm cells is significantly elevated in MG patients, whereas no significant changes are observed in other subsets or GZMK expression. Cytokine analysis reveals increased IL-21, GM-CSF, and IL-17A production by CD8 + T cells in MG patients. These phenotypic and functional alterations of CD8 + T cells persist during the acute phase of the disease, regardless of immunotherapy usage, and vary between ocular and generalized MG. Subgroup and correlation analyses further identify age-dependent and age-independent dysregulations of CD8 + T cells, indicating complex and subtype-specific roles of CD8 + T cells in the immunopathological processes underlying MG. Our findings provide novel insights into the involvement of CD8 + T cells in MG pathogenesis, laying a foundation for future research and potential therapeutic strategies targeting CD8 + T cells.

Transient EZH2 Suppression by Tazemetostat during In Vitro Expansion Maintains T-Cell Stemness and Improves Adoptive T-Cell Therapy

The histone methyltransferase enhancer of zeste homolog 2 (EZH2) plays important roles in T-cell differentiation, proliferation, and function. Previous studies have demonstrated that genetic deletion of EZH2 in CD8+ or total T cells impairs their antiviral and antitumor activities, cytokine production, and ability to expand upon rechallenge. Contrary to the detrimental role of deleting T cell-intrinsic EZH2, in this study, we demonstrated that transient inhibition of EZH2 in T cells prior to the phenotypic onset of exhaustion with a clinically approved inhibitor, tazemetostat (Taz), delayed their dysfunctional progression and preserved T-cell stemness and polyfunctionality but had no negative impact on cell proliferation. Taz-induced T-cell epigenetic reprogramming increased the expression of the self-renewal T-cell transcription factor TCF1 by reducing H3K27 methylation at its promoter preferentially in rapidly dividing T cells. In a murine melanoma model, T cells depleted of EZH2 induced poor tumor control, whereas adoptively transferred T cells pretreated with Taz exhibited superior antitumor immunity, especially when used in combination with anti-PD-1 blockade. Collectively, these data highlight the potential of transient epigenetic reprogramming by EZH2 inhibition to enhance adoptive T-cell immunotherapy.

Advances in the genetics of myasthenia gravis: insights from cutting-edge neuroscience research

Myasthenia gravis (MG) is an autoimmune disorder involving complex interactions between genetic and environmental factors. Genome-wide association studies (GWAS), transcriptome-wide association studies (TWAS), and other methods have identified multiple novel susceptibility loci and genes, providing crucial insights into the genetic etiology of MG. Moreover, the pivotal roles of epigenetic mechanisms, such as DNA methylation, histone modifications, and non-coding RNAs, in the pathogenesis of MG are gradually being unveiled. This review comprehensively summarizes the latest advances in MG genetic research, focusing on the discovery and validation of susceptibility genes, genetic heterogeneity and subtype-specific genetic factors, gene-environment interactions, epigenetic mechanisms, and progress in genetics-based diagnostic and prognostic biomarkers.

Antigen presentation for central tolerance induction

The extent of central T cell tolerance is determined by the diversity of self-antigens that developing thymocytes 'see' on thymic antigen-presenting cells (APCs). Here, focusing on insights from the past decade, we review the functional adaptations of medullary thymic epithelial cells, thymic dendritic cells and thymic B cells for the purpose of tolerance induction. Their distinct cellular characteristics range from unconventional phenomena, such as promiscuous gene expression or mimicry of peripheral cell types, to strategic positioning in distinct microenvironments and divergent propensities to preferentially access endogenous or exogenous antigen pools. We also discuss how 'tonic' inflammatory signals in the thymic microenvironment may extend the intrathymically visible 'self' to include autoantigens that are otherwise associated with highly immunogenic peripheral environments.

Circulating CD45RA-Foxp3++ Treg cells serve as a biomarker for predicting minimal clinical manifestations status of myasthenia gravis

AIMS

Regulatory T cells (Tregs) are key mediators of the induction of immune tolerance; however, the mechanisms by which they regulate myasthenia gravis (MG) are not fully understood. This study aimed to explore the characteristics of Tregs and their subpopulations in the peripheral blood of patients with minimal clinical manifestations (MM) of MG and identify biomarkers that predict MM-MG for treatment guidance.

MATERIALS AND METHODS

The clinical data of patients with general MG who visited our hospital were retrospectively analyzed. Age- and sex-matched volunteers were selected as healthy controls (HC). Flow cytometry was used to determine the proportion, function, and subpopulations of total Tregs. A correlation analysis was conducted for subpopulation proportions and MG disease severity.

KEY FINDINGS

A total of 27 cases of MM-MG, 40 cases of naїve-MG, and 33 cases of HC were included in this study. The number of total Tregs and the suppressive function of total Tregs were elevated in patients with MM-MG compared to those of patients with naїve-MG. Further analysis revealed that the frequency of CD45RA-Foxp3++ Tregs (a-Tregs) negatively correlated with quantitative myasthenia gravis (QMG) scores for patients with naїve-MG. In addition, the number of a-Tregs was significantly greater in patients with MM-MG than in patients with naїve-MG, and CD45RA-Foxp3+ Tregs expressed higher and lower levels of CTLA-4 and CXCR3, respectively.

SIGNIFICANCE

CD45RA-Foxp3++ Tregs were significantly more abundant and highly expressed surface inhibitory molecules in patients with MM-MG. This profile may serve as a predictive biomarker for MM-MG.

Single-cell sequencing has revealed a more complex array of thymic epithelial cells

Thymic epithelial cells participate in the maturation and selection of T lymphocytes. This review explores recent insights from single-cell sequencing regarding classifying thymic epithelial cells in both normal and neoplastic thymus. Cortical thymic epithelial cells facilitate thymocyte differentiation and contribute to positive selection. Medullary epithelial cells are distinguished by their expression of AIRE. Cells progress from a pre-AIRE state, containing precursors with cortical and medullary characteristics, termed junctional cells. Mature medullary epithelial cells exhibit promiscuous gene expression and after that downregulate AIRE mRNA. Post-AIRE cells can adopt a Hassall corpuscle-like phenotype or exhibit distinctive differentiation characteristics including tuft cells, ionocytes, neuroendocrine cells, and myoid cells.

Spatial transcriptomics elucidates medulla niche supporting germinal center response in myasthenia gravis-associated thymoma

Myasthenia gravis (MG) is etiologically associated with thymus abnormalities, but its pathology in the thymus remains unclear. In this study, we attempt to narrow down the features associated with MG using spatial transcriptome analysis of thymoma and thymic hyperplasia samples. We find that the majority of thymomas are constituted by the cortical region. However, the small medullary region is enlarged in seropositive thymomas and contains polygenic enrichment and MG-specific germinal center structures. Neuromuscular medullary thymic epithelial cells, previously identified as MG-specific autoantigen-producing cells, are enriched in the cortico-medullary junction. The medulla is characterized by a specific chemokine pattern and immune cell composition, including migratory dendritic cells and effector regulatory T cells. Similar germinal center structures and immune microenvironments are also observed in the thymic hyperplasia medulla. This study shows that the medulla and junction areas are linked to MG pathology and provides insights into future MG research.

Myasthenia gravis: the future is here

Myasthenia gravis (MG) stands as a prototypical antibody-mediated autoimmune disease: it is dependent on T cells and characterized by the presence of autoantibodies targeting proteins located on the postsynaptic surface of skeletal muscle, known as the neuromuscular junction. Patients with MG exhibit a spectrum of weakness, ranging from limited ocular muscle involvement to life-threatening respiratory failure. Recent decades have witnessed substantial progress in understanding the underlying pathophysiology, leading to the delineation of distinct subcategories within MG, including MG linked to AChR or MuSK antibodies as well as age-based distinction, thymoma-associated, and immune checkpoint inhibitor-induced MG. This heightened understanding has paved the way for the development of more precise and targeted therapeutic interventions. Notably, the FDA has recently approved therapeutic inhibitors of complement and the IgG receptor FcRn, a testament to our improved comprehension of autoantibody effector mechanisms in MG. In this Review, we delve into the various subgroups of MG, stratified by age, autoantibody type, and histology of the thymus with neoplasms. Furthermore, we explore both current and potential emerging therapeutic strategies, shedding light on the evolving landscape of MG treatment.

Single-Cell Sequencing Illuminates Thymic Development: An Updated Framework for Understanding Thymic Epithelial Tumors

Thymic epithelial tumors (TETs) are rare tumors for which treatment options are limited. The ongoing need for improved systemic therapies reflects a limited understanding of tumor biology as well as the normal thymus. The essential role of the thymus in adaptive immunity is largely effected by its epithelial compartment, which directs thymocyte (T-cell) differentiation and immunologic self-tolerance. With aging, the thymus undergoes involution whereby epithelial tissue is replaced by adipose and other connective tissue, decreasing immature T-cell production. Against this natural drive toward involution, a fraction of thymuses will instead undergo oncologic transformation, leading to the formation of TETs, including thymoma and thymic carcinoma. The rarity of these tumors restricts investigation of the mechanisms of tumorigenesis and development of rational treatment options. To this end, the development of technologies which allow deep molecular profiling of individual tumor cells permits a new window through which to view normal thymic development and contrast the malignant changes that result in oncogenic transformation. In this review, we describe the findings of recent illuminating studies on the diversity of cell types within the epithelial compartment through thymic differentiation and aging. We contextualize these findings around important unanswered questions regarding the spectrum of known somatic tumor alterations, cell of origin, and tumor heterogeneity. The perspectives informed by single-cell molecular profiling offer new approaches to clinical and basic investigation of thymic epithelial tumors, with the potential to accelerate development of improved therapeutic strategies to address ongoing unmet needs in these rare tumors.

The Proteostasis of Thymic Stromal Cells in Health and Diseases

The thymus is the key immune organ for the development of T cells. Different populations of thymic stromal cells interact with T cells, thereby controlling the dynamic development of T cells through their differentiation and function. Proteostasis represents a balance between protein expression, folding, and modification and protein clearance, and its fluctuation usually depends at least partially on related protein regulatory systems for further survival and effects. However, in terms of the substantial requirement for self-antigens and their processing burden, increasing evidence highlights that protein regulation contributes to the physiological effects of thymic stromal cells. Impaired proteostasis may expedite the progression of thymic involution and dysfunction, accompanied by the development of autoimmune diseases or thymoma. Hence, in this review, we summarize the regulation of proteostasis within different types of thymic stromal cells under physiological and pathological conditions to identify potential targets for thymic regeneration and immunotherapy.

Thymic gene expression analysis reveals a potential link between HIF-1A and Th17/Treg imbalance in thymoma associated myasthenia gravis

Myasthenia gravis (MG) is an immune-mediated disease frequently associated with thymic changes. Increased T helper 17 (Th17) cell activity and dysfunctional regulatory T (Treg) cells have been demonstrated in subgroups of MG. On the other hand, hypoxia-inducible factor 1 (HIF-1) has been shown to regulate the Th17/Treg balance by inducing Th17 differentiation while attenuating Treg development. To identify the underlying mechanisms of different thymic pathologies in MG development, we evaluated thymic samples from thymoma-associated myasthenia gravis (TAMG), MG with hyperplasia (TFH-MG) and thymoma without MG (TOMA) patients. Differential gene expression analysis revealed that TAMG and TFH-MG cells are associated with different functional pathways. A higher RORC/FOXP3 ratio provided evidence for Th17/Treg imbalance in TAMG potentially related to increased HIF1A. The hypoxic microenvironment in thymoma may be a driver of TAMG by increasing HIF1A. These findings may lead to new therapeutic approaches targeting HIF1A in the development of TAMG.

Unique association of anti-GABAA receptor encephalitis and myasthenia gravis in a patient with type A thymoma

Association between anti-GABAAR encephalitis and myasthenia gravis is extremely rare with few reported cases. Herein, we report a case of a female patient diagnosed with anti-GABAAR encephalitis and thymoma at the first admission. She was administered glucocorticoids for long-term immunotherapy, and thymectomy with biopsy demonstrated a type A thymoma. After 4 months, the symptoms of encephalitis were relieved, but she then developed post-thymectomy myasthenia gravis with anti-AChR and anti-titin dual positivity. Antibodies to connective tissue (anti-ANA, anti-PCNA) and those characteristics of paraneoplastic syndrome (anti-Ma2/Ta) were also positive. She received oral glucocorticoids and tacrolimus as immunosuppressive therapy, and myasthenic symptoms were stable during a 2-year follow-up. Our case revealed that anti-GABAAR encephalitis and myasthenia gravis can appear in patient with type A thymoma at different periods, which alerts physicians to take long-term follow-up for anti-GABAAR encephalitis with thymoma, even after thymectomy. Concurrent positivity for more than one antibody after thymectomy is rarely observed, and their contribution to the clinical course and treatment decision remains to be further investigated.

scAnnoX: an R package integrating multiple public tools for single-cell annotation

Background

Single-cell annotation plays a crucial role in the analysis of single-cell genomics data. Despite the existence of numerous single-cell annotation algorithms, a comprehensive tool for integrating and comparing these algorithms is also lacking.

Methods

This study meticulously investigated a plethora of widely adopted single-cell annotation algorithms. Ten single-cell annotation algorithms were selected based on the classification of either reference dataset-dependent or marker gene-dependent approaches. These algorithms included SingleR, Seurat, sciBet, scmap, CHETAH, scSorter, sc.type, cellID, scCATCH, and SCINA. Building upon these algorithms, we developed an R package named scAnnoX for the integration and comparative analysis of single-cell annotation algorithms.

Results

The development of the scAnnoX software package provides a cohesive framework for annotating cells in scRNA-seq data, enabling researchers to more efficiently perform comparative analyses among the cell type annotations contained in scRNA-seq datasets. The integrated environment of scAnnoX streamlines the testing, evaluation, and comparison processes among various algorithms. Among the ten annotation tools evaluated, SingleR, Seurat, sciBet, and scSorter emerged as top-performing algorithms in terms of prediction accuracy, with SingleR and sciBet demonstrating particularly superior performance, offering guidance for users. Interested parties can access the scAnnoX package at https://github.com/XQ-hub/scAnnoX.

Immune tolerance and the prevention of autoimmune diseases essentially depend on thymic tissue homeostasis

The intricate balance of immune reactions towards invading pathogens and immune tolerance towards self is pivotal in preventing autoimmune diseases, with the thymus playing a central role in establishing and maintaining this equilibrium. The induction of central immune tolerance in the thymus involves the elimination of self-reactive T cells, a mechanism essential for averting autoimmunity. Disruption of the thymic T cell selection mechanisms can lead to the development of autoimmune diseases. In the dynamic microenvironment of the thymus, T cell migration and interactions with thymic stromal cells are critical for the selection processes that ensure self-tolerance. Thymic epithelial cells are particularly significant in this context, presenting self-antigens and inducing the negative selection of autoreactive T cells. Further, the synergistic roles of thymic fibroblasts, B cells, and dendritic cells in antigen presentation, selection and the development of regulatory T cells are pivotal in maintaining immune responses tightly regulated. This review article collates these insights, offering a comprehensive examination of the multifaceted role of thymic tissue homeostasis in the establishment of immune tolerance and its implications in the prevention of autoimmune diseases. Additionally, the developmental pathways of the thymus are explored, highlighting how genetic aberrations can disrupt thymic architecture and function, leading to autoimmune conditions. The impact of infections on immune tolerance is another critical area, with pathogens potentially triggering autoimmunity by altering thymic homeostasis. Overall, this review underscores the integral role of thymic tissue homeostasis in the prevention of autoimmune diseases, discussing insights into potential therapeutic strategies and examining putative avenues for future research on developing thymic-based therapies in treating and preventing autoimmune conditions.

The Way Ahead: Lessons Learned from Decades of Cancer Research on Thymomas and Thymic Carcinomas

The history of thymoma (TH) research begins in the early 20th century, when Bell first recognized the epithelial nature of these tumors and their association with myasthenia gravis (MG) [...].

Evaluation of the effect of PET/CT Fluorodeoxyglucose inclusion on mortality and survival in operated thymoma patients

PURPOSE

In recent years, the use of fluorodeoxyglucose PET-computed tomography (PET-CT) has become widespread to evaluate the diagnosis, metabolism, stage and distant metastases of thymoma. In this study, it was aimed to investigate the connection of malignancy potential, survival and maximum standardized uptake value (SUV max ) measured by PET-CT before surgery according to the histological classification of the WHO in patients operated for thymoma. In addition, the predictive value of the Glasgow prognostic score (GPS) generated by C-reactive protein (CRP) and albumin values on recurrence and survival was investigated and its potential as a prognostic biomarker was evaluated.

METHODS

Forty-five patients who underwent surgical resection for thymoma and were examined with PET-CT in the preoperative period between January 2010 and January 2022 were included in the study. The relationship between WHO histological classification, tumor size and SUV max values on PET-CT according to TNM classification of retrospectively analyzed corticoafferents were evaluated. Preoperative albumin and CRP values were used to determine GPS.

RESULTS

The cutoff value for SUV max was found to be 5.65 in the patients and the overall survival rate of low-risk (<5.65) and high-risk (>5.65) patients was compared according to the SUV max threshold value (5.65) and found to be statistically significant. In addition, the power of PET/CT SUV max value to predict mortality (according to receiver operating characteristics analysis) was statistically significant ( P  = 0.048). Survival expectancy was 127.6 months in patients with mild GPS (O points), 96.7 months in patients with moderate GPS (1 point), and 25.9 months in patients with severe GPS (2 points).

CONCLUSION

PET/CT SUV max values can be used to predict histological sub-type in thymoma patients, and preoperative SUV max and GPS are parameters that can provide information about survival times and mortality in thymoma patients.

Single-cell transcriptome landscape of circulating CD4+ T cell populations in autoimmune diseases

CD4+ T cells are key mediators of various autoimmune diseases; however, their role in disease progression remains unclear due to cellular heterogeneity. Here, we evaluated CD4+ T cell subpopulations using decomposition-based transcriptome characterization and canonical clustering strategies. This approach identified 12 independent gene programs governing whole CD4+ T cell heterogeneity, which can explain the ambiguity of canonical clustering. In addition, we performed a meta-analysis using public single-cell datasets of over 1.8 million peripheral CD4+ T cells from 953 individuals by projecting cells onto the reference and cataloging cell frequency and qualitative alterations of the populations in 20 diseases. The analyses revealed that the 12 transcriptional programs were useful in characterizing each autoimmune disease and predicting its clinical status. Moreover, genetic variants associated with autoimmune diseases showed disease-specific enrichment within the 12 gene programs. The results collectively provide a landscape of single-cell transcriptomes of CD4+ T cell subpopulations involved in autoimmune disease.

Myasthenia gravis: the changing treatment landscape in the era of molecular therapies

Myasthenia gravis (MG) is an autoimmune disorder that affects the neuromuscular junction, leading to muscle weakness and fatigue. MG is caused by antibodies against the acetylcholine receptor (AChR), the muscle-specific kinase (MuSK) or other AChR-related proteins that are expressed in the postsynaptic muscle membrane. The standard therapeutic approach for MG has relied on acetylcholinesterase inhibitors, corticosteroids and immunosuppressants, which have shown good efficacy in improving MG-related symptoms in most people with the disease; however, these therapies can carry a considerable burden of long-term adverse effects. Moreover, up to 15% of individuals with MG exhibit limited or no response to these standard therapies. The emergence of molecular therapies, including monoclonal antibodies, B cell-depleting agents and chimeric antigen receptor T cell-based therapies, has the potential to revolutionize the MG treatment landscape. This Review provides a comprehensive overview of the progress achieved in molecular therapies for MG associated with AChR antibodies and MuSK antibodies, elucidating both the challenges and the opportunities these therapies present to the field. The latest developments in MG treatment are described, exploring the potential for personalized medicine approaches.

A guide to thymic selection of T cells

The thymus is an evolutionarily conserved organ that supports the development of T cells. Not only does the thymic environment support the rearrangement and expression of diverse T cell receptors but also provides a unique niche for the selection of appropriate T cell clones. Thymic selection ensures that the repertoire of available T cells is both useful (being MHC-restricted) and safe (being self-tolerant). The unique antigen-presentation features of the thymus ensure that the display of self-antigens is optimal to induce tolerance to all types of self-tissue. MHC class-specific functions of CD4+ T helper cells, CD8+ killer T cells and CD4+ regulatory T cells are also established in the thymus. Finally, the thymus provides signals for the development of several minor T cell subsets that promote immune and tissue homeostasis. This Review provides an introductory-level overview of our current understanding of the sophisticated thymic selection mechanisms that ensure T cells are useful and safe.

Exacerbation of Thymoma-Associated Myasthenia Gravis Following Efgartigimod Treatment Related to Anti-acetylcholine Receptor Antibody Overshoot: A Report of Two Cases

Myasthenia gravis (MG), a chronic, autoimmune disease affecting the neuromuscular junction, arises from various autoantibodies, including those against the acetylcholine receptor (AChR). Recently, efgartigimod, a human IgG1 antibody Fc fragment engineered to reduce the pathogenic IgG autoantibody level, was developed as a treatment for MG. However, the long-term effects of the treatment are still unclear. The present report describes two novel cases of thymoma-associated MG exacerbation following efgartigimod treatment related to anti-AChR antibody overshoot. Both cases shared certain characteristics, including anti-AChR antibody positivity and post-thymectomy status. After a few cycles of efgartigimod treatment, their MG deteriorated, and their anti-AChR antibody titer exceeded the level before efgartigimod therapy. Prior studies show that anti-AChR antibody titer does not correlate with the disease severity of MG. However, previous studies have reported antibody overshoot following plasma exchange, which, like efgartigimod, reduces the level of plasma IgG and autoantibodies. Thus, MG exacerbation with anti-AChR antibody overshoot may be an adverse effect of both efgartigimod and plasma exchange. When clinical symptoms in patients with thymoma-associated MG receiving efgartigimod deteriorate despite low IgG, assessing the anti-AChR antibody level can be important for reconsidering the treatment strategy.

[Thymoma-associated generalized myasthenia gravis complicated with anti-VGKC complex antibody-associated limbic encephalitis: a case report]

We present a case of a 54-year-old woman. She was attending our department for thymoma-associated generalized myasthenia gravis. While she was treated with intravenous immunoglobulins for the exacerbation of myasthenic symptoms, she suddenly lost her consciousness for the first time and continued to have mild disorientation along with anterograde and retrograde amnesia afterwards. The symptoms improved after steroid pulse therapy. After searching for autoantibodies, she was diagnosed with anti-VGKC complex antibody-associated limbic encephalitis. As one-third of cases are complicated by thymoma, anti-VGKC complex antibody-positive limbic encephalitis has the aspect of a paraneoplastic neurological syndrome. In this case, masses suspected to be a recurrence of thymoma were found. In cases of thymoma, involvement of anti-VGKC complex antibodies should be considered when central nervous system symptoms appear, and when anti-VGKC complex antibodies are positive, recurrence or exacerbation of thymoma should be considered.

High-Throughput CSF Proteomics and Machine Learning to Identify Proteomic Signatures for Parkinson Disease Development and Progression

BACKGROUND AND OBJECTIVES

This study aimed to identify CSF proteomic signatures characteristic of Parkinson disease (PD) and evaluate their clinical utility.

METHODS

This observational study used data from the Parkinson's Progression Markers Initiative (PPMI), which enrolled patients with PD, healthy controls (HCs), and non-PD participants carrying GBA1, LRRK2, and/or SNCA pathogenic variants (genetic prodromals) at international sites. Study participants were chosen from PPMI enrollees based on the availability of aptamer-based CSF proteomic data, quantifying 4,071 proteins, and classified as patients with PD without GBA1, LRRK2, and/or SNCA pathogenic variants (nongenetic PD), HCs, patients with PD carrying the aforementioned pathogenic variants (genetic PD), or genetic prodromals. Differentially expressed protein (DEP) analysis and the least absolute shrinkage and selection operator (LASSO) were applied to the data from nongenetic PD and HCs. Signatures characteristics of nongenetic PD were quantified as a PD proteomic score (PD-ProS), validated internally and then externally using data of 1,556 CSF proteins from the LRRK2 Cohort Consortium (LCC). We further tested the PD-ProS in genetic PD and genetic prodromals and examined associations with clinical progression.

RESULTS

Data from 279 patients with nongenetic PD (mean ± SD, age 62.0 ± 9.6 years; male 67.7%) and 141 HCs (age 60.5 ± 11.9 years; male 64.5%) were used for PD-ProS derivation. From 23 DEPs, LASSO determined weights of 14 DEPs for the PD-ProS (area under the curve [AUC] 0.83, 95% CI 0.78-0.87), validated in an independent internal validation cohort of 71 patients with nongenetic PD and 35 HCs (AUC 0.81, 95% CI 0.73-0.90). In the LCC, only 5 of the 14 DEPs were also measured. Notably, these 5 DEPs still distinguished 34 patients with nongenetic PD from 31 HCs with the same weights (AUC 0.75, 95% CI 0.63-0.87). Furthermore, the PD-ProS distinguished 258 patients with genetic PD from 365 genetic prodromals. Finally, regardless of genetic status, the PD-ProS independently predicted both cognitive and motor decline in PD (dementia, adjusted hazard ratio in the highest quintile [aHR-Q5] 2.8 [95% CI 1.6-5.0]; Hoehn and Yahr stage IV, aHR-Q5 2.1 [95% CI 1.1-4.0]).

DISCUSSION

By integrating high-throughput proteomics with machine learning, we identified PD-associated CSF proteomic signatures crucial for PD development and progression.

TRIAL REGISTRATION INFORMATION

ClinicalTrials.gov (NCT01176565). A link to the trial registry page is clinicaltrials.gov/ct2/show/NCT01141023.

CLASSIFICATION OF EVIDENCE

This study provides Class II evidence that the CSF proteome contains clinically important information regarding the development and progression of Parkinson disease that can be deciphered by a combination of high-throughput proteomics and machine learning.

Unraveling molecular networks in thymic epithelial tumors: deciphering the unique signatures

Thymic epithelial tumors (TETs) are a rare and diverse group of neoplasms characterized by distinct molecular signatures. This review delves into the complex molecular networks of TETs, highlighting key aspects such as chromosomal abnormalities, molecular subtypes, aberrant gene mutations and expressions, structural gene rearrangements, and epigenetic changes. Additionally, the influence of the dynamic tumor microenvironment on TET behavior and therapeutic responses is examined. A thorough understanding of these facets elucidates TET pathogenesis, offering avenues for enhancing diagnostic accuracy, refining prognostic assessments, and tailoring targeted therapeutic strategies. Our review underscores the importance of deciphering TETs' unique molecular signatures to advance personalized treatment paradigms and improve patient outcomes. We also discuss future research directions and anticipated challenges in this intriguing field.

Peripheral immune landscape for hypercytokinemia in myasthenic crisis utilizing single-cell transcriptomics

BACKGROUND

Myasthenia gravis (MG) is the most prevalent autoimmune disorder affecting the neuromuscular junction. A rapid deterioration in respiratory muscle can lead to a myasthenic crisis (MC), which represents a life-threatening condition with high mortality in MG. Multiple CD4+ T subsets and hypercytokinemia have been identified in the peripheral pro-inflammatory milieu during the crisis. However, the pathogenesis is complicated due to the many types of cells involved, leaving the underlying mechanism largely unexplored.

METHODS

We conducted single-cell transcriptomic and immune repertoire sequencing on 33,577 peripheral blood mononuclear cells (PBMCs) from two acetylcholine receptor antibody-positive (AChR +) MG patients during MC and again three months post-MC. We followed the Scanpy workflow for quality control, dimension reduction, and clustering of the single-cell data. Subsequently, we annotated high-resolution cell types utilizing transfer-learning models derived from publicly available single-cell immune datasets. RNA velocity calculations from unspliced and spliced mRNAs were applied to infer cellular state progression. We analyzed cell communication and MG-relevant cytokines and chemokines to identify potential inflammation initiators.

RESULTS

We identified a unique subset of monocytes, termed monocytes 3 (FCGR3B+ monocytes), which exhibited significant differential expression of pro-inflammatory signaling pathways during and after the crisis. In line with the activated innate immune state indicated by MC, a high neutrophil-lymphocyte ratio (NLR) was confirmed in an additional 22 AChR + MC patients in subsequent hemogram analysis and was associated with MG-relevant clinical scores. Furthermore, oligoclonal expansions were identified in age-associated B cells exhibiting high autoimmune activity, and in CD4+ and CD8+ T cells demonstrating persistent T exhaustion.

CONCLUSIONS

In summary, our integrated analysis of single-cell transcriptomics and TCR/BCR sequencing has underscored the role of innate immune activation which is associated with hypercytokinemia in MC. The identification of a specific monocyte cluster that dominates the peripheral immune profile may provide some hints into the etiology and pathology of MC. However, future functional studies are required to explore causality.

Histogenetic and disease-relevant phenotypes in thymic epithelial tumors (TETs): The potential significance for future TET classification

Thymic epithelial tumors (TETs) encompass morphologically various subtypes. Thus, it would be meaningful to explore the expression phenotypes that delineate each TET subtype or overarching multiple subtypes. If these profiles are related to thymic physiology, they will improve our biological understanding of TETs and may contribute to the establishment of a more rational TET classification. Against this background, pathologists have attempted to identify histogenetic features in TETs for a long time. As part of this work, our group has reported several TET expression profiles that are histotype-dependent and related to the nature of thymic epithelial cells (TECs). For example, we found that beta5t, a constituent of thymoproteasome unique to cortical TECs, is expressed mainly in type B thymomas, for which the nomenclature of cortical thymoma was once considered. Another example is the discovery that most thymic carcinomas, especially thymic squamous cell carcinomas, exhibit expression profiles similar to tuft cells, a recently discovered special type of medullary TEC. This review outlines the currently reported histogenetic phenotypes of TETs, including those related to thymoma-associated myasthenia gravis, summarizes their genetic signatures, and provides a perspective for the future direction of TET classification.

Myasthenia-like paraneoplastic syndrome with multiple cranial nerve tumor infiltration: A case report and literature review

RATIONALE

Approximately 0.001% of patients with cancer have paraneoplastic nerve system syndrome, which can affect the central nervous system, neuromuscular junction, or peripheral nervous system. Although myasthenia gravis (MG) may exist as a thymic paraneoplastic syndrome (PNPS), its association with primary lung cancer remains unknown.

PATIENT CONCERNS

A 55-year-old female presented with slurred speech, weakness in chewing, sporadic difficulty in swallowing, and weakness in both lower limbs for half a year.

DIAGNOSES

Based on cerebrospinal fluid and electromyography findings, we present the case of a female patient diagnosed with overlapping multicranial nerve tumor infiltration and MG-like neurological PNPS secondary to lung adenocarcinoma.

INTERVENTIONS

The patient received intrathecal injections of pemetrexed and neurotrophic (vitamin B) therapy before ceasing chemoradiotherapy and chose cabozantinib on her own.

OUTCOMES

Weakness of the proximal limbs, choking cough, and chewing problems did not improve significantly.

LESSONS

Although it is unclear why MG coexists with lung cancer, it is probable that MG is a paraneoplastic condition. Cerebrospinal fluid testing should be carried out along with electrophysiological, serological, and pharmacological procedures pertinent to the diagnosis of MG to thoroughly examine if people simultaneously experience MG-like PNPS and tumor growth. Starting immunotherapy and anticancer medication at the same time that tumor development and MG-like syndrome are discovered is crucial.

An unusual ectopic thymoma clonal evolution analysis: A case report

Thymomas and thymic carcinomas are rare and primary tumors of the mediastinum which is derived from the thymic epithelium. Thymomas are the most common primary anterior mediastinal tumor, while ectopic thymomas are rarer. Mutational profiles of ectopic thymomas may help expand our understanding of the occurrence and treatment options of these tumors. In this report, we sought to elucidate the mutational profiles of two ectopic thymoma nodules to gain deeper understanding of the molecular genetic information of this rare tumor and to provide guidance treatment options. We presented a case of 62-year-old male patient with a postoperative pathological diagnosis of type A mediastinal thymoma and ectopic pulmonary thymoma. After mediastinal lesion resection and thoracoscopic lung wedge resection, the mediastinal thymoma was completely removed, and the patient recovered from the surgery and no recurrence was found by examination until now. Whole exome sequencing was performed on both mediastinal thymoma and ectopic pulmonary thymoma tissue samples of the patient and clonal evolution analysis were further conducted to analyze the genetic characteristics. We identified eight gene mutations that were co-mutated in both lesions. Consistent with a previous exome sequencing analysis of thymic epithelial tumor, HRAS was also observed in both mediastinal lesion and lung lesion tissues. We also evaluated the intratumor heterogeneity of non-silent mutations. The results showed that the mediastinal lesion tissue has higher degree of heterogeneity and the lung lesion tissue has relatively low amount of variant heterogeneity in the detected variants. Through pathology and genomics sequencing detection, we initially revealed the genetic differences between mediastinal thymoma and ectopic thymoma, and clonal evolution analysis showed that these two lesions originated from multi-ancestral regions.

Cellular mechanisms and clinical applications for phenocopies of inborn errors of immunity: infectious susceptibility due to cytokine autoantibodies

INTRODUCTION

With a growing knowledge of Inborn error immunity (IEI), immunological profiling and genetic predisposition to IEI phenocopies have been developed in recent years.

AREAS COVERED

Here we summarized the correlation between various pathogen invasions, autoantibody profiles, and corresponding clinical features in the context of patients with IEI phenocopies. It has been extensively evident that patients with anti-cytokine autoantibodies underly impaired anti-pathogen immune responses and lead to broad unregulated inflammation and tissue damage. Several hypotheses of anti-cytokine autoantibodies production were summarized here, including a defective negative selection of autoreactive T cells, abnormal germinal center formation, molecular mimicry, HLA class II allele region, lack of auto-reactive lymphocyte apoptosis, and other possible hypotheses.

EXPERT OPINION

Phenocopies of IEI associated with anti-cytokine autoantibodies are increasingly recognized as one of the causes of acquired immunodeficiency and susceptibility to certain pathogen infections, especially facing the current challenge of the COVID-19 pandemic. By investigating clinical, genetic, and pathogenesis autoantibodies profiles associated with various pathogens' susceptibilities, we could better understand the IEI phenocopies with anti-cytokine autoantibodies, especially for those that underlie life-threatening SARS-CoV-2.

Genetic profile of thymic epithelial tumors in the Japanese population: an exploratory study examining potential therapeutic targets

Background

Thymic epithelial tumors (TETs) are prone to developing in East Asian populations. However, little is known about the genomic profile of TETs in East Asian populations, and the genomic aberrations in TETs have not yet been fully clarified. Thus, molecular targeted therapies for patients with TETs have not been established. This prospective study was conducted to explore the genetic abnormalities of surgically resected TETs in a Japanese cohort and to identify clues for carcinogenesis and potential therapeutic targets in TETs.

Methods

Genetic profiles of TETs were investigated using fresh-frozen specimens resected from operable cases with TETs. DNA sequencing was performed using a next-generation sequencing (NGS) gene panel test with Ion Reporter™ and CLC Genomics Workbench 11.0. The mutation sites were further confirmed by Sanger sequencing, digital droplet polymerase chain reaction (ddPCR), and TA cloning for validation.

Results

Among 43 patients diagnosed with anterior mediastinal tumors between January 2013 and March 2019, NGS and validation analyses were performed in 31 patients [29 thymomas and two thymic cancers (TCs)] who met the study criteria. Of these, 12 cases of thymoma types A, AB, B1, and B2 harbored the general transcription factor 2-I (GTF2I) mutation (L424H). Conversely, the mutation was not detected in type B3 thymoma or TC, suggesting that the GTF2I mutation existed in indolent types of TETs. Rat sarcoma viral oncogene (RAS) mutations were detected in three cases [Harvey RAS (HRAS) in two cases of type AB thymoma and neuroblastoma RAS (NRAS)] in one case of type B1 thymoma), and additional sex combs like 1 (ASXL1) mutation was present in one case of TC. All RAS mutations were observed in GTF2I-mutated cases.

Conclusions

The GTF2I mutation (L424H) is the most frequently occurring mutation in the limited histology of thymoma, consistent with those in the non-Asian population. HRAS and NRAS mutations co-occurred in cases harboring the GTF2I mutation. These findings suggest that the existence of the GTF2I mutation might be related to indolent types of TETs, and RAS mutations could be candidates as therapeutic targets in TETs.

Inflammation and autoimmune myasthenia gravis

Myasthenia gravis (MG) is a neuromuscular autoimmune disorder characterized by chronic but intermittent fatigue of the eye- and general body muscles. Muscle weakness is caused primarily by the binding of an autoantibody to the acetylcholine receptors, resulting in blockage of normal neuromuscular signal transmission. Studies revealed substantial contributions of different proinflammatory or inflammatory mediators in the pathogenesis of MG. Despite these findings, compared to therapeutic approaches that target autoantibody and complements, only a few therapeutics against key inflammatory molecules have been designed or tested in MG clinical trials. Recent research focuses largely on identifying unknown molecular pathways and novel targets involved in inflammation associated with MG. A well-designed combination or adjunct treatment utilizing one or more selective and validated promising biomarkers of inflammation as a component of targeted therapy may yield better treatment outcomes. This review briefly discusses some preclinical and clinical findings of inflammation associated with MG and current therapy approaches and suggest the potential of targeting important inflammatory marker(s) along with current monoclonal antibody or antibody fragment based targeted therapies directed to a variety of cell surface receptors.

Revisiting Aire and tissue-restricted antigens at single-cell resolution

The thymus is a highly specialized organ that plays an indispensable role in the establishment of self-tolerance, a process characterized by the "education" of developing T-cells. To provide competent T-cells tolerant to self-antigens, medullary thymic epithelial cells (mTECs) orchestrate negative selection by ectopically expressing a wide range of genes, including various tissue-restricted antigens (TRAs). Notably, recent advancements in the high-throughput single-cell analysis have revealed remarkable heterogeneity in mTECs, giving us important clues for dissecting the mechanisms underlying TRA expression. We overview how recent single-cell studies have furthered our understanding of mTECs, with a focus on the role of Aire in inducing mTEC heterogeneity to encompass TRAs.