Acquired aplastic anaemia (AA) is a heterogeneous disease characterized by bone marrow haematopoietic failure, and its pathogenesis is multifactorial, involving immune dysregulation, genetic susceptibility and environmental factors. Single-nucleotide polymorphisms (SNPs) are common single-base genomic variants that are frequent, stable and readily detectable, making them useful markers for studying genetic susceptibility to disease. Specific SNPs may contribute to immune abnormalities, bone marrow microenvironmental imbalance and dysfunction of haematopoietic stem and progenitor cells (HSPCs) in AA by regulating gene expression and influencing molecular functions. In this review, we systematically summarize the association between SNPs in key genes and the susceptibility, severity, treatment response and prognosis of AA, aiming to provide new insights into early risk prediction, disease management and potential gene-based intervention strategies for AA.
The Nuclear Factor Kappa B (NF-kB) signalling pathway is essential for regulating inflammation, cell survival, and adaptive immune responses through its canonical (NF-κB1-associated) and noncanonical (NF-κB2-associated) branches. The canonical pathway mediates rapid and broad reactions to immune stimuli, whereas the noncanonical pathway is activated by specific signals and contributes to lymphoid organ development, B-cell maturation including germinal centre activity, T-cell differentiation, thymic selection and antiviral defence. NF-κB transcription factors consist of five subunits: NF-kB1 (p105/p50), NF-kB2 (p100/p52), RelA, RelB and c-Rel-and heterozygous variants in NFKB1 or NFKB2 genes result in a wide range of immune dysregulation. NFKB1 mutations have been associated with common variable immunodeficiency, autoinflammatory or rheumatologic manifestations, Epstein-Barr virus-related lymphoproliferation, gastrointestinal involvement and susceptibility to recurrent or opportunistic infections. Clinical features of NFKB2 deficiency show considerable variability depending on mutation location, but recurrent infections and hypogammaglobulinemia remain the most frequently reported findings. Despite growing recognition of NF-κB-related inborn errors of immunity, the phenotypic spectrum continues to expand and genotype-phenotype correlations remain challenging. In this study, we describe seven individuals from five families with NFKB1 or NFKB2 variants and demonstrate considerable clinical and immunological heterogeneity, including marked intrafamilial variability.
Immunometabolism, an emerging field exploring metabolic reprogramming and functional regulation in immune cells, offers a lens for understanding complex diseases. This review delineates core concepts, key signalling nodes-emphasising the mechanistic target of rapamycin (mTOR) as an integrator of metabolic and immune signals-research and intervention strategies across metabolic and infectious diseases. Immune cells display metabolic plasticity: At rest, they depend mainly on mitochondrial oxidative phosphorylation, but swiftly shift to aerobic glycolysis upon activation to fuel effector functions. Pro-inflammatory subsets like Th1 cells and M1 macrophages lean heavily on glycolysis, whereas regulatory T cells favour fatty acid oxidation. Central pathways-glycolysis, the tricarboxylic acid (TCA) cycle, and amino acid metabolism-directly shape immune activation and inflammation via intermediates and regulatory enzymes. For example, succinate and itaconic acid are critical in inflammation control, while fatty acid and cholesterol metabolism dictate immune cell fate. In metabolic disorders such as obesity, diabetes, fatty liver disease, and atherosclerosis, immune metabolic reprogramming is the main driver of chronic low-grade inflammation and tissue injury. During infection, a metabolic tug-of-war ensues: Pathogens hijack host metabolism for survival, and the host counters by reprogramming its own metabolism. The idea of "trained immunity" highlights how metabolism-epigenetics crosstalk endows innate immunity with memory-like capacity. These insights inform therapeutic avenues-modulating metabolic pathways, nutritional interventions, and microbiome targeting-with wide potential. Challenges remain, including the complexity of in vivo networks and the need for precise interventions. Yet advances in single-cell multi-omics and metabolic flux analysis will deepen mechanistic understanding and enable breakthroughs in precision strategies.
Th17-cells are crucial for defence against fungal and bacterial infections and deficiency characterises certain inborn errors of immunity (IEI), including STAT3-related Hyper IgE syndrome (HIES) and STAT1-related Chronic Mucocutaneous Candidiasis (CMC). Standardised methods for clinical Th17-cell quantification are limited. We developed a flow cytometric assay for quantifying Th17-cells in peripheral blood based on PMA/ionomycin stimulation and intracellular IL-17 labeling and evaluated its precision, robustness and longitudinal stability. A reference interval was established in 51 healthy adults and the impact of age and sex was assessed. The assay was applied to 31 patients carrying STAT1 or STAT3 variants or presenting phenotypes for which Th17-cell quantification is informative. Diagnostic performance was analysed using receiver operating characteristic (ROC) curves and Matthew's Correlation Coefficients (MCC). The assay showed high intra- and inter-assay precision (CV 5.1% and 10%) and Th17-cell fractions remained stable after 72 h of post-fixation storage. Delayed pre-fixation reduced precision. Age and sex did not significantly influence Th17-cell fractions, supporting a unified Th17-cell reference interval of T-helper cells [0.21%-1.7%]. Compared with healthy controls, Th17-cell fractions were significantly lower in patients with STAT3 variants, patients with HIES or with both. ROC and MCC analyses indicated that Th17-cell fractions above 0.44% reliably excluded pathogenic variants or associated phenotypes in all patient groups. This validated Th17-cell assay is robust, reproducible and suitable for clinical use. It can guide genetic testing in IEI by identifying patients with Th17-cell deficiencies and excluding variants or phenotypes unlikely to be causative.
We aimed to evaluate the sensitivity and specificity of Recent Thymic Emigrant (RTE) levels for diagnostic discrimination among various Inborn Errors of Immunity (IEI) subgroups. We analysed 205 paediatric patients diagnosed with IEI at the Paediatric Immunology and Allergy Department of Başakşehir Çam and Sakura City Hospital in Istanbul between January 2021 and January 2024. An age- and sex-matched control group consisting of 31 healthy children was also included for comparison. Demographic, clinical and laboratory data were evaluated. Reduced RTE levels were identified in 39% of all patients. Low RTE levels were most pronounced in patients with syndromic combined immunodeficiency (77%) and immune dysregulation (100%), and were also observed at high frequencies in combined immunodeficiency (CID) (60%) and autoinflammatory disorders (57.1%). For the syndromic CID group, the diagnostic performance of RTE yielded an area under the curve (AUC) of 0.80, with a sensitivity of 92% and a specificity of 52%. In the immune dysregulation group, the AUC was 0.79, with a sensitivity of 83.5% and a specificity of 57.1%. Assessment of RTE levels represents a valuable diagnostic biomarker, particularly for patients within the syndromic CID and immune dysregulation categories. This parameter may contribute meaningfully to clinical practice by facilitating early diagnosis, guiding genetic testing and enabling assessment of thymic function. Incorporating thymic output assessment into routine immunophenotyping panels may shorten the diagnostic timeline for IEI and allow earlier initiation of appropriate therapies.
Viruses activate host defences by alerting interferon and other alarms. Viruses seeking latency must curtail this. Infected subjects would then have minimal immune system activation and remain healthy. However, a minority cannot prevent emergence of associated diseases. This conundrum remains despite our understanding (i) that interferon specifically suppresses the translation of viral mRNAs, but not host mRNAs, and (ii) that for the latent state only one latency-maintaining mRNA may be needed. Critical are mRNA loadings with purine (R) bases, relative to pyrimidine bases (Y). Base composition and structural studies have established the genome-wide potential of duplex DNA (hence transcripts thereof) to extruded stem-loops, the stems of which require parity between R and Y bases. Sometimes conflicting with coding demands, parity-violations (R > Y) decrease this potential in exons (and hence in mRNAs). Thus, one mRNA (EBNA-1) of the Epstein-Barr virus (EBV) is successful in not alerting hosts to immune awareness. However, Y-rich transcripts might occasionally arise in the highly polymorphic 'junk DNA', long known as pervasively transcribed. Thus, within a minor subset of the infected population, some may, by chance, have randomly mutated to create pyrimidine-loaded regions that would form forbidden double-stranded RNA duplexes with purine-loaded EBNA-1 mRNAs. Thus, immune systems would awaken. Other viruses, differing in types/extents of latency, have evolved different survival strategies. Thus, mRNAs of the extremely latent human T cell leukaemia virus (HTLV1) are Y-loaded (Y > R), but a single latency transcript is highly R-loaded. In contrast, most mRNAs of less extremely latent retrovirus (HIV1) are expressed with R > Y.
Autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED) is a rare monogenic autoimmune disease caused by loss-of-function mutations in the Autoimmune regulator gene and the subsequent impairment of negative selection in the thymus. Previous studies have identified many T cell abnormalities in APECED patients, with increased signs of activation and failure of regulation. These findings, however, have been demonstrated using traditional flow cytometry studies, prone to human misinterpretation of multidimensional data. Here we present an unsupervised flow cytometry analysis of CD4+ T cells in 20 APECED patients. Our workflow consists of an optimized sequence of well documented unsupervised analysis algorithms for data quality control, batch correction and clustering with multiple options evaluated. We show the overall increase in T cell activation to extend from the previously reported CD8+ compartment to both the T helper and regulatory T cells. We demonstrate the regulatory T cells in APECED to adopt a population distribution dominated by cells of low suppressive potential and present a novel CD45RAneg, CCR7neg, CD31high, CD127mid population unique to APECED. In general, however, we find the population structure of the APECED CD4+ T cell compartment largely similar to that of the controls as supported by both our clustering and dimensionality reduction analyses. Our analysis replicates previous findings and provides novel information on APECED while also presenting an optimized unsupervised workflow for flow cytometry analysis in general. Our approach offers multiple advantages over manual flow cytometry analysis with its rigorous data quality control, well-documented batch correction and optimized automated clustering.
Identifying sensitive and specific blood biomarkers for early warning of severe COVID-19 remains a critical clinical need. Based on previous findings of elevated cytokines in bronchoalveolar lavage fluid and blood, we developed a novel luciferase immunosorbent assay (LISA) that selectively quantifies biologically active full-length suPAR and can eliminate interference from inactive fragments measured by conventional ELISA. Compared with conventional ELISA, LISA showed a lower detection limit (5.08 vs. 45.72 pg/mL) and a wider linear range (45.72-100,000.00 vs. 1234.46-11,111.11 pg/mL). In adult COVID-19 patients, suPAR levels were significantly elevated in severe cases (p < 0.001) and correlated positively with NLR and SII (p = 0.003 for each), and with IL-6 (p < 0.001), but negatively with lymphocyte count (p = 0.004). suPAR outperformed conventional inflammatory markers in predicting severe disease (AUC = 0.785) and adverse outcomes (AUC = 0.912), supporting its role as an independent predictor. In paediatric COVID-19 patients, suPAR remained superior to other single peripheral blood biomarkers for severity prediction, despite weaker correlations with inflammatory indices. This study establishes a reliable method for quantifying functionally intact suPAR and demonstrates its age-dependent predictive value, highlighting its potential for individualized risk stratification in COVID-19 patients.
Porphyromonas gingivalis (P. gingivalis), has been implicated in exacerbating inflammatory arthritis through its virulence factors. Understanding the role of these factors could inform strategies to mitigate both periodontal and synovial inflammation. This study aimed to investigate the prevalence of P. gingivalis virulence factors and their potential impact on disease activity in patients with periodontitis, rheumatoid arthritis (RA), or both conditions. Patients with RA (n = 22), RA plus periodontitis (n = 22), periodontitis (n = 10), and healthy controls (n = 35), were compared for C-reactive protein levels, anti-cyclic citrullinated peptide IgG, peptidylarginine-deiminase (PAD)2/4 activity and anti-P. gingivalis virulence-associated gingipain antibodies. All patients with periodontitis were compared for P. gingivalis, Tannerella forsythia and Prevotella intermedia colony-forming units, and gene variants of P. gingivalis, including PAD (P.PAD), major fimbriae (fimA), lysine-gingipain (kgp), and receptor antigen gene B (ragB). Higher mean clinical periodontal attachment loss was observed with P.PAD type 1 (p = 0.033). The major fimbriae and lysine-gingipain gene variants showed distinct distributions between groups. Anti-gingipain IgG levels showed positive correlations with RA disease activity. Despite limitations, this study supports a role for P. gingivalis in exacerbating periodontitis and RA underscoring the importance of P. gingivalis virulence factors in disease modulation and highlighting potential therapeutic strategies. Further research is needed to elucidate mechanistic pathways and develop effective interventions. Trial Registration: ISRCTN 17950307; https://doi.org/10.1186/ISRCTN17950307.
Enzymes like peptidylarginine deiminase 4 (PAD4) generate citrullinated epitopes that are crucial in triggering and driving the anti-citrullinated protein antibody (ACPA) response in rheumatoid arthritis. Here, we assessed whether serum PAD4-potentiating activity is associated with subsequent arthritis development among ACPA-positive individuals during the pre-clinical phase. The study included 267 ACPA-positive individuals from the Karolinska Risk-RA cohort, among whom 101 (37.8%) developed arthritis within the observational period (range 22-60 months). We measured the ability of serum to potentiate PAD4 activity by quantifying the generation of citrullinated products using high-performance HPLC. Study participants were then classified as PAD4act-positive or -negative, and PAD4 status analysed in relation to onset of arthritis, clinical characteristics (ESR, CRP and DAS28) and established risk factors (HLA-DRB genotype, smoking). PAD4act-positivity was identified in 35 individuals, with a significant proportion (21, p = 0.0049) developing arthritis. Kaplan-Meier analysis demonstrated that individuals with PAD4act-positivity had increased rate of progressing to arthritis (p = 0.0022). Additionally, PAD4act-positive individuals were more likely to possess at least one copy of the HLA-DRB shared epitope allele (p = 0.045). Notably, PAD4act-positivity did not associate with pre-clinical CRP, ESR, DAS28, or smoking status. These findings suggest that serum PAD4-potentiating activity may help stratify arthritis risk and time to onset among ACPA-positive at-risk individuals.
The UNC13D gene encodes Munc13-4, a key regulator of cytotoxic granule exocytosis in effector immune cells, enabling the release of perforin and granzymes that are essential for cytotoxic function and immune surveillance. Loss-of-function mutations in UNC13D result in immune dysregulation syndromes, most notably familial hemophagocytic lymphohistiocytosis (fHLH, also referred to as FHL). This review provides a comprehensive overview of UNC13D, including its structural characteristics, biological functions, and spectrum of pathogenic variants. We summarize the mechanistic roles of Munc13-4 in granule-mediated cytotoxicity and examine the clinical correlations between UNC13D mutations and fHLH type 3 (FHL3). Furthermore, we discuss emerging evidence linking UNC13D dysfunction to a broader range of diseases, highlighting its clinical relevance and potential as both a diagnostic biomarker and therapeutic target. Overall, this review aims to bridge the gap between molecular mechanisms and clinical translation in UNC13D-related disorders.
Recombination-activating genes (RAG1 and RAG2) encode lymphoid-specific proteins that are essential for V(D)J recombination during early T- and B-lymphocyte development. Biallelic mutations in these genes result in a broad spectrum of primary immunodeficiency phenotypes, ranging from classical severe combined immunodeficiency (SCID) to combined immunodeficiency, immune dysregulation, autoimmunity, and inflammatory complications. The immunological phenotype varies widely, from T-B-NK+ severe combined immunodeficiency (SCID) to combined immunodeficiency (CID), or near-normal T and B cell counts, and even antibody deficiencies despite preserved pathogen-specific antibody responses. In this cohort, we aimed to characterize the clinical, immunological, and genetic features, as well as the disease course, of patients diagnosed with RAG1 and RAG2 deficiencies.
The initiation of adaptive immunity requires antigen presentation in immune inductive sites. Classical dendritic cells (cDC) sense peripheral immune response inducing cues and migrate to the tissue-draining lymph nodes upon engagement, where they present acquired antigen to cognate T cells. Vaccines include adjuvants, which enable cDC activation and migration, both essential steps in the cascade leading to adaptive immunity. We here show that the expression of MyD88, the adapter molecule downstream of most toll-like receptors (TLR), is essential for the migration of cDCs in response to several stimuli and that its restricted expression to the TLR-sensing cDC subset is sufficient for the migration of that subset. As efficacious oral vaccines are primarily needed for use in newborns, we further quantify and characterise neonatal intestinal cDCs in five-day-old mice and show that they follow the same rules and patterns as we identified for cDCs in the adult intestines. Together, our data suggest strong conservation of immune-inducing cues across ages and provide fundamental knowledge aiding adjuvant choice for neonatal vaccination strategies.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection significantly affects innate immune responses, particularly those of natural killer (NK) cells, which play an important role in antiviral defence. This review combines phenotypic, functional, and transcriptomic findings to explain the disruption of NK cell subsets in COVID-19. Flow cytometry studies have shown generalised lymphopenia and a significant reduction in the CD56bright and CD56dimCD16+ subsets. This change is linked to an increase in the CD56dimCD16- and CD56-CD16+ populations, which correlate with disease severity. At the molecular level, there is an imbalance between activating and inhibitory receptors. This includes increases in NKG2A, PD-1, and LAG-3, along with decreases in NKp30, NKp46, and NKG2D. These findings are consistent with an exhausted phenotype and weakened cytotoxicity. Single-cell RNA sequencing (scRNA-seq) studies have identified an increase in proliferative, cytotoxic, and platelet-associated CD56dim NK subpopulations in severe cases and a reduction of CD56bright cells. Transcriptomic profiling showed that upregulation of interferon-stimulated genes (ISGs) and inflammatory pathways driven by STAT1/3, NF-κB activation, and transforming growth factor-beta (TGF-β) signalling suppresses NK effector functions. Collectively, these findings suggest a model in which progressive NK cell dysfunction may be associated with the immunopathogenesis of COVID-19. The integration of multi-omic and phenotypic approaches provides a comprehensive view of NK cell responses to SARS-CoV-2 and suggests potential biomarkers and therapeutic targets to restore NK cell antiviral activity.
Itaconate, derived from cis-aconitate decarboxylation by immune-responsive gene 1 (IRG1; also called cis-aconitate decarboxylase 1, ACOD1), is an intermediate metabolite of the tricarboxylic acid (TCA) cycle in the mitochondria. The production of itaconate in myeloid cells is rapidly increased to high levels in pathological conditions, such as infection and cancer. It is well known that itaconate plays an essential role in regulating macrophage-mediated inflammation and immune response through multiple mechanisms, such as regulating signal transduction and protein modification. As the first responders upon infections and injuries, neutrophils contribute to pathogen clearance and inflammation by several mechanisms, such as phagocytosis, producing reactive oxygen species (ROS), and forming neutrophil extracellular traps (NETs). Increasing evidence shows that neutrophils can also produce itaconate, which in turn modulates neutrophil activation, thereby affecting the elimination of pathogens, the resolution of inflammation, and tumour progression. In this review, we summarize the recent advancements in understanding the effects of endogenous itaconate and its derivatives on neutrophil responses, with a focus on the underlying mechanisms and potential therapeutic applications in infectious and inflammatory diseases.
Pregnant individuals were prioritised for COVID-19 research due to concerns about increased susceptibility and limited clinical trial data. This narrative review synthesises evidence on maternal infection, immunological adaptations, placental susceptibility, and antibody transfer following maternal SARS-CoV-2 vaccination. Symptomatic COVID-19 during pregnancy increases risks of severe outcomes, whereas vertical transmission remains rare. Placental pathology is characterised mainly by maternal vascular malperfusion and inflammation, with limited evidence of direct viral infection. Maternal vaccination-particularly with mRNA vaccines-induces robust IgG responses with efficient transplacental and lactational transfer, conferring passive neonatal protection. Key uncertainties include optimal vaccine timing, durability of neonatal immunity, and variant-specific responses. Strengthening standardised research and ensuring inclusion of pregnant individuals is essential for global maternal health policy.
Immune checkpoint inhibitors (ICIs) have reshaped cancer treatment, offering durable remissions for a minority of patients. Yet their success has come with a difficult trade-off: a large proportion of patients develop immune-related adverse events (irAEs), sometimes severe, and often without gaining clinical benefit. These reactions signal a disruption of peripheral tolerance that is not easily explained by traditional models in which negative selection of autoreactive T cells maintains self-restraint. Under ICI therapy, patients' own T cells can behave in ways that resemble the alloreactive responses seen in chronic graft-versus-host disease (cGVHD), producing a pattern of tissue injury that mirrors this well-studied transplant complication. This parallel offers a fresh way to think about why irAEs occur and how they might be prevented. Despite arising from fundamentally different immunologic triggers, comparative transcriptomic analyses reveal that cGVHD and irAEs induced by ICIs converge on a common molecular ecosystem dominated by interferon-conditioned tissue states. Early clinical experience with ultra-low-dose ICI regimens supports this idea, showing that meaningful antitumor activity can be preserved while dramatically reducing toxicity. We suggest that viewing ICI-induced autoimmunity through a cGVHD-like lens may help guide safer dosing strategies and broaden access to immunotherapy worldwide.
Interleukin-40 (IL40) is a recently described 27 kDa cytokine encoded by C17orf99, originally suggested to play a role in B-cell biology, but its function is largely unknown. However, elevated serum levels have been reported in rheumatic diseases. Most published studies focus on IL40 measurements in serum/plasma using commercial sandwich ELISAs. Here we found large discrepancies between two IL40 ELISAs (Mybiosource and Abbexa), with Abbexa reporting significantly higher plasma levels. In our investigation, IL40 (Abbexa) was not elevated in patients with ANCA-associated vasculitis, early or established rheumatoid arthritis (RA), or RA patients who had developed B cell lymphoma (RA-L), compared to healthy donors. Yet, we found significant correlation of Abbexa IL40 levels with BAFF and APRIL. We next compared the binding of IL40 between the two commercial assays. Pre-adsorption experiments showed that the Mybiosource capture antibody bound the same target as the Abbexa capture antibody but did not detect the same IL40. Moreover, neither assay detected the reciprocal IL40 kit reference nor mammalian expressed recombinant IL40. In contrast, a Human Protein Atlas (HPA) antibody towards the unstructured C-terminal of IL40, despite being only partly validated by HPA, detected recombinant IL40 in Western blot and ELISA. We speculate that there may be different structural or modified forms of IL40. The discrepancy between the IL40 Abbexa results and the literature also highlights the difficulties in interpreting results from commercial antibodies and assays.
The link between allergic conditions and common variable immunodeficiency (CVID) is still unclear. Only a few studies suggest allergic diseases are more prevalent in CVID patients than in the general population, and the role of IgE remains poorly defined. This study aims to evaluate the prevalence of allergic conditions in CVID and the role of serum IgE and IgA levels. This prospective, cross-sectional, case-control study enrolled Italian adult CVID patients to investigate allergic conditions' frequency and relationships between IgE, IgA, and clinical phenotypes. Analyses of diagnostic/prognostic accuracy were performed with ROC curves. We documented an allergic disease in 26.6% of 60 CVID patients, most commonly allergic rhinitis (56.2%) and bronchial asthma (12.5%). CVID patients with allergy had higher IgE levels (+8.9 kU/L, p = 0.006) than non-allergic ones, but lower than allergic individuals without CVID. IgE deficiency was observed in 65% of CVID patients, with a strong correlation between IgE and IgA levels (r = 0.7, p < 0.001). Low IgE (< 2.5 kU/L) and IgA levels (< 7 mg/dL) were significantly associated with lymphoproliferative (p < 0.001) and granulomatous phenotypes (p = 0.005), achieving an AUC of 94% and 81% for predicting lymphoproliferation and granulomatosis, respectively. The prevalence of allergic conditions in CVID patients is lower compared with previous studies. Low IgE levels served as a good biomarker for CVID and CVID-phenotypes. Combined serum IgE and IgA assessment improved prognostic stratification.
