Journal of Clinical Immunology

Background VEXAS syndrome is a late onset autoinflammatory disease caused by somatic UBA1 mutations and characterized by heterogeneous systemic and hematologic manifestations. We aimed to describe all identified Belgian cases through a national multicenter cohort. Methods We conducted a retrospective study across four Belgian tertiary centers. Clinical, biological, genetic, therapeutic, and outcome data were collected using standardized anonymized case report forms. Analyses were descriptive. Results Twenty-one male patients were identified between January 2018 and May 2025. General symptoms such as Fatigue, weight loss and sweating occurred in 95% of cases. The most frequent manifestations were cutaneous (85.7%), hematologic (76.2%), articular (66.7%), thromboembolic (57.1%), chondritis (42.9%), ophthalmologic (38.1%), pulmonary (38.1%). Other manifestations also included vasculitis (61.9%). At diagnosis, 95% had anemia, macrocytic in 57%, and 28.6% had thrombocytopenia. Corticosteroids were the main first line therapy. Second line treatments included anti IL 6 agents (46.7%), JAK inhibitors (20%), and azacitidine (14.3%). Complete remission occurred in 50% of patients receiving anti IL 6 therapy and in 33% treated with either JAK inhibitors or azacitidine. Two patients underwent allogeneic stem cell transplantation, one died from infectious complications. Twenty six infectious episodes were recorded, including opportunistic infections. Six patients (28.6%) died during follow-up, four from infectious complications. Conclusion This first Belgian national cohort confirms the clinical heterogeneity of VEXAS syndrome and highlights substantial infectious morbidity and mortality. Access to targeted second-line therapies, particularly anti IL-6 agents and JAK inhibitors, remains challenging despite apparent clinical benefit.

The genetic risk factors of immune cytopenias are unclear. Immune cytopenias have been reported in various genetic contexts: 1) inherited error of immunity genes, mainly due to rare germline variants, 2) systemic lupus erythematosus, associated with common germline variants, 3) hematological malignancies, and 4) clonal hematopoiesis, the latter two due to somatic variants. However, the respective contribution and interaction of these variants remain to be investigated. Here, we used two large biobanks with whole genome sequencing data to systematically investigate the genetic contribution to immune cytopenia. We found that the four types of genetic variants independently contribute to immune cytopenia risk. We notably found that carriers of variants in some autosomal recessive genes of inherited error of immunity had an increased risk of immune cytopenia. Additionally, common variant-mediated risk of systemic lupus erythematosus also increased the risk of immune cytopenia. Overall, a third to a half of patients with immune cytopenia carried at least one of the four genetic risk variants investigated. Combining the four variants allowed stratifying the risk of immune cytopenia in both general and high-risk population. In general population, the 10-year incidence of immune cytopenia in the lowest and highest risk groups was 0.08% and 1.5%, respectively. In sum, this work identified that different genetic risk factors can lead to immune cytopenia. A large proportion of individuals with immune cytopenia carried an underlying genetic risk factor. Finally, combining these genetic risk factors enabled risk stratification.

Background Monogenic autoinflammatory disorders arise from genetic defects that pathologically activate innate immunity. IRAK4, a serine/threonine kinase in the Myddosome pathway, mediates IL 1 and Toll like receptor signaling, driving proinflammatory cytokine and type I interferon responses. While biallelic loss of function IRAK4 variants cause an immunodeficiency, recent reports implicate biallelic IRAK4 variants in severe neuro and systemic autoinflammation (NASA). We investigated a child with a similar phenotype and screened unsolved autoinflammatory leukoencephalopathies in the Myelin Disorders Biorepository Project (MDBP). Methods Individuals with unexplained autoinflammatory leukoencephalopathy and no unifying molecular diagnosis were identified in the Myelin Disorders Biorepository Project (MDBP), and genome sequencing was reanalyzed to prioritize rare, protein altering and splice affecting variants. Candidate variants and their splicing consequences were interrogated with short read and targeted long read RNA sequencing, benchmarked against control PBMC and normal tissue transcriptomes. Nonsense mediated decay of transcripts was also assessed. Clinical, genetic, and treatment data were extracted by standardized deep phenotyping, and brain MRI was reviewed in consensus by two pediatric neuroradiologists. Results We identified six patients from five unrelated families with biallelic, rare IRAK4 variants presenting with severe, persistent autoinflammation without immunodeficiency. Variants included two homozygous and three compound heterozygous changes. All patients had a concordant clinical and radiologic syndrome: episodic, waxing and waning encephalopathy with refractory seizures; neuroimaging showed transient white matter edema that evolved to gliosis, superimposed on marked calcifications and ensuing cerebral atrophy. Biomarkers indicated neuroinflammation and anemia in all cases. Median age at neurologic symptom onset was 12.96 years (IQR 9.44). Immune suppressive therapies achieved partial benefit, but most patients had ongoing seizures, persistent neuroinflammation, and progressive disease, and without treatment, loss of life. Conclusion In these six patients, a strongly concordant clinical and radiological phenotype emerges of IRAK4-mediated autoinflammation, expanding the phenotypic and mutational spectrum of IRAK4 related disease. Further studies are needed to define mechanisms and optimal treatments.

Autoantibodies neutralizing type I IFNs (AAN-IFN-I) have been found in significant proportions of cases of severe, critical, and fatal COVID-19 pneumonia. We performed a systematic review of 54 studies reporting auto-Abs against type I IFNs and a meta-analysis of 20 studies reporting auto-Abs neutralizing type I IFNs published between 2020 and 2026. The meta-analysis included data for 11,380 SARS-CoV-2-infected individuals from Europe, North America, South America, Asia, the Middle East, North Africa and international multicenter cohorts, including 7,814 with severe or critical disease (69%). The pooled prevalence of AAN-IFN-I was estimated at 7.9% (95% CI, 6.0-10.4). Disease severity was strongly associated with AAN-IFN-I prevalence (OR, 11.7; 95%CI, 7.6-17.9; P=5x10^-29). The pooled prevalence of AAN-IFN-I reached 11.4% (95% CI, 10.2-12.7%) in patients with severe or critical COVID-19 and 15.3% (95% CI, 12.1-19.2%) in those who died. The prevalence of AAN-IFN-I increased with age in patients with severe, critical, or fatal COVID-19. AAN-IFN-I probably accounted for about 1.1 million of the 7.1 million deaths from COVID-19. AAN-IFN-I are strong, common, global determinants of life-threatening COVID-19 pneumonia.

Large genomically annotated acute myeloid leukaemia (AML) datasets exist, but population-based contemporary cohorts remain scarce. Here we report clinicopathological, genomic, and outcome data from Danish AML patients. 2,512 AML patients were identified between 2015-2022, of whom 33.8% had available NGS data (NGS+). In patients [≤]70 years, baseline characteristics and outcomes were comparable between NGS+ and NGS- groups. In patients >70 years, more NGS+ patients received intensive treatment, but survival was similar among intensively treated patients. The distribution of mutations varied significantly by age and sex, with older age and male sex exhibiting higher frequencies of adverse-risk gene mutations. In intensively treated NGS+ patients, ELN2017 stratified 5-year OS: 58.4% (favorable), 43.4% (intermediate), and 28.2% (adverse), with hazard ratios (HRs) of 0.63 (favorable) and 1.45 (adverse) relative to intermediate. ELN2022 yielded corresponding OS rates of 56.9%, 51.8%, and 29.7%, with HRs of 0.78 and 1.86. The two models had comparable predictive performance for OS in a time-dependent model. In conclusion, outcomes of intensively treated AML patients were comparable irrespective of NGS status, underscoring the representativeness of the REFORM-AML database for the Danish AML population. Age and male sex correlated with adverse-risk mutations, and both ELN2017 and ELN2022 robustly predicted survival.

Background: Patients receiving anti-TNF treatment for chronic inflammatory disease display impaired antibody responses, but it remains unclear how immune memory formation is affected. We evaluated antibody responses and memory B cells (Bmem) after COVID-19 booster vaccination in inflammatory bowel disease (IBD) patients receiving anti-TNF treatment. Methodology: Blood was sampled at baseline, 1, and 6 months after WH1/BA.5 bivalent or XBB.1.5 monovalent vaccination from 27 IBD patients receiving intravenous anti-TNF and 44 controls. Neutralizing antibodies were measured using an infectious virus assay. SARS-CoV-2 spike receptor binding domain (RBD)-specific serum IgG was quantified by ELISA, and RBD-specific Bmem were immunophenotyped by flow cytometry using recombinant proteins from ancestral, Omicron BA.1, BA.5, XBB.1.5, and JN.1 variants. Results: Serum IgG to vaccine RBD and neutralizing antibodies in patients increased pre to 1 month post-vaccination, but were lower than controls. Ancestral-, BA.5- and XBB.1.5-specific Bmem increased after vaccination but were significantly lower in patients than controls. Within RBD-specific Bmem, frequencies of recently activated CD21lo cells were increased after vaccination, and were higher in patients than controls. Fewer antigen-specific Bmem in patients expressed IgG4, and more expressed IgG3 or IgD following vaccination. Following vaccination, more RBD-specific Bmem recognized multiple viral variants. However, patients had fewer Bmem that could bind to subvariants than controls. Conclusion: Antibody and Bmem responses to COVID-19 booster vaccination in anti-TNF-treated IBD patients displayed reduced capacity, durability and cross-reactivity, suggesting impaired immune memory for protection against breakthrough infection. This supports the recommendation for annual booster vaccination to prevent severe disease and viral spread.

Juvenile systemic sclerosis (jSSc) is a rare autoimmune disease marked by skin fibrosis and multi-organ involvement. Autologous stem cell transplantation (ASCT) is an emerging therapy for severe, treatment-refractory jSSc, but its effects on immune cell dynamics remain poorly understood. PBMCs were collected from three patients with jSSc before ASCT and at 6, 12, and 24 months post-ASCT. Patient and healthy control samples were profiled using cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq). We focused on monocytes, given their role in fibrosis-promoting inflammation. To detect longitudinal trends, pseudobulked gene expression (log scale) was regressed against time since ASCT. This approach identified widespread changes in jSSc monocytes, including decreased expression of systemic sclerosis-linked genes, such as SERPINE1. On the pathway level, NF-{kappa}B-associated inflammatory signaling was elevated in jSSc monocytes at baseline relative to healthy controls and decreased progressively post-ASCT. Genes related to mitochondrial function and oxidative phosphorylation progressively increased in expression after ASCT, suggesting a shift in metabolic state. Compositional changes in monocyte subpopulations were also identified and may have contributed to longitudinal gene expression patterns. Together, these findings characterize the dynamic immune changes in jSSc following ASCT and highlight a widely applicable longitudinal modeling framework for single-cell data.

The extent to which rare and common genetic variants jointly contribute to the risk of acute myeloid leukemia (AML) still remains relatively unexplored in large-scale biobank whole-genome sequencing cohorts. Here, we leverage the latest sequencing and phenotypic data from the All of Us Research Program to identify variants, genes, and gene-sets associated with AML. We performed set-based association tests for rare protein-coding variants (Ncases=265 and Ncontrols=169,706) and single-variant association tests for common variants (Ncases=265 and Ncontrols=169,705) utilizing the large European-like ancestry sample. For the rare-variant set-based tests conducted using SAIGE-GENE+, four genes were statistically significant: DNMT3A, TET2, SRSF2, and IDH2 (Bonferroni-corrected Cauchy p-value < 0.05). We also constructed multiple rare-variant burden risk scores using different gene-sets to identify those with a substantial rare-variant burden for AML. Gene-sets derived from Genomic Data Commons whole-genome sequencing data, comprising two distinct groups-genes observed to harbor somatic mutations in AML and genes observed to harbor somatic mutations across all cancer types-showed a statistically significant rare-variant burden (Bonferroni-corrected p-value < 0.05). Ultimately, these findings demonstrate that leveraging whole-genome sequencing in large-scale biobanks enables the identification of rare protein-coding variants, genes, and gene sets associated with AML.

Acquired aplastic anaemia is caused by immune-mediated loss of haematopoietic stem and progenitor cells (HSPCs), but the regulatory states that sustain cytotoxic immunity and their relationship to inherited susceptibility remain incompletely understood. We integrated two single-cell RNA-sequencing cohorts spanning healthy, non-severe and severe aplastic anaemia with single-cell chromatin accessibility profiling, genome-wide association meta-analysis, Bayesian fine-mapping and stratified LD-score regression. Single-cell transcriptomics revealed a coordinated shift across the immune and haematopoietic compartments. Cytotoxic CD8 and {gamma}{delta} T cells converged on a shared NKG7/CCL5/PRF1 effector program, indicating that cytotoxic differentiation extends across T-cell lineages. Effector-memory T cells combined inflammatory signalling with SOCS, DUSP, TNFAIP3, RGS1 and TOX, consistent with sustained stimulation accompanied by extensive feedback regulation. With increasing disease severity, these inflammatory states were further coupled to hypoxic, oxidative and unfolded-protein-response programmes, suggesting qualitative remodeling of the immune compartment rather than uniform amplification of perforin-granzyme expression. Single-cell chromatin accessibility provided a regulatory counterpart to these transcriptional states. Naive and memory-associated cells retained TCF7/LEF1/BACH2 accessibility, whereas cytotoxic cells acquired coordinated accessibility across CCL5, NKG7, PRF1, granzymes and killer-receptor loci. Pseudotime, motif activity and integrated RNA-chromatin profiles positioned AP-1, NFAT and TBX21 along this transition, linking loss of memory-associated regulation to acquisition of cytotoxic effector competence. Genetic meta-analysis independently recovered association at the HLA-B region, reinforcing antigen presentation as the principal inherited susceptibility axis. Fine-mapping additionally prioritized a non-HLA locus without resolving its effector gene, while stratified LD-score regression found no detectable preferential enrichment of common-variant heritability within effector-memory or cytotoxic regulatory elements. Integrated with the cellular data, these findings support a mechanistic hierarchy in which HLA-linked antigen presentation establishes the selective context, persistent cytotoxic T-cell state remodeling maintains pathogenic immune pressure, and IFN{gamma}-responsive HSPC suppression translates this pressure into haematopoietic failure.

De novo mutations underlying early-onset systemic autoinflammatory diseases have identified key regulators of innate immunity, including pathways that drive IL-1-mmediated inflammation. Here we describe two unrelated girls presenting in infancy with systemic inflammation and sterile lung abscesses, who harbor the same de novo gain-of-function mutation in dysferlin (DYSF; p.P1449L) Myeloid expression of DYSF P1449L enhances COP-I binding, promotes dysferlin retention in the ER-Golgi, and disrupts vesicle trafficking and membrane homeostasis. Dysferlin-mutant monocytes and M2-like macrophages exhibit ectopic perinuclear NLRP3 inflammasome activation, increased IL-1{beta} production, and inflammatory cell death. Mutant M2-like macrophages further display defects in membrane expansion, exocytosis, efferocytosis, and debris clearance, promoting neutrophil recruitment and DAMP-signal amplification that culminate in sterile abscess formation. These findings identify dysferlin as a regulator of membrane homeostasis in myeloid cells, establish defective membrane-stress adaptation as trigger of NLRP3 inflammasome activation, and define a novel IL-1 mediated autoinflammatory disease caused by gain-of-function DYSF mutations.

Purpose: Adults with high- or very high-risk acute leukemia (AL) or myelodysplastic syndrome (MDS) face substantial relapse risk after allogeneic hematopoietic stem-cell transplantation. We evaluated single-unit cord blood (CB) transplantation after ex vivo expansion with UM171 in this population. Patients and Methods: Two prospective, single-arm phase II trials at four centers enrolled 64 adults with high- or very high-risk AL or MDS; 60 received a UM171-expanded CB transplant and comprised the analysis population. CB units were preferentially selected at a 5/8 HLA match to maximize the graft versus leukemia effect. Patients received intermediate- or high-intensity conditioning with tacrolimus/mycophenolate mofetil graft-versus-host-disease (GVHD) prophylaxis. Endpoints included safety, feasibility, non-relapse mortality (NRM), relapse-free survival (RFS), overall survival (OS), GVHD, GVHD-free relapse-free survival (GRFS), chronic GVHD-free relapse free survival (CRFS). Results: Thirty-two percent of patients had undergone previous transplantation, 17% of patients with AL were not in remission and 24% of those with AML/MDS had TP53 mutations. Of 62 patients who remained eligible for transplantation, 60 had a graft successfully manufactured and infused. Median times to neutrophil and platelet engraftment were 17 and 38 days, respectively. NRM was 5.1% at day 100 and 15.2% at 1 year. Two-year cumulative incidence of relapse was 22.3%. Two-year OS and RFS were 63.9% and 60.4%, respectively. Grade III-IV acute GVHD incidence was 20.3% at 1 year and moderate-to-severe chronic GVHD incidence was 6.8% at 2 years. Conclusion: UM171-expanded CB transplantation was feasible and provided prompt engraftment, durable disease control, and infrequent clinically significant chronic GVHD in adults with high- and very high-risk AL/MDS. Comparative studies are warranted to define its role relative to contemporary donor platforms.

Down syndrome, caused by trisomy 21, is characterized by chronic interferon-associated inflammation and immune dysregulation, yet the contribution of human secondary lymphoid organs to shaping this immune landscape remains unclear. Using multimodal single-cell and spatial profiling of human tonsils, we identify extensive remodeling of immune organization in trisomy 21. CD4 T cells are skewed away from canonical follicular helper (TFH) programs toward inflammatory TFH1-like and cytotoxic helper states enriched for interferon-responsive transcriptional programs. Tonsillar TFH cells exhibit increased interferon-{gamma} and interleukin-21 production, indicating inflammatory skewing toward type 1 helper immunity. These alterations are accompanied by changes in dendritic cell and CD8 T-cell compartments, reduced follicular size, increased extrafollicular TFH1-B-cell proximity and altered B-cell differentiation trajectories. Together, our findings identify trisomy 21 as a unique human context to investigate how chronic interferon-associated inflammation reshapes lymphoid tissue organization and adaptive immune cell fate decisions.

In TLR7-driven macrophage activation syndrome (MAS), inflammatory hemophagocytes (iHPCs) differentiate from Ly6CHI monocytes, phagocytose red blood cells and promote disease, including anemia and thrombocytopenia. We demonstrate here that IRF5 is required for iHPC differentiation and MAS in TLR7-overexpressing (TLR7.1) mice. Both constitutive and myeloid-specific Irf5 deletion reduced iHPCs and improved anemia, thrombocytopenia and survival. Furthermore, therapeutic inhibition of IRF5 ameliorated MAS features and reduced splenic and circulating iHPCs. While cell-intrinsic IRF5 expression was required for iHPC differentiation, it was not required for TLR7.1 Ly6CHI monocyte differentiation and monocyte transcriptional programs. We further show that the transcriptome and chromatin landscape changed dramatically as iHPCs differentiated from TLR7.1 Ly6CHI monocytes. Many transcriptional programs gained in iHPCs were enriched in genes associated with IRF5-binding accessible chromatin regions, including those associated with NF-kB signaling, cytokine and chemokine production, and complement activation. Our data suggest that IRF5 collaborates with other transcription factor families, including NF-kB, ETS and AP1 members, to regulate iHPC gene programs. Together, our findings demonstrate that expression of IRF5 in myeloid cells is critical for MAS, for iHPC differentiation, and acts broadly across iHPC-specific gene programs in TLR7-driven inflammation.

Background: Sickle cell anaemia (SCA) is characterised by chronic haemolysis, inflammation, platelet activation, and recurrent vaso-occlusive complications. Mean platelet volume (MPV) is a readily available platelet index, but evidence regarding its relationship with disease severity in paediatric SCA remains limited and inconsistent, particularly in African populations. Objective: To evaluate the relationship between MPV and disease severity among children with SCA in Kwara State, North-Central Nigeria. Methods: This hospital-based cross-sectional study included 51 clinically stable children with confirmed SCA consecutively recruited from the paediatric haematology clinic of Children Emergency Specialist Hospital, Ilorin. Complete blood count, including MPV, was performed using a Rayto RT-7600 automated haematology analyser. Disease severity was assessed using a composite clinical and laboratory scoring system based on a previously described method. Pearson's correlation, Spearman's rank correlation, simple linear regression, and the Kruskal-Wallis test were used as appropriate. Statistical significance was set at p < 0.05. Results: Of 51 participants, 14 (27.5%) had mild, 33 (64.7%) moderate, and 4 (7.8%) severe disease. Mean MPV was 9.34 +/- 0.76 fL (range, 8.0-11.2). Pearson's correlation showed a weak positive, non-significant linear relationship with severity score (r = 0.231, p = 0.103), whereas Spearman's analysis showed a weak positive monotonic association (rho = 0.286, p = 0.042). Regression explained 5.3% of severity-score variation (R2 = 0.053, p = 0.103). MPV did not differ significantly across severity categories (H = 2.163, p = 0.339). MPV correlated inversely with haemoglobin (r = -0.556, p < 0.001) and positively with platelet count (r = 0.307, p = 0.029). Conclusion: MPV showed a weak relationship with disease severity but inconsistent statistical evidence across analyses. The limited explained variance and absence of significant differences between severity categories do not support MPV as a standalone severity marker. Larger longitudinal studies are warranted. Keywords: Sickle cell anaemia; Mean platelet volume; Disease severity; Platelet indices; Paediatric haematology; Cross-sectional study; Nigeria.

Accurate discrimination between viral, bacterial, and inflammatory diseases in febrile children remains a major clinical challenge that contributes to diagnostic uncertainty, inappropriate antimicrobial use, and suboptimal clinical management. Host blood transcriptomics offer a promising strategy to improve diagnostic precision. The present study represents the largest integrative multi-cohort pediatric study of transcriptomic biomarker discovery, validation, and confirmation reported to date, integrating harmonized public transcriptomic datasets with an independent confirmation cohort comprising well-phenotyped patients to identify parsimonious host-response signatures for differentiating viral, bacterial, and inflammatory diseases. Transcriptomic signatures were derived from an integrated retrospective microarray multi-cohort (n=1,683), independently validated in a retrospective RNA-seq cohort (n=767), and confirmed by digital PCR in an independent cohort (n=29), demonstrating reproducibility across patient populations, transcriptomic technologies, and analytical platforms. The analysis identified binary signatures and a unified multiclass classifier that consistently achieved high diagnostic accuracy across all three study phases and outperformed more than 30 published host transcriptomic signatures. Decision curve analysis showed substantially greater clinical net benefit than C-reactive protein across clinically relevant decision thresholds. These findings provide a strong foundation for clinically deployable molecular diagnostics to improve patient triage, antimicrobial stewardship, and precision medicine in childhood infections.

Shingles (herpes zoster), caused by reactivation of varicella zoster virus (VZV), affects approximately one third of the global population. Besides environmental factors, host genetics play a role in determining susceptibility to shingles. Here, we performed a large-scale genome-wide association study (GWAS) meta-analysis of shingles across five cohorts comprising 72,935 cases and 1,644,597 controls of European ancestry. We identified seven genome-wide significant loci, including novel associations at IGHG1, IFNAR2, MPV17L2 (IL12RB1), BACH2, and RHOBTB1, implicating MHC class I antigen presentation, type I interferon signaling, humoral immunity, and T-cell memory maintenance as key genetic determinants of shingles susceptibility. HLA fine-mapping identified eight independently associated HLA alleles, mapping predominantly to HLA-B (HLA-B*44:02), with additional associations at HLA-C (HLA-C*02:02) and an independent association at HLA-DQB1 (HLA-DQB1*05:02). Gene set analysis and stratified LD score regression identified significant enrichment of shingles heritability in immune tissues and pathways. Phenome-wide association study, genetic correlation analysis, and bidirectional two-sample Mendelian randomization identified causal effects of shingles on stroke, herpes simplex infection, and systemic lupus erythematosus, and suggested pain conditions and arthrosis as risk factors for shingles. These findings advance understanding of the genetic architecture of VZV reactivation and its causal relationships with other diseases.

Introduction: The application of pharmacogenomics (PGx) in pediatrics is limited by the lack of age-oriented interpretation approaches, as algorithms developed for adults do not account for ontogenetic changes in the activity of drug-metabolizing enzymes and transport proteins. The aim of this study was to evaluate the clinical applicability of pharmacogenomic data in Russian children, assess the concordance between genotype-based recommendations and the ontogenetic status of drug-metabolizing enzymes, and develop recommendations for the generation of age-oriented PGx reports. Methods: We analyzed whole-exome sequencing (WES) data from 524 pediatric patients and 635 newborns, filtering pharmacogenomic annotations according to PharmGKB/ClinPGx evidence levels (1A-2B) and the presence of the 'Pediatrics' tag. The concordance between genotype-based recommendations and the ontogenetic status of drug-metabolizing enzymes was assessed in newborns. In a pediatric subgroup of 100 patients, a retrospective analysis of medical records was performed to evaluate the structure of pharmacotherapy and the frequency of adverse drug reactions (ADRs). A 'PGx-ADR-cost' database was created, and the relative population burden index was calculated for 27 gene-variant-drug-ADR associations. Results: Clinically relevant annotations (requiring drug avoidance or dose modification) accounted for only 5% of all initial pharmacogenomic annotations in both cohorts; 67.6% (pediatric cohort) and 67.2% (neonatal cohort) of these were related to alleles with altered function. Concordance between genotype-based recommendations and the ontogenetic status of drug-metabolizing enzymes in newborns was observed in only 5 of 14 (35.71%) gene-drug pairs. ADRs were identified in 21% of the 100 pediatric patients; however, only two cases could be explained by high-evidence PharmGKB/ClinPGx annotations. Ranking by relative population burden identified UGT1A1*28-irinotecan-induced neutropenia and HLA-A*31:01-carbamazepine-induced severe cutaneous reactions as priority associations. Conclusions: Age represents a critical factor in the interpretation of pharmacogenomic data in children, as current approaches to PGx reporting do not adequately incorporate the ontogenetic context. We propose a pediatric PGx interpretation model that includes mandatory reporting of patient age, ontogenetic adjustment, evidence-level stratification, and multidisciplinary clinical assessment. Prospective validation is required to confirm the clinical utility of the proposed approach.

Epstein-Barr virus (EBV) reprograms B cells in autoimmune disease. Reprogrammed EBV+ B cells activate nearby B and CD4+ T cells, via upregulated antigen presentation and costimulatory machinery, to drive autoimmune pathology. EBV reactivation is a known correlate of long COVID, which is a heterogeneous condition that can bear similarities to autoimmune disease. However, the mechanisms underpinning this association remain unresolved. We report on EBV metabolically reprogrammed B cells in patients with COVID-19. We find EBV+ B cells provide stimulatory signals to bystander B and CD4+ T cells. SARS-CoV-2 infected participants exhibiting elevated fractions of EBV+ B cells present, at convalescence, with dysregulated lipid profiles, increased autoantibody titers, and post-acute symptomology likely reflective of this metabolic reprogramming and cell-cell interactions. Enrichment of our EBV+ B cell signatures seen in patients with COVID-19 is similar in patients with lupus and multiple sclerosis suggesting a potentially shared pathway of EBV-driven dysfunction across diseases.

Clonal hematopoiesis (CH), an aging-related expansion of hematopoietic stem cell (HSC) clones, is associated with hematologic malignancy, cardiovascular disease, and mortality. Most clonal expansions, however, occur in the absence of known driver mutations. Passenger mutations reveal positive selection in HSCs and provide a quantitative, driver-agnostic phenotype that increases statistical power over dichotomized driver-based definitions. We used somatic passenger mutation burden as a quantitative phenotype to map the genetic, phenotypic, and geographic correlates of CH across 791,067 blood whole-genome sequences from UK Biobank (UKB) and the All of Us Research Program (AoU). Multi-ancestry meta-analysis of genome-wide association studies in both cohorts identified 81 loci associated with passenger mutation burden, including 42 novel loci. Rare-variant analyses additionally implicated MBD2, PRKACB, PUF60, and related epigenetic and transcriptional regulators of clonal fitness. Together, common and rare germline associations converged with canonical CH drivers on shared pathways regulating DNA methylation, chromatin, RNA splicing, and genome maintenance. Sex and ancestry stratified analyses revealed the shared and population-specific determinants of CH, including loci undetected in the pooled analysis. Associated variants were concentrated in regulatory elements active in hematopoietic stem and progenitor cells, linking germline associations to relevant cell states and lineages. Phenome-wide analyses revealed distinct consequences of inherited CH liability and observed passenger burden, with passenger burden strongly associated with incident hematologic malignancy and mortality and germline risk showing additional nonhematologic associations. Finally, spatial modelling of passenger mutation burden across U.S. regions revealed persistent geographic heterogeneity incompletely explained by income, air quality, or chemotherapy prevalence, pointing to additional unmeasured environmental exposures. Overall, through parallel analyses of two population-scale biobanks, we characterize the multi-ancestry genetic architecture of CH and reveal convergence of germline and somatic variation on shared pathways governing clonal expansion in aging blood.

Background and objectivesMyasthenia gravis associated with antibodies against muscle-specific kinase (MuSK-MG) is a well-characterized IgG4-autoimmune disease, however, the mechanisms driving IgG4 predominance remain poorly understood. This study investigated whether promoter DNA methylation of cytokine genes involved in IgG4 class switching is associated with this immune response. MethodsPeripheral blood mononuclear cells were isolated from MuSK-MG patients (n=36), acetylcholine receptor myasthenia gravis (AChR-MG) patients as disease controls (n=7), and sex-matched healthy controls (n=12). Promoter DNA methylation of IL4, IL10, and IL13 was assessed by methylation-sensitive high-resolution melting and relative cytokine mRNA expression by qPCR. Associations with clinical variables, and antibody levels were subsequently evaluated. ResultsMuSK-MG patients showed lower median IL13 promoter methylation compared with healthy controls (p = 0.004). Median IL4 promoter methylation was also reduced in MuSK-MG compared with healthy controls (p < 0.001) and AChR-MG disease controls (p < 0.001), whereas no differences were observed for IL10 promoter methylation. Relative mRNA expression of IL4 (p = 0.0005), IL10 (p = 0.0462), and IL13 (p = 0.0002) was increased in MuSK-MG compared with AChR-MG. Compared with healthy controls, only IL4 expression remained significantly increased (p < 0.0001). Promoter methylation was inversely correlated with relative mRNA expression for IL4 (p < 0.0001), while IL13 showed a similar but non-significant trend (p = 0.054), no association was observed for IL10. Multivariable analysis demonstrated that treatment at sampling was independently associated with lower IL10 and IL13 promoter methylation, whereas no associations were observed with age, sex, disease phase, or disease duration. Promoter methylation did not correlate with total serum IgG4 or anti-MuSK IgG4 levels. DiscussionMuSK-MG is associated with selective hypomethylation of IL4 and IL13 promoters accompanied by increased cytokine gene expression, while IL10 promoter methylation remains unchanged. The association between treatment and IL10 and IL13 promoter methylation suggests that immunosuppressive therapy may influence epigenetic regulation in MuSK-MG. Together, these findings support a role for epigenetic dysregulation of Th2-associated cytokines in the immunological environment associated with IgG4 subclass switch. To our knowledge, this is the first study investigating IL4, IL10, and IL13 promoter DNA methylation in MuSK-MG.