Journal of Clinical Immunology

Background: Human papillomaviruses (HPVs) pose a severe threat to global public health by driving nonmelanoma skin cancer (NMSC) and cervical cancer, with NMSC being one of the most common cancers worldwide. Epidermodysplasia verruciformis (EV) is an inborn error of immunity characterized by an increased susceptibility to persistent infection of cutaneous HPV and a high risk of NMSC. The genetic basis remains unknown in many patients with EV. Methods: We collected four unrelated pedigrees with EV. Genetic analysis identified five variants in JAK1 encoding the Janus kinase 1. Ex vivo models and patient-derived tissue were employed to evaluate the functional effects of JAK1 variants and delineate the pathogenic mechanisms. Results: We identified different variants in JAK1 in four pedigrees with dominant EV. Genetic analysis revealed five novel variants in JAK1, three of which resulted in nonsense-mediated mRNA decay (NMD). Functional assays identified a decreased phosphorylation of the signal transducers and activators of transcription (STATs), impaired interferon responses, and defective T cell activation. Immune dysregulation in patients, characterized by a reduced CD4/CD8 T cell ratio, decreased CD8 naive T cell proportion, and accumulated memory T cells, implies impaired antiviral immunity against HPV. Conclusions: Our findings confirm that JAK1 loss-of-function (LOF) variants underlie susceptibility to cutaneous HPV infection. [Funded by the National Natural Science Foundation of China (81788101, 81230015, 82394420, and 82394423), the National Key Research and Development Program of China (2022YFC2703900), the CAMS Innovation Fund for Medical Sciences (2021-I2M-1-018), and the Regione Lombardia, Italy (Innovative Research Project 1137-2010)].

Severe combined immunodeficiency (SCID) is a heterogeneous, recessive disorder, associated with the onset of severe, recurrent infections in the first few months of life. SCID is fatal if left untreated, but outcomes can be significantly improved by prompt diagnosis and treatment, particularly prior to onset of infection. Consequently, SCID is already included in many newborn screening programmes around the world, as well as multiple international genomic newborn screening (gNBS) research programmes. However, there is a vital need to estimate penetrance of SCID variants in population cohorts, to mitigate the potential consequences of reporting low penetrance variants in a genotype-first gNBS setting. This study aimed to assess the penetrance and prevalence of these variants in the UK Biobank population cohort. Whole genome sequencing data from 490,640 individuals was used to interrogate 16 SCID genes for potentially causal variation. We identified 4206 carriers of single heterozygous pathogenic variants ([~]1% of cohort), but only 6 individuals double heterozygous, homozygous or hemizygous for relevant pathogenic variants. 3 individuals would be expected to require further testing had they been identified by gNBS, suggesting that fewer than 1 in 100,000 newborns might require follow-up testing due to SCID variants. Following detailed variant curation, we were able to identify only 2 unabected individuals likely to be harbouring biallelic pathogenic variants, potentially indicative of reduced penetrance. Nonetheless, SCID remains an excellent candidate for inclusion in gNBS studies, due its severity, clinical actionability and expected low false positive rate, although care should be taken when reporting hypomorphic variants.

The emergence of vaccine covered serotypes causing invasive pneumococcal disease (IPD) is a serious concern worldwide. We investigated the unexpected rise of serotype 4 causing IPD primarily in non-vaccinated young adults after the COVID-19 pandemic that further spread to adults [≥] 65 years in recent years. For this purpose, we conducted a retrospective study of serotype 4 IPD cases (n=827) reported in Spain between 2009 and 2024. Whole-genome sequencing was performed to assess clonal lineages and phylogenetic relationships. Clinical and epidemiological data were compared between serotype 4 and all other serotypes causing IPD. Epidemiological and genomic analysis confirmed that the rise started as an abrupt cluster of IPD cases in Seville (Andalusia) in the year 2022 due to the ST15063 within GPSC12 lineage. This outbreak initially caused pneumonia episodes that required hospitalization in young individuals associated with high rates of tobacco smoking, alcohol, and inhaled drugs such as cannabis and cocaine, followed by a general distribution pattern throughout the country in the following years, affecting the elderly population. Experimental studies to evaluate potential underlying mechanisms confirmed that ST15063 serotype 4 strains displayed enhanced infection rates of human lung cells that significantly increased in the presence of cigarette smoke exposure and by influenza H3N2 virus coinfection, but not with H1N1. These findings highlight the need for targeted vaccination strategies not only against pneumococcus but also against respiratory viruses such as influenza, RSV and COVID-19 and demonstrate the importance of molecular surveillance to establish effective interventions in high-risk populations.

UNC93B1 is a crucial chaperone protein for the trafficking of TLRs and regulates antigen presentation in dendritic cells (DCs), which activates downstream immune responses. Here, we identified a novel homozygous gain-of-function (GOF) UNC93B1 variant in an early-onset lupus patient. The patient presented with elevated level of inflammation and auto-antibody, and organ damage. The Unc93b1R95L/R95L transgenic mice also exhibited with autoimmune and autoinflammatory phenotypes. The transcriptional analysis revealed increased inflammation and elevated activation of DCs in the patients PBMCs and bone marrow-derived DCs (BMDCs) from Unc93b1R95L/R95L mice. In addition to the selected TLR7/8 activation in previously reported UNC93B1 GOF variants, the single-cell transcriptome and flow cytometry of splenocytes from Unc93b1R95L/R95L mice demonstrated increased phagocytosis activity and T helper cell differentiation with altered ICAM and MHC signaling in DCs and T cells, respectively. These results suggest UNC93B1 GOF variant enhances antigen presentation from DCs to T cells in the pathogenesis of immune dysregulation. Our study expands the pathogenic variants spectrum of UNC93B1 and offers insight into the underlying mechanism of antigen presentation in immune dysregulation caused by UNC93B1 beyond its trafficking function of TLRs.

Cancer-related genomic instability (GI) may cause genetic alterations in spermatozoa, implying health issues not only in cancer survivors, but also in their children [1, 2]. We therefore studied Loss of Y chromosome (LOY), considered as hallmark of GI [3-15], in spermatozoa and blood from survivors of childhood and testicular cancer (CC, TC), and controls (CTRL). We found that LOY was statistically significantly more frequent in spermatozoa from cancer survivors than in controls (Odds Ratio [OR]=2.2 for CC vs. CTRL and OR=2.4 for TC vs. CTRL). Furthermore, LOY was about an order of magnitude more prevalent in spermatozoa than in blood among 18-53-year-old males within all cohorts. Our findings suggest that LOY in spermatozoa might be a clinically useful marker of GI, reduced fertility and disease predisposition in males. Introducing LOY in spermatozoa as a biomarker opens a new research avenue into disease prevention and the causes and consequences of LOY.

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) and long COVID are complex chronic conditions that often follow infectious triggers with overlapping clinical features but poorly defined pathophysiological relationships. This study aimed to identify disease-specific immune signatures through multiparameter immunophenotyping of monocytes, dendritic cells, and T-cell subsets. A total of 207 participants were included (ME/CFS: n = 103; long COVID: n = 63; healthy controls: n = 41). Peripheral blood mononuclear cells were analyzed using multiparameter flow cytometry. Statistical analyses included non-parametric testing, age-adjusted ANCOVA, correlation network analysis, and principal component analysis (PCA). Long COVID was characterized by increased M2-like monocyte polarization, elevated CD80 expression across monocyte subsets, expansion of dendritic cells, and reduced expression of activation markers, indicating persistent immune activation with features of immune exhaustion. In contrast, ME/CFS exhibited reduced costimulatory molecule expression, impaired CCR7-mediated immune cell trafficking, and less coordinated activation patterns, consistent with a state of immune suppression. Correlation network analysis revealed more extensive and integrated immune interactions in long COVID, while PCA identified distinct immunophenotypic components and enabled moderate discrimination between the two conditions. These findings demonstrate that ME/CFS and long COVID are characterized by distinct immune profiles, supporting the concept of divergent immunopathological mechanisms. The identified signatures may contribute to biomarker development and guide targeted therapeutic approaches.

Patients with myasthenia gravis (MG) may produce autoantibodies neutralizing type I interferons (AAN-I-IFN), which have been shown to underlie severe viral diseases, including critical COVID-19 pneumonia, in patients without MG. We studied an international cohort of 85 unvaccinated SARS-CoV-2-infected MG patients with no antiviral treatment. Hypoxemic pneumonia occurred in 48 of these patients, including 22 (45.8%) with AAN-I-IFN, which neutralized both IFN-2 and IFN-{omega} in 14 (29.2%) patients. Six (16.2%) of the remaining 37 patients had AAN-I-IFN, which neutralized both IFN-2 and IFN-{omega} in three patients. The risk of hypoxemic pneumonia was greater in MG patients with AAN-I-IFN neutralizing 10 ng/mL of both IFN-2 and IFN-{omega} (odds ratio and 95% confidence interval (OR [95% CI]): 12.7 [2.1-78.9], p=0. 0010) or IFN-2 at any dose (4.7 [1.5-15.0], p=0.0054) than in those without such autoantibodies. The risk of AAN-I-IFN production was much higher in MG patients than in the general population (28.9 [10.8-77.7], p=4.9x10-27). Fourteen patients had thymoma, which increased the risk of AAN-I-IFN (64% versus 27%, (OR [95% CI]: 5.6 [1.6-19.4], p=0.0050) and hypoxemic pneumonia (9.2 [1.9-44.2]; p=0.0019). Thymoma is, thus, associated with a higher risk of producing AAN-I-IFN, and these autoantibodies are associated with a higher risk of developing life-threatening COVID-19 pneumonia in patients with MG.

Infection with SARS-CoV-2 can lead to long COVID, a chronic multisystemic condition estimated to affect approximately 400 million people worldwide. Although underlying mechanisms remain elusive, aberrant ongoing inflammation driven by Epstein-Barr virus (EBV) reactivation and persistent SARS-CoV-2 viral reservoirs have been hypothesized. We compared cellular and humoral immune responses to SARS-CoV-2 and EBV between participants with neuropsychiatric long COVID and recovered individuals. Peripheral blood mononuclear cells (PBMCs) and sera were collected from 27 long COVID individuals with [≥]2 neuropsychiatric symptoms and 27 matched recovered participants at 3-6 months post-COVID-19 symptom onset (PSO). PBMCs were assessed for IFN-{gamma}, IL-2, TNF, and granzyme B T-cell responses against SARS-CoV-2, EBV, and human cytomegalovirus (HCMV). Sera were evaluated for neutralizing activity against live ancestral SARS-CoV-2 and EBV, and EBV reactivation was assessed by early antigen-diffuse IgG. We observed no significant differences in SARS-CoV-2-, EBV-, or HCMV-specific T-cell responses or live virus neutralization between long COVID and recovered groups at 3-6 months PSO. EBV reactivation was additionally only detected in one neuropsychiatric long COVID participant. However, reduced EBV neutralizing capacity at 3-6 months significantly associated with fatigue at 12 months PSO. Anti-EBV viral capsid antigen IgG levels were also significantly diminished in long COVID participants and similarly trended lower in those reporting fatigue at 12 months PSO. We therefore detected no differences in SARS-CoV-2- or EBV-specific T-cell responses or serological neutralizing capacity between neuropsychiatric long COVID and recovered participants; however, diminished EBV-specific humoral immunity may serve as a prognostic marker for neuropsychiatric long COVID development. IMPORTANCEWe performed a comprehensive analysis of cellular and humoral immune responses to SARS-CoV-2, Epstein-Barr virus, and human cytomegalovirus in individuals with neuropsychiatric long COVID, a subgroup that remains poorly characterized. Although no differences in virus-specific T-cell immunity were observed between long COVID and recovered individuals, diminished Epstein-Barr virus neutralization at 3-6 months was associated with persistent or relapsing fatigue at 12 months post-COVID-19 symptom onset. Anti-viral capsid antigen IgG antibody levels were also significantly lower in neuropsychiatric long COVID participants at 3-6 months and similarly trended lower in those reporting fatigue at 12 months post-symptom onset. Together, these findings suggest that impaired humoral immunity to Epstein-Barr virus may contribute to the development or persistence of neuropsychiatric long COVID and highlight a promising future direction for mechanistic studies.

Dengue virus (DENV) is a major burden to global public health, affecting hundreds of millions annually. Children represent the major proportion of global dengue cases, ranging from asymptomatic or subclinical presentation to dengue fever (DF) and severe dengue hemorrhagic fever or shock syndrome (DHF/DSS). The factors that distinguish this range of disease severity are still poorly understood. To identify biomarkers of severity, we analyzed the plasma proteome of acute DENV infected children including both subclinical and hospitalized cases. Proteins associated with the acute-phase response, innate immune and lysosomal activation, and components of the coagulation cascade showed marked differences between hospitalized and subclinical cases during early infection. Longitudinal profiling demonstrated that endothelial dysfunction emerges early, with PTX3 showing the strongest and most rapid upregulation in hospitalized patients, supporting its potential role as a marker of imminent vascular involvement. When comparing severe (DHF/DSS) and classical DF hospitalized cases, CLEC11A displayed the highest fold change at hospital admittance. We used machine-learning analysis to predict disease severity at the acute phase of infection, distinguishing subclinical from hospitalized cases and patients that develop classical dengue fever or severe disease based on the identified complement regulators and inflammatory markers. The panel of identified plasma proteins shed light on the mechanisms of dengue related disease progression and may provide a handle to predict disease severity based on blood markers present during the acute phase of infection.

Background: Prolonged SARS-CoV-2 infection in immunocompromised individuals may accelerate virus evolution within the host, raising concerns about the virus evading immunity, developing resistance, and forming novel variants of concern. However, the determinants and public health implications of within-host viral evolution in this population remain incompletely understood. Methods: We performed longitudinal analyses of SARS-CoV-2 genomes from 91 patients with COVID-19 who were classified as being severely or moderately immunocompromised. Using serial measurements of viral RNA loads and infectious titers, we modeled the shedding dynamics of the virus and stratified the infected cases by upper respiratory virus shedding duration to assess associations with within-host evolutionary dynamics. Results: Shedding modeling identified two profiles of shedding duration: intermediate and long. The long shedding profile (shedding lasting >21 days) was found in 14.8% of moderately immunocompromised cases and 72.1% of severely immunocompromised cases. Frequent single-nucleotide variants accumulated specifically in severely immunocompromised individuals with the long shedding phenotype, correlating positively with shedding duration. By contrast, mutations remained limited in moderately immunocompromised individuals with the long shedding phenotype and in severely immunocompromised individuals with the intermediate shedding phenotype. We identified mutations in the spike receptor-binding domain associated with monoclonal antibody resistance; however, we found no fitness-enhancing mutations for inter-host transmission, and antiviral drug resistance mutations were rare. Instead, mutations were introduced frequently and randomly across the entire viral genome. Conclusions: Prolonged upper respiratory virus shedding exceeding 21 days combined with severe immunocompromise is a risk factor of the accumulation of within-host SARS-CoV-2 mutations. Although no variants of concern emerged, the introduction of genome-wide random mutations suggests that the risk for novel variant generation cannot be excluded. These findings highlight the need for intensive antiviral strategies to limit shedding duration to less than 21 days in severely immunocompromised patients, and for immunological investigations to elucidate the host factors underlying residual shedding control in those who achieve clearance within this threshold.

Multiple sclerosis (MS) is an immune-mediated demyelinating disease of the central nervous system affecting 2.8 million people worldwide. Both genetic and environmental factors contribute to MS risk, with Epstein-Barr virus (EBV) infection being an important environmental factor. To better clarify the role of EBV in MS, we examined its impact on gene expression, chromatin accessibility, and transcription factor binding in primary B cells and EBV-transformed B cells derived from patients with MS and healthy controls. RNA-seq and ATAC-seq analyses revealed extensive MS-dependent gene expression and chromatin accessibility differences in EBV-transformed, but not in primary B cells. These changes are largely accounted for by the expression levels of EBNA2, an EBV-encoded transcriptional regulator previously implicated in MS. ChIP-seq analysis revealed that EBNA2 binding with its interacting human partners RBPJ, EBF1, and PU.1 is highly enriched at MS genetic risk loci, with extensive EBNA2 allelic binding and increased enrichment at MS genetic risk loci in MS-derived cells. Our findings demonstrate that enhanced EBNA2 activity in MS alters human gene expression, chromatin accessibility, and transcription factor binding in an MS-dependent manner. Collectively, this study provides new insights into the molecular mechanisms through which EBV, particularly EBNA2, interacts with host genetic risk to contribute to MS pathogenesis.

The primary route of SARS-CoV-2 entry is via respiratory epithelium. However, many COVID-19 patients developed dermatological lesions, and SARS-CoV-2 RNA has been detected in the patients skin. Inflammatory skin diseases, psoriasis and atopic dermatitis (AD), significantly increased the risk of COVID-19. To evaluate the potential role of skin in SARS-CoV-2 host interactions, we utilized 3D human skin organoids (HSO) generated from human epidermal keratinocytes, as well as neonatal skin explants. HSO were treated with cytokines involved in acute and chronic skin inflammation and cytokine storm in severe COVID-19 disease, TNF-, IL-6, IL-1{beta}, and IFN-{gamma}, individually and in combination. HSO were also treated with Th1 (TNF- + IL-17) and Th2 (IL-4 + IL-13) cocktails inducing pro-psoriasis and pro-AD HSO changes, respectively. All individual cytokines, and especially their combinations, elevated the expression of ACE2 and TMPRSS2 at mRNA/protein levels. The Th2 induced only TMPRSS2, the Th1 predominantly induced ACE2. Topically applied Spike-pseudotyped lentiviral Tomato reporter, which binds ACE2 similarly to SARS-CoV-2, successfully infected control and cytokine-treated HSO as well as neonatal skin explants. Cytokine treatment, especially TNF- + IL-6 + IL-1{beta} + IFN-{gamma} and the Th1, significantly increased viral entry. Transcriptomic analysis further revealed partial overlap between gene expression signatures induced by Spike-mediated entry in inflamed HSO and those observed in lung tissue from COVID-19 patients, supporting the biological relevance of skin models. Together, these findings demonstrate that inflammation enhances the permissiveness of human skin to SARS-CoV-2 entry, suggesting that the skin may represent a previously underappreciated interface in viral host interactions.

Red blood cell (RBC) alloimmunization is a clinically significant complication in transfused patients whose immunological determinants remain incompletely understood. Type I interferon (IFN-I) signaling drives RBC alloimmunization in murine models, and systemic lupus erythematosus (SLE) is characterized by constitutive IFN-I hyperactivation alongside elevated alloimmunization rates. We analyzed three publicly available SLE RNA-seq cohorts (GSE72509, GSE112087, GSE122459; whole blood and PBMC; total n = 150 SLE) in a pre-specified discovery-replication-validation design. A 14-gene IFN-I signature score was computed per sample; differential expression, gene set enrichment analysis, and Spearman correlation were performed independently per cohort. IFN-I scores were significantly elevated in SLE versus healthy controls in all three cohorts (p < 0.01 each). IFN-high SLE patients showed 665 differentially expressed genes, with enrichment of alloimmunization-associated and plasmablast differentiation gene sets confirmed by GSEA. The alloimmunization signature score correlated significantly with IFN-I score across all three independent cohorts ({rho} = +0.77, +0.51, +0.60; all FDR q < 0.05); Tfh differentiation showed no association in any cohort. To our knowledge, this represents the first human transcriptomic evidence that IFN-I pathway activity in SLE is coupled to alloimmunization-associated immune programs in vivo. These findings identify IFN-I score as a candidate biomarker of alloimmunization susceptibility in SLE and provide translational rationale for prospective studies incorporating transfusion outcome data.

BackgroundInflammatory bowel disease (IBD) is a chronic inflammatory disorder characterized by gut microbial dysbiosis and immune dysregulation. While compositional changes in the microbiome are well studied, the functional mechanisms through which microbes influence host signalling remain poorly understood. PurposeThis study aimed to investigate microbial-host molecular mimicry in IBD and to elucidate its role in modulating immune and neuronal pathways through a newly proposed Microbial Signal Recognition and Neuronal Mimicry (SRNM) axis. MethodsShotgun metagenomic datasets from IBD patients and healthy controls were analyzed using a custom Molecular Mimicry In Silico Pipeline (MMIP). Reads were assembled, annotated, and subjected to protein homology mapping, Gene Ontology enrichment, PFAM domain analysis, and taxonomic profiling to identify microbial proteins mimicking human functional pathways. ResultsIBD-associated microbiomes exhibited significantly higher functional complexity and enrichment of eukaryote-like proteins compared to healthy controls. Microbial proteins mimicking host pathways involved in neuron projection development, signal recognition particle (SRP)-mediated protein targeting, immune signaling, and stress responses were markedly enriched in IBD. Key human-like targets included TRPV1, CAMK2D, SNCA, MTCP1, TCL1B, and PEAK3. PFAM analysis revealed overrepresentation of kinase domains, zinc-finger motifs, ankyrin repeats, and ABC transporters. These signatures were predominantly contributed by IBD-enriched taxa such as Gammaproteobacteria, Fusobacteria, and Betaproteobacteria. ConclusionThis study identifies a previously unrecognized SRNM axis in IBD, revealing how microbial molecular mimicry may influence neuroimmune signaling and disease pathogenesis, and highlight potential targets for microbiome-based therapeutic intervention.

Kabuki syndrome (KS) is a congenital developmental disorder caused by germinal pathogenic variants in the lysine methyltransferase 2D (KMT2D, KS1) or lysine demethylase 6A (KDM6A, KS2) genes. Kabuki patients display mental retardation, multiorgan malformations and immune dysregulation - ranging from immunodeficiency to autoimmunity - which strongly compromises their life expectancy. We explored whether the complex immunological scenario of Kabuki syndrome 1 subjects (Ks) could be ascribed to an altered generation of CD4+FOXP3+ regulatory T cells (Tregs). We report that pediatric Ks carrying KMT2D pathogenic variants show a significant reduction of Tregs. DNA methylation analysis reveals a specific methylation pattern at the FOXP3 distal enhancer that correlates with decreased FOXP3 transcription early during Treg cell induction and promotes T helper (Th)-2 lineage differentiation. Finally, in vitro T cell demethylation rescues FOXP3 expression and Treg induction in Ks, offering a novel potential therapeutic perspective. Our findings connect KMT2D loss-of-function to the inhibition of human FOXP3 gene transcription and provide novel molecular insights to explain the immunological phenotype in Ks, thus pinpointing this syndrome as a novel Tregopathy.

The emergence and spread of highly pathogenic avian influenza H5N1 subtypes have raised global concerns due to their ability to cross species barriers and occasional spillover to humans. The viruses primarily infect wild birds and poultry, which have caused significant, sporadic outbreaks in mammals including dairy cattle. Influenza D virus is a recently identified influenza virus that mainly affects cattle with frequent spillover to other species such as swine. Despite the availability of poultry vaccines, there are no H5N1 and Influenza D vaccines for cattle or other potentially affected livestock. Given a history of frequent influenza pandemics originating from avian and mammalian hosts, there is an urgent need for enhanced surveillance, biosecurity, and the development of antivirals and vaccines. Here we describe the development of a novel hybrid alphavirus-influenza pseudovirion (Ha-IV), which is a non-replicating influenza virus-like particle composed of viral structural proteins and an RNA genome derived from a fast-expressing alphaviral vector. As a proof-of-concept, we assembled Ha-IV pseudoviruses based on influenza D and influenza A and B subtypes, and demonstrated their infectivity. In addition, we validated an influenza A pseudovirus based on the H5N1 clade 2.3.4.4b strain, A/Texas/37/2024, for rapid quantification of neutralization antibodies within 4 to 18 hours. Furthermore, we used the pseudovirus to quantify infected cow sera and performed a correlation study with the classic hemagglutinin inhibition assay (HIA). We demonstrate that the Ha-IAV pseudovirus-based assay is consistent with HIA in identifying protective antibody responses. Our results demonstrate that this new Ha-IV pseudovirus provides a rapid tool for quantifying the infectivity of emerging HA mutants and for assessing neutralizing antibody responses.

The continuous renewal of healthy epidermis depends on the finely regulated proliferation of basal keratinocytes and subsequent differentiation as the newly formed cells move upwards through the different layers of the epidermis. Perturbations in keratinocyte differentiation may lead to cornification disorders. We investigated seven dogs of different breeds belonging to four independent families that showed striking multifocal tree bark-like skin lesions. Histopathologically, lesional skin was characterized by pronounced epidermal and infundibular hyperkeratosis with epidermal and sebaceous gland hyperplasia. We therefore tentatively termed the phenotype phloiokeratosis, derived from the Greek word phloios for tree bark and keratosis indicating abnormal keratinization. Whole genome sequencing of DNA from affected dogs revealed four independent variants in the SUV39H1 gene encoding the SUV39H1 histone lysine methyltransferase, an H3K9 methyltransferase, which is involved in epigenetic silencing of chromatin. Phloiokeratosis is inherited as an X-chromosomal semi-dominant trait. Four of the affected dogs in our study were heterozygous females and had lesion patterns reminiscent of Blaschko lines. In two of them, trio analyses experimentally confirmed de novo mutation events in the SUV39H1 gene. Previously, Suv39h1-/- knockout mice had been reported to have normal skin. So far, no human patients with SUV39H1 loss-of-function variants have been reported. The findings in SUV39H1 mutant dogs with phloiokeratosis for the first time link SUV39H1 deficiency to a heritable skin phenotype. Our study highlights the essential role of SUV39H1-mediated epigenetic silencing during normal keratinocyte differentiation and provides a unique model for further investigations. Author SummaryThe integrity of the skin depends on a balanced equilibrium of keratinocyte proliferation, differentiation, and sloughing of terminally differentiated cells into the environment requiring finely regulated changes in the global transcriptome of differentiating keratinocytes. We investigated seven dogs belonging to four different families with a new disorder of cornification characterized by tree bark-like outgrowths of the epidermis. Histopathological examinations confirmed that the outermost layer of the epidermis was thickened in affected dogs. The genetic analysis yielded four different SUV39H1 loss-of-function variants in the affected dogs from the four families. The SUV39H1 gene encodes an enzyme that is involved in the epigenetic silencing of chromatin. The newly characterized inherited skin disease in dogs is the first clinical phenotype that has been linked to SUV39H1 deficiency. Most likely, SUV39H1 deficiency leads to delayed epigenetic silencing and consequently delayed differentiation of keratinocytes. Dogs with this rare skin disease provide an improved understanding of the essential role of SUV39H1 in the epigenetic control of gene expression in skin.

Mycetoma is a neglected tropical disease caused by various bacterial and fungal pathogens that has a significant health impact across a broad geographically defined "mycetoma belt" spanning South America, Africa and Asia. Histologically, mycetoma is characterised by invasive and destructive granuloma development in the skin, deep tissues and bone, leading to tissue destruction, deformities and high morbidity. The presence of macroscopic, highly compacted pathogen microcolonies, or "grains," is a key diagnostic feature, and the formation of grains supports pathogen persistence and disease chronicity. However, there is a paucity of information on immune responses in mycetoma patients and on the relative importance of phylogeny and/or grains in establishing the local immune landscape. Here, we used spatial proteomics to examine the distribution of 43 immune-related proteins in surgical biopsies from 11 patients with mycetoma of bacterial (Actinomycetoma; Actinomadura pelletierii and Streptomyces somaliensis; n=6) and fungal (Eumycetoma; Madurella mycetomatis; n=5) origin. Using mixed-effects modelling, an exploratory analysis across species and pathogen classes revealed few significant differences in immune marker expression. In contrast, and independently of pathogen class, the cellular infiltrate closest to grain boundaries had higher per-cell expression of CD66b+, ARG1, and VISTA. The preferential accumulation of CD66b+ARG1+VISTA+ cells at grain boundaries was confirmed by quantitative immunofluorescence analysis. Hence, the local tissue microenvironment surrounding the mycetoma grain represents a specialised immunosuppressive niche, with parallels to the tumour microenvironment.

RIG-I is a cytosolic immune receptor that provides the first line of defense by detecting viral RNA and triggering antiviral responses. Its physiological role in humans remains unclear, as no patients with complete RIG-I deficiency have yet been reported. We identified a critically ill COVID-19 patient with severe RIG-I deficiency caused by heterozygous RIG-I G731R, a novel dominant loss-of-function variant. The G731R mutation in helicase motif VI disrupts the arginine finger, impairing the ATPase activity of RIG-I, but not its RNA-binding ability. However, viral RNA binding fails to expose the signaling domains, thereby impairing the IFN-{beta} response of G731R. Instead, G731R competes with wild-type RIG-I, exerting a dominant negative effect. The loss-of-function is caused by bulky-charged substitutions at G731, as alanine or leucine substitution results in an unexpected gain-of-function phenotype. These findings highlight the importance of uncompromised RIG-I function for human antiviral immunity and the pleiotropic effects of single mutations.

Coccidioidomycosis presents clinically as a spectrum ranging from self-limiting Uncomplicated Valley Fever (UVF) in most cases to life-threatening Disseminated Coccidioidomycosis (DCM) in rare individuals. A few patterns of immunologic deficits allowing for dissemination have been identified, though the specific defects in most individuals with DCM remain undefined. We hypothesized that chronic antigen exposure in DCM engenders a state of T cell exhaustion. From a cohort of over 300 subjects with confirmed diagnoses of coccidioidomycosis, circulating T cell phenotypes were characterized via flow cytometry and Coccidioides-specific T cell responses were measured using the Activation-Induced Marker (AIM) assay. Male sex was significantly associated with disseminated disease (odds ratio 2.5; 95% CI: 1.5 - 4.0). 52% of subjects showed Coccidioides-specific T cell responses in our AIM assay. We noted a significant difference in subjects sampled in the first year of diagnosis, where only 8% of DCM subjects had T cell responses during this time, as compared to 44% of UVF subjects (p = 0.04). Among DCM patients with detectable AIM responses, CD4+ T cells demonstrated an exhausted phenotype with elevated PD-1 expression compared to UVF subjects. In vitro PD-1 blockade augmented IFN{gamma} production in most tested DCM subjects. These findings suggest that dissemination may occur in some individuals during a period of impaired antigen-specific T-cell activity. Importantly, these responses can be augmented in vitro by PD-1 blocking antibodies, supporting further study of immune checkpoint therapy as an adjunct to antifungal treatment in disseminated coccidioidomycosis.