Marko Radic

There are credible signs that COVID-19 is surging again in certain parts of the world, despite the fact that many countries have reduced surveillance and mandatory reporting, implying that the case numbers are likely under-estimated. In this context, the emergence of SARS-CoV-2 variants shapes the antigenic landscape faced by the human immune system, repeatedly re-selecting suitable responses. Whereas most SARS-CoV-2 viruses trigger protective B-cell responses, a subset of subjects exhibit deregulated Bcell activation, including responses marked by extrafollicular B cell expansion, impaired germinal center formation, and autoreactivity. These observations suggest that a breakdown in immune tolerance, possibly mediated by pro-inflammatory cytokines and TLR stimulation, may activate autoreactive B-cell clones. Given the rapid appearance of SARS-CoV-2 variants with potential immune-evasive mutations, repeated activation of B cells may increase the risk of tolerance disruption.It is estimated that approximately 10-20 % of subjects who have been infected with SARS-CoV-2 will develop long COVID19. However, there is little understanding of what causes this condition. It could be due to persistence of the SARS-CoV-2 virus in the organism or to variants exhibiting an abundance of spike mutations. Additionally, several autoantibodies have been associated with long COVID occurrence, symptoms, and severity [1; 2; 3; 4]. This Research Topic Community Series aims to provide further insight into how variant-driven antigenic stimulation skews B cell fates toward pathological trajectories, affects the balance between effective immunity and immune-tolerance, and promotes self-reactivity.B cells play several key roles in the immune response to SARS-CoV-2. B cells produce neutralizing antibodies that bind to the virus and block its entry into human cells and reduce viral replication. B cells act as antigen-presenting cells to T helper cells, and this B-T cell collaboration is essential for strong, durable immunity. During infection, B cells undergo affinity maturation in germinal centers, a process that improves antibody affinity and helps maintain durable, potent antibody responses. Following infection or vaccination, B lymphocytes give rise to memory B cells that can quickly produce antibodies during a future exposure to the virus, providing lasting immunity and/or faster recovery. In severe cases, hyperactive or exhausted B cell responses are present, and a subset of B cells, termed, ageassociated B cells or extrafollicular B cells, may become overactive and contribute to inflammation. In this Research Topic Community Series, the role of B cells during SARS-CoV-2 reinfection is discussed [5].Studies of inborn errors of immunity (IEI) can lead to refinements of clinical and immunological characteristics of diseases and novel therapeutic approaches. Since 2020, several research groups have identified monogenic defects that predispose individuals-often previously healthy-to life-threatening COVID-19 pneumonia. Genetic defects that increase the risk for severe COVID-19 include the type I Interferon (IFN-I) pathway (TLR3, TLR7, IRF7, IRF9, IFNAR1, IFNAR2, UNC93B1, TICAM1, and TBK1).Mutations or loss-of-function variants in these genes can lead to uncontrolled viral replication and severe disease. Paradoxically, some IEIs, like XLA, result in moderate or mild disease. Identification of highly conserved SARS-CoV-2 targets that are highly immunogenic, but do not elicit auto-reactivity, represents a key step in designing anti-COVID-19 vaccines. In this Research Topic Community Series, scanning the entire spike amino acid sequence for linear epitopes that meet these requirements led to identification of multiple linear epitopes and a highly conserved region that elicits potentially pathogenic autoantibodies [6]. Investigation of the humoral response of COVID-19 patients with IEI enabled detection of IgG and IgM antibodies against the SARS-CoV-2 spike protein, and the presence of specific receptor-binding domain-positive (RBD+) IgG+ memory B cells after vaccination against SARS-Cov2 [7]. These observations could help developing safer pan-coronavirus vaccines.Research has identified several SARS-CoV-2 proteins and epitopes that elicit strong adaptive immune responses, remain highly conserved across variants, and exhibit minimal similarity to human proteinsreducing the likelihood of molecular mimicry and autoimmune cross-reactivity. Regions reported to be highly conserved across variants, immunogenic, and not associated with significant auto-reactivity have been described in the nucleocapsid (N) Protein, the S2 Subunit of the Spike (S) protein, membrane (M) protein, non-Structural Proteins (NSPs) involved in replication, and ORF3a. Epitopes most associated with concern are located primarily in certain regions of Spike S1, and parts of N. By contrast, S2, M, and essential NSPs show minimal homology to self peptides, no strong associations with post-COVID-19 autoimmune sequelae, and their structures are stable across variants, probably because of reduced pressure for immune escape. In this Research Topic Community Series, investigation of SARS-CoV-2 vaccine-induced immunity indicates a wide heterogeneity in the magnitude of the receptor-binding domain (RBD)-specific neutralizing responses, and illustrate that antibody levels largely depend on prior exposure to SARS-CoV-2, the number of vaccine doses, and the type of vaccine received [8].Several published reports have identified autoantibodies whose appearance in COVID-19 patients coincided with the infection. Conversely, it has long been suspected that infections may provide a trigger for autoimmune disease. Researchers have used antigen arrays to screen for many antibody specificities to draw parallels with known targets associated with specific autoimmune diseases. Titi et al. provide the next level of insight in this Research Topic Community Series [9]. They...

Chimeric antigen receptor (CAR) T cell therapy has been highly effective in eradicating malignant B cells in cancer, and this success has prompted an extension of the approach to areas beyond oncology. In pioneering studies, CAR T cells targeting the B cell marker CD19 demonstrated robust efficacy as treatment for the autoimmune disease systemic lupus erythematosus. Patients who received anti-CD19 CAR T cells experienced remission of most or all clinical manifestations and discontinued prior medications. These results have spurred intense interest in extending these observations to larger patient cohorts and other autoimmune conditions. More nuanced strategies for use of CARs in autoimmunity have also been developed. Here, we offer insight into the role of B cells in the pathophysiology of autoimmunity and present an overview of preclinical studies and clinical trials that use engineered cell therapy for autoimmune disorders. In discussing the prospects and challenges of this emerging field, a view emerges in which the promise of clinical efficacy invites careful consideration of potential pitfalls.

The clinical success of chimeric antigen receptors (CARs) in treating lymphoid malignancies [1] and their emerging efficacy in autoimmune diseases [2], has fundamentally transformed cellular receptor engineering from a research frontier into a therapeutic reality. This progress is catalyzing a broader reappraisal of the approach to diseases driven by aberrant cellular immunity. Yet realizing the full potential of these technologies demands more than incremental advances in engineering; it requires deeper integration across basic science, translational research, and clinical disciplines spanning oncology, rheumatology, nephrology, and neurology. The need for such convergence, along with the obstacles that impede it, has been thoughtfully examined in several recent reviews [3]. This Research Topic was conceived to bridge the disciplinary boundaries that often separate the scientists and clinicians driving this rapidly evolving field. The goal was to advance engineered receptor therapies toward broader applications in both autoimmunity and cancer. The collected articles report on conceptual advances and original experimental findings across the therapeutic landscape of chimeric receptors.Cheever et al., contribute original data on a chimeric autoantibody receptor (CAAR) that presents the extracellular domain of the thyroid-stimulating hormone receptor (TSHR) as molecular bait to attract and eliminate TSHR-reactive B cells. Their demonstration of CAARmediated cytotoxicity against anti-TSHR B cells in vitro establishes the critical first step toward CAAR T cell therapy for Graves' disease. The data provide a proof of concept that exemplifies the precision-targeting logic now being extended across autoimmune conditions.Three reviews map the growing landscape of cellular therapies for immune dysregulation. Zheng et al. survey advances in both CAR-T and CAR-macrophage platforms for autoimmune diseases, comparing their capacity to selectively eliminate autoreactive immune populations while weighing therapeutic advantages against translational hurdles. Kümmel et al.. turn to regulatory T cells, examining how antigen-specific CAR-Treg engineering might restore immune tolerance in inflammatory bowel disease; they outline strategies targeting circulating carcinoembryonic antigen, flagellin, and IL-23R, while candidly assessing developmental challenges. Wu et al. provide a broader synthesis of how CAR-T therapy, born in oncology, is now transforming autoimmune treatment, with CD19targeted approaches inducing rapid, durable remissions in refractory cases. Their review also surveys emerging CAR-NK, CAAR-T, and CAR-Treg modalities alongside management of cytokine release syndrome and immune effector cell-associated neurotoxicity syndrome.The transition from hematologic to solid malignancies remains the field's most formidable frontier. Stavrou et al. assess the current state of CAR-T applications in osteosarcoma and rhabdomyosarcoma, acknowledging the substantial obstacles these tumors present while highlighting promising clinical trials on the horizon. Andreou et al. dissect why solid tumors resist CAR-T therapy so effectively, focusing on how the tumor microenvironment impedes trafficking, infiltration, and antigen targeting. They evaluate strategies to remodel stromal and vascular barriers, enhance CAR-T precision and persistence, and mitigate off-tumor toxicity, offering a roadmap toward more effective, personalized solid-tumor immunotherapies.Finally, Kuo et al. extend the conversation beyond conventional lymphocyte engineering to innate lymphoid cells (ILCs). Their review details ILC subset diversity, tissue residency, and phenotypic plasticity, positioning these cells as both biomarkers and therapeutic targets. Strategies under exploration, ex vivo expansion, pluripotent stem cell-derived ILCs, CARengineered ILCs, cytokine modulation, and checkpoint blockade, suggest new avenues for intervention, though challenges of cellular heterogeneity and manufacturing scalability remain.The articles assembled in this Research Topic illuminate both the remarkable progress and the formidable challenges that define cellular receptor engineering today. From CAARmediated targeting of autoreactive B cells in Graves' disease to CAR-Treg strategies for inflammatory bowel disease, from the persistent puzzle of solid tumor microenvironments to the untapped potential of innate lymphoid cells, these contributions collectively map a therapeutic frontier in active expansion.Several themes emerge across this collection. First, the conceptual architecture pioneered in hematologic malignancies is proving remarkably adaptable, yielding new modalities (CAR-macrophages, CAR-Tregs, CAR-ILCs) tailored to distinct pathophysiologies. Second, autoimmune applications are no longer a speculative extension of oncology successes but a clinical reality generating durable remissions in previously refractory disease. Third, the solid tumor challenge demands not incremental refinement but fundamental innovation in how we navigate immunosuppressive microenvironments.What unites these diverse efforts is a shared recognition: diseases long considered manageable at best, such as certain cancers, autoimmune conditions, or chronic inflammatory disorders, may now be curable through precise cellular reprogramming. Realizing this possibility will require exactly the kind of cross-disciplinary dialogue this Research Topic seeks to foster. We hope these articles serve not as a summary of current knowledge but as a catalyst, stimulating new collaborations between basic science, translational research, and clinical applications across oncology, rheumatology, nephrology, neurology, and beyond.

The COVID-19 pandemic remains a serious public health problem globally. During winter influenza seasons, more aggressive SARS-CoV-2 infections and fatalities have been documented, indicating that influenza co-infections may significantly impact the disease outcome of COVID-19. Both influenza and SARS-CoV-2 viruses share many similarities in their transmission and their cellular tropism for replication in the human respiratory tract. However, the complex intricacies and multi-faceted dynamics of how the two pathogens interact to ensure their survival in the same lung microenvironment are still unclear. In addition, clinical studies on influenza co-infections in COVID-19 patients do not provide conclusive evidence of how influenza co-infection mechanistically modifies disease outcomes of COVID-19. This review discusses various viral as well as host factors that potentially influence the survival or synergism of these two respiratory pathogens in the infected lung microenvironment.

The COVID-19 pandemic remains a serious public health problem globally. During winter flu seasons, more aggressive SARS-CoV-2 infections with fatalities have been documented, indicating that influenza co-infections may significantly impact the disease outcome of COVID-19. Both influenza and SARS-CoV-2 viruses share many similarities in their transmission and cellular tropism for their replication in the human respiratory tract. However, it is still unclear how the two pathogens interplay to ensure their survival in the same lung microenvironment. In addition, clinical studies on influenza co-infections in COVID-19 patients do not provide conclusive evidence on how influenza co-infection mechanistically modifies the disease outcome in COVID-19. This mini-review discusses various viral as well as host factors that potentially influence the survival or synergism of these two respiratory pathogens in the infected lung microenvironment.

Pulmonary fibrosis, severe alveolitis, and the inability to restore alveolar epithelial architecture are primary causes of respiratory failure in fatal COVID-19 cases. However, the factors contributing to abnormal fibrosis in critically ill COVID-19 patients remain unclear. This study analyzed the histopathology of lung specimens from eight COVID-19 and six non-COVID-19 postmortems. We assessed the distribution and changes in extracellular matrix (ECM) proteins, including elastin and collagen, in lung alveoli through morphometric analyses. Our findings reveal the significant degradation of elastin fibers along the thin alveolar walls of the lung parenchyma, a process that precedes the onset of interstitial collagen deposition and widespread intra-alveolar fibrosis. Lungs with collapsed alveoli and organized fibrotic regions showed extensive fragmentation of elastin fibers, accompanied by alveolar epithelial cell death. Immunoblotting of lung autopsy tissue extracts confirmed elastin degradation. Importantly, we found that the loss of elastin was strongly correlated with the induction of neutrophil elastase (NE), a potent protease that degrades ECM. This study affirms the critical role of neutrophils and neutrophil enzymes in the pathogenesis of COVID-19. Consistently, we observed increased staining for peptidyl arginine deiminase, a marker for neutrophil extracellular trap release, and myeloperoxidase, an enzyme-generating reactive oxygen radical, indicating active neutrophil involvement in lung pathology. These findings place neutrophils and elastin degradation at the center of impaired alveolar function and argue that elastolysis and alveolitis trigger abnormal ECM repair and fibrosis in fatal COVID-19 cases. Importantly, this study has implications for severe COVID-19 complications, including long COVID and other chronic inflammatory and fibrotic disorders.

Excessive release of neutrophil extracellular traps (NETs) has been reported in various human pathologies, including COVID-19 patients. Elevated NET levels serve as a biomarker, indicating increased coagulopathy and immunothrombosis risks in these patients. Traditional immunoassays employed to quantify NET release focus on bulk measurements of released chromatin in simplified microenvironments. In this study, we fabricated a novel NET-array device to quantify NET release from primary human neutrophils with single-cell resolution in the presence of the motile bacteria Pseudomonas aeruginosa PAO1 and inflammatory mediators. The device was engineered to have wide chambers and constricted loops to measure NET release in variably confined spaces. Our open NET-array device enabled immunofluorescent labeling of citrullinated histone H3, a NET release marker. We took time-lapse images of primary healthy human neutrophils releasing NETs in clinically relevant infection and inflammation-rich microenvironments. We then developed a computer-vision-based image processing method to automate the quantification of individual NETs. We showed a significant increase in NET release to Pseudomonas aeruginosa PAO1 when challenged with inflammatory mediators tumor necrosis factor-α [20 ng mL⁻¹] and interleukin-6 [50 ng mL⁻¹], but not leukotriene B₄ [20 nM], compared to the infection alone. We also quantified the temporal dynamics of NET release and differences in the relative areas of NETs, showing a high percentage of variable size NET release with combined PAO1 – inflammatory mediator treatment, in the device chambers. Importantly, we demonstrated reduced NET release in the confined loops of our combined infection–inflammation microsystem. Ultimately, our NET-array device stands as a valuable tool, facilitating experiments that enhance our comprehension of the spatiotemporal dynamics of NET release in response to infection within a defined microenvironment. In the future, our system can be used for high throughput and cost-effective screening of novel immunotherapies on human neutrophils in view of the importance of fine-tuning NET release in controlling pathological neutrophil-driven inflammation.

Neutrophil adhesion to endothelia, entry into tissues and chemotaxis constitute essential steps in the immune response to infections that drive inflammation. Neutrophils bind to other cells and migrate via adhesion receptors, notably the α _M β ₂ integrin dimer (also called Mac-1, CR3 or CD11b/CD18). Here, the response of neutrophils to integrin engagement was examined by monitoring the activity of peptidylarginine deiminase 4 (PAD4). Histone H3 deimination was strongly stimulated by manganese, an integrin-activating divalent cation, even in the absence of additional inflammatory stimuli. Manganese-induced cell attachment resulted in neutrophil swarm formation that paralleled histone deimination, whereas antibodies that impair integrin binding prevented both cell adhesion and histone deimination. Manganese treatment led to putative deimination of profilin, a protein that functions as an actin-organizing hub, as detected by two-dimensional gel electrophoresis and citrulline immunoblotting. Cl-amidine, a covalent inhibitor of PAD4, and GSK484, a specific PAD4 inhibitor, blocked profilin deimination. Neutrophil migration toward leukotriene B4 and toward synovial fluid from a rheumatoid arthritis patient were inhibited by chloramidine, thus supporting the contribution of deimination to chemotaxis. The data, based on a simplified system for integrin activation, imply a mechanism whereby integrin attachment coordinates neutrophil responses to inflammation and orchestrates deimination of nuclear and cytoskeletal proteins. This article is part of the Theo Murphy meeting issue ‘The virtues and vices of protein citrullination’.