Clinical Immunology

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.

Antiphospholipid syndrome (APS) and systemic sclerosis (SSc) are immune-mediated multisystem autoimmune diseases with distinct clinical phenotypes but overlapping pathogenic themes, including immune dysregulation, chronic inflammation, and endothelial injury. Using peripheral blood transcriptome datasets from the Gene Expression Omnibus (GSE102215: 9 APS/9 controls; GSE231691: 49 SSc/18 controls), we performed differential expression analysis within each cohort (limma; |log2FC|>1, P<0.05) and identified 281 genes dysregulated in the same direction in both diseases (100 upregulated and 181 downregulated). Enrichment analyses highlighted interferon-related and cytokine/inflammatory signaling programs in APS and SSc. To derive a compact diagnostic signature, we combined random forest feature ranking with a single-hidden-layer artificial neural network, prioritizing five shared candidate biomarkers (S100A8, IER5L-AS1, LTK, PRR5-ARHGAP8, and PCDH1). Each gene showed consistent case-control differences in both cohorts (P<0.001) and achieved good discrimination (AUC>0.75), with S100A8 performing most consistently (AUC=0.98 in APS; AUC=0.88 in SSc). CIBERSORT deconvolution indicated a myeloid-skewed blood profile in both diseases, characterized by higher neutrophil and monocyte/macrophage signals; SSc additionally showed stronger inferred CD4+ T cell and NK cell signals. S100A8 expression correlated with inferred neutrophil abundance in both cohorts (APS r=0.62; SSc r=0.58; P<0.05). Finally, miRNA-target prediction and DSigDB drug-signature enrichment generated regulatory and pharmacologic hypotheses, including immune-regulatory miRNAs (e.g., miR-155 and miR-146a) and candidate compounds (celecoxib, tamibarotene, HMN-176, and XMD14-99). Overall, these results nominate shared blood transcriptional markers and immune correlates across APS and SSc for follow-up validation.

Systemic Lupus Erythematous (SLE) is a chronic autoimmune disorder, broadly characterized by systemic inflammation along with heterogeneous clinical manifestations, severe morbidity, moribund organ failure and eventual mortality. In our study, SLE patients displayed higher percentage of activated, inflamed and hyper polarized CD8+ T cells, dysregulated CD8+ T cell differentiation, significantly elevated serum inflammatory cytokines, higher accumulation of cellular ROS when compared to healthy controls. Importantly, these hyper inflammatory/hyper polarized CD8+ T cells responded better to an anti-oxidant than to an oxidant. Terminally differentiated Tc1 cells also showed plasticity upon Oxidant/antioxidant treatment but was in contrast to the SLE CD8+ T cell response. Our studies suggest that the differential phenotype and redox response of SLE CD8+ T cells and Tc1 cells could be attributed to their cytokine environs during their respective differentiation and eventual activation environs. Polarisation of Tc1 cells with IL-21 drove hyper cytoxicity without hyper polarisation suggesting that SLE inflammatory environment could drive the extreme aberrancy in SLE CD8+ T cell.

Systemic Lupus Erythematosus (SLE) is an autoimmune disease characterized by systemic inflammation involving various immune cell types. Monocytes, pivotal in promoting and regulating inflammation in SLE, differentiate from classical monocytes into intermediate monocytes and non-classical monocytes, assuming diverse roles. In this study, we investigated the epigenetic and transcriptomic profiles of these three monocyte subsets in an SLE cohort. In addition to common DNA methylation and transcriptomic alterations, we identified monocyte subset-specific alterations, especially in DNA methylation, which reflect an impact of SLE on the monocyte differentiation process. SLE classical monocytes exhibited a stronger proinflammatory profile, with an interferon signature and were primed for macrophage differentiation. SLE non-classical monocytes displayed a phenotype related to T cell differentiation regulation, and a Th17-promoting phenotype. Changes in monocyte proportions, DNA methylation and expression occurred in relation to disease activity and involved the STAT1 pathway. Integrating bulk datasets with single-cell RNA-seq data of SLE patients further supported the interferon signature in classical monocytes, associating intermediate and non-classical populations with exacerbated complement activation pathways. Our results indicate a subversion of the epigenome and transcriptome in monocyte differentiation toward non-classical subsets in SLE, impacting function, in relation to disease activity and progression.

ObjectiveSystemic lupus erythematosus (SLE) is the prototypical systemic autoimmune disease, with a poor long-term prognosis. The type I interferon (IFN) signature, a prominent feature of SLE, is not an ideal therapeutic target or outcome predictor. To explore immunological pathways in SLE more precisely, we performed integrative analysis of transcriptomics, epigenomics, and genomics using each immune cell subset from peripheral blood. MethodsWe sorted 18 immune cell subsets and identified the mRNA expression profiles and genetic polymorphisms in 107 SLE patients and 92 healthy controls. Open chromatin information was also taken by ATAC-seq analysis. Combined differentially expressed genes (DEGs) and expression quantitative trait loci (eQTL) analysis was conducted to find key driver genes in SLE pathogenesis. ResultsWe found transcriptomic, epigenetic, and genetic importance of oxidative phosphorylation (OXPHOS)/mitochondrial dysfunction in SLE memory B cells. Particularly, we identified an OXPHOS-regulating gene, PRDX6, as a key driver in SLE B cells. Prdx6-deficient B cells showed upregulated mitochondrial respiration as well as antibody production. We revealed OXPHOS signature was associated with type I IFN signaling-related genes (ISRGs) signature in SLE memory B cells. Furthermore, the gene sets related to innate immune signaling among ISRGs presented correlation with OXPHOS and these two signatures showed associations with SLE organ damage as well as specific clinical phenotypes. ConclusionThis work elucidated the potential prognostic marker for SLE. Since OXPHOS consists of the electron transport chain, a functional unit in mitochondria, these findings suggest the importance of mitochondrial dysfunction as a key immunological pathway involved in SLE.

ObjectiveSjogrens disease (SjD) is a systemic autoimmune disorder characterized by lymphocytic infiltration of exocrine glands, resulting in xerostomia, keratoconjunctivitis sicca, fatigue, arthralgia, and systemic organ involvement. This study aimed to characterize the metabolic and immune dysregulation of SjD using a multi-omics approach, focusing on the metabolic environment and B-cell transcriptomic responses. MethodsTranscriptomic, methylomic, and metabolomic datasets from whole blood, plasma, and urine of 293 SjD patients and 508 controls were analyzed from the PRECISESADS study. B-cell transcriptomes were included to link systemic metabolic alterations to cell-intrinsic immune programs. Multi-omics factor analysis (MOFA) was used to integrate data and identify discriminant molecular drivers. ResultsMulti-omics integration revealed metabolic rewiring involving the urea cycle, glutamine/arginine metabolism, and NAD depletion linked to interferon signaling. Among the strongest contributors, plasma lysophosphatidic acids (LPA) emerged as key discriminants associated with interferon-driven activation. B-cell transcriptomes showed upregulation of LPA-related genes (CERS6, INPP1, TRIP6), and its receptor LPAR6. Importantly, in this study LPAR6 protein expression was confirmed in B cells for the first time. Secondary findings included alterations in sphingosine-1-phosphate (S1P) metabolism, suggesting a broader lysophospholipid signaling axis. ConclusionsThis study identifies the LPA-LPAR6 signaling axis as a potential metabolic driver of B-cell activation and interferon-associated inflammation in SjD, highlighting a previously unrecognized immunometabolic pathway. These findings highlight LPA-LPAR6 as a candidate target for therapeutic modulation in SjD, while also implicating S1P signaling as a complementary regulatory mechanism.

BackgroundLow-dose interleukin-2 (IL-2) shows promise as a treatment for restoring functional and numerical deficits of regulatory T (Treg) cells in patients with various autoimmune diseases. Several clinical trials testing low-dose IL-2 in systemic lupus erythematosus (SLE) have been completed, with a comprehensive review of these trials currently lacking. ObjectiveWe aimed to conduct a systematic synthesis of findings from clinical trials regarding the clinical efficacy and safety of using low-dose IL-2 in patients with SLE. Furthermore, we intended to determine the sensitivity of different responder indices for IL-2-induced clinical improvement in SLE. MethodsFollowing the Preferred Reporting Items for Systematic Reviews and Meta-Analyses, we searched the Scopus and MEDLINE databases for articles reporting trials testing low-dose IL-2 in patients with SLE published between January 2010 and September 2022. To evaluate the risk of bias, we applied a modified version of the Downs and Black assessment tool. ResultsWe retrieved 1,018 articles, six of which we analyzed including four open-label studies and two randomized controlled trials following a detailed review process. The studies included a total of 230 patients, of which 150 received low dose IL-2 and 80 received placebo. Although the open-label studies demonstrated an expansion of Treg cells that coincided with a clinical response, the predefined primary endpoints for clinical efficacy were not achieved in the randomized controlled trials. In general, treatment with low-dose IL-2 appears to be safe and tolerated well. ConclusionLow-dose IL-2 therapy appears to be a promising strategy for treating SLE; however, larger trials are still necessary to assess clinical responses in patients with such a heterogeneous disease.

Paediatric acute-onset neuropsychiatric syndrome (PANS) is characterised by infection-provoked abrupt and dramatic onset of obsessive compulsive disorder (OCD) or eating restriction, along with neurodevelopmental regression. Although the aetiology of PANS remains uncertain, due to a prevailing neuroimmune hypothesis some children receive the immune modulator intravenous immunoglobulin (IVIg). Using single-cell RNA sequencing of peripheral immune cells, we examined gene expression in five children with PANS (mean age 10.2 years, range 5-17, 60% male) who were receiving open-label IVIg. Maternal autoimmunity (n=3) and familial neurodevelopmental/neuropsychiatric disorders (n=5) were present. The index PANS event occurred age 1.8-13 years, characterised by abrupt eating restriction (n=5), developmental regression (n=4), and OCD (n=3). Single-cell RNA sequencing (144,470 cells) was performed in five patients pre- and post-IVIg, and four controls (mean age 13.5 years, range 11-16, 50% male). In PANS pre-IVIg compared to neurotypical controls, there were downregulated immune pathways (defense response, innate immunity, secretory granules) in most cell types. However, NK cells exhibited upregulated immune pathways (response to corticosteroid), supporting a baseline immune dysregulation. In PANS pre-IVIg compared to controls, ribosomal pathways were upregulated in neutrophils and CD8 T cells, but downregulated in NK cells. Post-IVIg, the previously downregulated immune pathways were upregulated in most cell types, and the baseline ribosomal pathway abnormalities were reversed. Additionally, histone modification pathways (histone methyltransferase, chromatin) were downregulated in neutrophils and NK cells post-IVIg. We propose PANS is an epigenetic immune-brain disorder with cellular epigenetic, ribosomal, and immune dysregulation. Therefore, epigenetic and immune-modulating therapies, such as IVIg, may have a critical role in treating this disabling disorder. HighlightsO_LIFive children with PANS receiving monthly IVIg who had clinical benefit were studied C_LIO_LIThree young boys had a regressive (autistic) phenotype, whereas the older two girls had OCD C_LIO_LISingle-cell RNA sequencing showed epigenetic, ribosomal, and immune dysregulation in PANS C_LIO_LIIVIg treatment had epigenetic and immune-modulating effects in PANS C_LIO_LIIVIg altered gene expression of histone methyltransferase and chromatin genes C_LI

Post-COVID syndrome (PCS) has emerged as a significant health concern with persisting symptoms. A subset of PCS patients develops severe myalgic encephalomyelitis/chronic fatigue syndrome (pcME/CFS). Dysregulated autoantibodies (AABs) have been implicated in PCS, contributing to immune dysregulation, impairment of autonomous nerve and vascular function. As recently shown in autoimmune diseases, IgG fractions translate disease-specific pathways into various cells. Therefore, we asked whether IgG fractions from PCS patients could be applied in-vitro to identify specific cytokine responses for PCS patients without (nPCS) and with pcME/CSF. To assess this, we have stimulated monocyte cell lines with IgG fractions from PCS patients. Our findings reveal distinct cytokine responses induced by patient derived AABs which are suggested in vascular and immune dysfunction. In contrast to nPCS, pcME/CSF AABs induced enhanced neurotrophic responses, characterized by significant cytokine correlations involving brain-derived neurotrophic factor (BDNF), glial cell-derived neurotrophic factor (GDNF) and tumor necrosis factor superfamily member 14 (LIGHT). Further, AAB-induced cytokine levels correlate with clinical symptoms. This study emphasizes a contribution of AABs in PCS, in mitigating long-term immune dysregulation, and a need for therapies modulating IgG-induced signaling pathways.

Multisystem Inflammatory Syndrome in Children associated with COVID-19 (MIS-C) is a late complication of pediatric COVID-19, which follows weeks after original SARS-CoV-2 infection, regardless of its severity. It is characterized by hyperinflammation, neutrophilia, lymphopenia and activation of T cells with elevated IFN-{gamma}. Observing production of autoantibodies and parallels with systemic autoimmune disorders, such as systemic lupus erythematodes (SLE), we explored B cell phenotype and serum levels of type I, II and III interferons, as well as the cytokines BAFF and APRIL in a cohort of MIS-C patients and healthy children after COVID-19. We documented a significant elevation of IFN-{gamma}, but not IFN- and IFN-{lambda} in MIS-C patients. BAFF was elevated in MIS-C patient sera and accompanied by decreased BAFFR expression on all B cell subtypes. The proportion of plasmablasts was significantly lower in patients compared to healthy post-COVID children. We noted the presence of ENA Ro60 autoantibodies in 4/35 tested MIS-C patients. Our work shows the involvement of humoral immunity in MIS-C and hints at parallels with the pathophysiology of SLE, with autoreactive B cells driven towards autoantibody production by elevated BAFF. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=175 SRC="FIGDIR/small/22275245v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@166327dorg.highwire.dtl.DTLVardef@7cde7forg.highwire.dtl.DTLVardef@1f3a3b2org.highwire.dtl.DTLVardef@803175_HPS_FORMAT_FIGEXP M_FIG C_FIG Summary sentenceElevated serum BAFF in children with MIS-C supports the state of polyclonal B cell activation and autoimmune phenomena characterizing this disease.

ObjectiveTo define cellular and molecular mechanisms distinguishing active systemic lupus erythematosus (SLE) from remission by profiling autoreactive antinuclear antigen- positive (ANA+) and non-autoreactive B cells subsets in three cohorts: active disease (SLE-A), long-term, drug free remission (SLE-R), and healthy controls (HC). MethodsPeripheral blood B cells were phenotyped by flow cytometry, including ANA reactivity. Single-cell RNA sequencing (scRNA-seq) was performed on sorted ANA+ and ANA- subsets. ResultsSeven transcriptomic B cell clusters were resolved: quiescent (Naive 1, Marginal Zone B cells [MZB], IgG Memory 1) and activated (Age-Associated B cells [ABCs], Naive 2, IgM Memory, IgG Memory 2). SLE-A showed expansion of activated clusters, MZB contraction, and a higher IgG:IgM B cell ratio. SLE-R exhibited an "immunological reset," distinct from healthy homeostasis, with reduced ABCs and IgG Memory 2, persistence of Naive 2, and partial restoration of MZB and Naive 1. Interferon- (IFNa) signaling was elevated across clusters in SLE-A (SLE-A > SLE-R > HC), whereas TNF signaling was enriched in activated clusters across cohorts, with minimal differences between SLE-R and SLE-A. IFNa and TNF scores were inversely correlated. B cells predominantly expressed TNFR2, suggesting immunomodulatory TNF effects in remission. ANA+ cells in HC and SLE-R showed enriched Fc{gamma}RIIb inhibitory and IL-4/STAT6 signaling, suggesting reinstated regulatory control. DiscussionCompared to SLE-A, SLE-R was characterized by partial reversion to HC homeostasis with residual activation. These findings delineate immunologic features of remission and suggest therapeutic opportunities, including modulation of TNFR2, Fc{gamma}RIIb, and IL-4 to help sustain remission. What is already known on this topicSome patients with SLE achieve complete clinical remission without treatment, referred as immune reset; the mechanisms that underlie this state have not been well characterized. Healthy individuals and patients with Systemic Lupus Erythematosus (SLE) normally harbor similar frequencies of autoreactive B cells; the checkpoints that regulate activation of these cells are not fully defined. What this study addsB cells, stratified by their reactivity to nuclear antigens (ANA), from active SLE (SLE-A), drug-free remission (SLE-R), and healthy controls (HC) were analyzed using single cell sequencing and flow cytometry. We identified B cells states associated with disease activity; SLE-R displayed a distinct profile that differed from SLE-A and HC. TNF signaling was present in activated B cell subsets in SLE-A and SLE-R. This persistence in SLE-R may reflect an immunomodulatory function of TNF on TNFR2, which is expressed on B cells. ANA+ cells in SLE-R and HC were enriched for inhibitory Fc{gamma}RIIb and IL-4/STAT6 programs. How this study might affect research, practice or policyThe signatures identified help define the "immunological reset" state in patients with SLE-R. We also identified pathways, such as type I IFN, TNFR2, Fc{gamma}RIIb, IL-4/STAT6 as potential targets for maintaining remission.

Uveitis is a common cause of blindness and classified as infectious or non-infectious types. Non-infectious uveitis is often secondary to systemic autoimmune diseases, with Behcets disease (BD) and Vogt-Koyanagi-Harada disease (VKHD) as the two most common causes. Uveitis in BD and VKHD often show similar clinical manifestations, but the underlying immunopathogenesis remains unclear. We collected immune cell infiltrates in aqueous humour of BD and VKHD uveitis patients and analysed them by single-cell RNA paired with T cell receptor (TCR) sequencing. T cells were found as the dominant immune cell infiltration. Intriguingly, a majority of CD4+ in T cell infiltrates was only observed in VKHD but not in BD. In agreement with this discrepancy between VKHD and BD, T cell clonality analysis and Clonotype Neighbour Graph Analysis (CoNGA) also revealed a selective expansion of pro-inflammatory CD4+ T cell clones in VKHD. In contrast, BD showed a selective expansion of pro-inflammatory CD8+ T cell clones. Our study reveals distinct immunopathogenesis of uveitis driven by CD4+ T cells in VKHD and by CD8+ T cells in BD, and therefore suggests differential approaches for their diagnosis and therapy.

BackgroundSystemic lupus erythematosus (SLE) is a spontaneous systemic auto-immune condition for which the inciting factors and genetic basis are generally unknown. Although heterogeneous in its manifestations and severity, SLE involves chronic inflammation along with sustained autoantibody production. The root causes and pathophysiology of the inflammation and breaches of tolerance are incompletely understood, but neutrophils are thought to be important elements of the pathophysiology. Type I interferons (IFN) in the bloodstream and an IFN-stimulated gene (ISG) signature in circulating leukocytes, including neutrophils, are common features in many patients. Earlier work has provided evidence of increased levels of transcripts derived from transposable elements (TEs) in peripheral blood cells of SLE patients. Using six leukocyte types, including neutrophils, we tested the correlation of TE expression with disease severity and explored the relationships between increased ISG and TE expression with attention to the genomic locations of the expressed TEs. ResultsWe reanalysed previously published data from neutrophils and other leukocytes of SLE patients sub-divided into ISG-high (termed IFNpos, n=12) and ISG-low (termed IFNneg, n=11) patients in the original study, examining RNA-seq data from B and T lymphocytes, conventional and plasmacytoid dendritic cells (DC), monocytes and PMN of IFNpos and IFNneg SLE patients compared to healthy controls. SLE patients pre-stratified as IFNneg showed no significant increase in TE expression. All IFNpos cell types had similar amounts of total TE-encoded RNA, but among the 6 cell types, PMN had the highest number of differentially expressed TEs and ISGs in IFNpos SLE patients compared to healthy controls. There was a strong correlation between expression of several specific TE families and disease activity assessed at the time of the visit. Most upregulated TEs ([~]80%) were present in introns of upregulated genes, and [~]67% of these were ISGs. By mapping expressed TEs in ISGs, we found that high intronic TE expression correlated strongly with increased ISG expression as well as with splicing alterations in annotated exons flanking expressed TEs. Consistent with autonomous TE expression, upregulated TEs were also observed at intergenic sites distant from annotated genes, perhaps due to weakening of heterochromatin integrity. ConclusionsOur findings show a strong association and suggest mechanistic relationships between increased TE expression and IFN responses in multiple types of leukocytes centrally involved in SLE pathogenesis. Although limited by short-read RNA-seq technology, our analyses support selective upregulation of some TEs independent from the regulation of conventional genes, concurrent with many intron-localized TEs whose expression tracks with ISGs. The data emphasize the need for long-reads sequencing to understand the causes and consequences of high TE expression in SLE and other autoimmune/inflammatory disorders. Important questions include whether TE expression in introns of ISGs and other genes is independently regulated or reflects exonization or partial intron retention, and how frequently it correlates with splicing variations in adjacent exons.

The Fc{gamma} receptors (Fc{gamma}Rs) act as modulators of the immune system and have previously been shown to play a role in immune disorders such as systemic lupus erythematosus and immune thrombocytopenic purpura. Thus far, their role in primary immunodeficiencies (PID), including common variable immunodeficiency disorders (CVID), has not been studied. In this paper we explored whether there is an association between the following single nucleotide polymorphisms (SNPs) and CVID: FCGR2A H131R (rs1801274), FCGR2B I232T (rs1050501), and FCGR3A F158V (rs396991). We compared the genotypes of a cohort of 83 patients with PID, including 56 with CVID, against controls. We found a significant difference between our mixed PID cohort and controls at the FCGR2A H131R SNP (X2 =7.884, p=0.019). There was not a significant difference at either of the other SNPs studied. Further, we examined the effect of FCGR SNPs on the incidence of the most common CVID complications within our cohort: anaemias, organ-specific autoimmunity, bronchiectasis, splenomegaly, granulomata, and cytopenias. We found no significant association between SNPs and the development of these complications. In summary, we have shown that there is a link between the FCGR2A H131R SNP and the development of a PID.

Systemic lupus erythematosus (SLE) is associated with infection susceptibility and altered innate immune function. Monocyte metabolism is linked to appropriate cytokine release and bacterial containment. We investigated cytokine production and metabolic programming in the monocyte population from SLE patients and healthy controls following lipopolysaccharide (LPS) stimulation. SLE monocytes displayed increased IL-10, TNF, and IL-8 production, with impaired IL-1{beta} induction. Metabolic profiling revealed altered substrate use, with increased glucose dependence and reduced fatty acid and amino acid oxidation after LPS stimulation. SLE patients exhibited reduced numbers of classical monocytes, expansion of intermediate monocytes, and dysregulated subset-specific metabolic reprogramming in response to LPS. This descriptive study provides a cornerstone for (i) understanding infection susceptibility in SLE, (ii) subset-resolved immunometabolic profiling as a tool in autoimmunity, and (iii) developing future metabolic-targeted therapeutic strategies HighlightsO_LIDescriptive mapping shows SLE monocytes are proinflammatory with glucose dependence after LPS C_LIO_LIClassical and intermediate SLE subsets show divergent baseline metabolic preferences versus healthy C_LIO_LISLE subsets display aberrant LPS responses, i.e.. increased glucose and reduced fatty acid oxidation C_LIO_LIThis study provides a cornerstone for subset-resolved immunometabolism in infection susceptibility. C_LI

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.

Systemic lupus erythematosus (SLE) is an autoimmune disorder that results in an attack by bodys immune system of its own tissues, causing chronic inflammation and tissue damage. T cells play a key role in the pathogenesis of SLE, as they secrete pro-inflammatory cytokines as well as mediate direct effects on target tissues. Recently, CD4-positive T cells with cytotoxic potential were showed to be involved in autoimmune disease progression and tissue damage. However, whether this cell type expands and plays effector functions in SLE patients remain to be elucidated. Analyzing single-cell RNA sequencing (scRNA-Seq) data and flow cytometry data, we find that cytotoxic CD4+CD28- T cells are present in SLE patients. We also show that these cells expand most prominently in patients affected by lupus nephritis, and they exhibit cytotoxic activity against human renal glomerular endothelial cells in vitro. In addition, our study suggests that Interleukin-15 (IL-15) promotes the expansion, proliferation and cytotoxic function of CD4+CD28- T cells in SLE patients. Tofacitinib, a selective JAK3 inhibitor, inhibits the effect of IL-15 on CD4+CD28- T cells. Together, our study clearly demonstrated that CD4+ CD28- T cells characterized by proinflammatory properties and cytolytic function expand in SLE patients. The pathogenic potential of these CD4+ CD28- T cells is driven by IL-15/IL-15R/JAK3/STAT5 signaling pathway, which may open new avenues for therapeutic intervention to prevent progression of SLE patients.

Long-COVID (LC) is a serious clinical condition characterised by debilitating fatigue together with a wide array of symptoms that significantly reduce the quality of life of patients. Currently no holistic or even symptom specific treatment options are available, likely due to both a lack of insight into the disease processes that drive LC symptoms and an extreme heterogeneity in patients profiles. We characterised patients and post infection controls, with respect to their immunological profiles with a non-exhaustive panel of biomarkers rationalised based on their potential role in driving symptoms. We observed that the patients symptoms could be grouped into 4 clusters suggesting possible stratification. Systemic inflammation persisted and did not normalize over time in LC. This was not related to persistent SARS-CoV-2 infection, as the presence of circulating N-protein was detected similarly in both patients and controls. No obvious deviation in B-cells and monocytes profiles were observed with minor changes for NK-cells (CD62L+/CD16+/HLA-DR+). Major changes affected CD4+T-cells (and to a lesser extent CD8+T-cells) with respect to exhaustion (PD1+/LAG3+/CD44+), regulation (Treg) and differentiation (naive/memory-CD62L+). Several candidate biomarkers (cytokines, microRNAs, phosphate metabolism) were present more frequently in LC at high levels and provided information on underlying disease processes. While frequencies of candidate autoantibody+ participants were not different, levels of some antibodies were higher in LC. Yet none of these candidates stood out as a universal biomarker for LC, with the exception of CRP (73% cases), and loss of Treg (50%). However, we confirmed that several overlapping underlying aetiologies may be involved in this complex disease. Specific groups of biomarkers also associated with the 4 cluster of patients. Although to be taken with caution due to small numbers, 3 biomarkers discriminated controls from patients (Treg/CD4+PD1+/CD4+CD161+), others were associated with symptoms recovery (low IL10/IL12/IL4 and high miR766) or deterioration (high CD4+CD38+/ CD8+naiveCD62L+/low IL2) over 12 months. This study provides rational for developing targeted therapeutic strategies as well as biomarkers to stratify LC patients most likely to respond.

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a debilitating but poorly-understood disease. ME/CFS symptoms can range from mild to severe, and include immune system effects alongside incapacitating fatigue and post-exertional disease exacerbation. In this study, we examined immunological profiles of people living with ME/CFS by flow cytometry, focusing on cytotoxic cells, to determine whether people with mild/moderate (n= 43) or severe ME/CFS (n=53) expressed different immunological markers. We found that people with mild/moderate ME/CFS had increased expression of cytotoxic effector molecules alongside enhanced proportions of early-immunosenescence cells, determined by the CD28-CD57- phenotype, indicative of persistent viral infection. In contrast, people with severe ME/CFS had higher proportions of activated circulating lymphocytes, determined by CD69+ and CD38+ expression, and expressed more pro-inflammatory cytokines, including IFN{gamma}, TNF and IL-17, following stimulation in vitro, indicative of prolonged non-specific inflammation. These changes were consistent across different cell types including CD8+ T cells, mucosal associated invariant T cells and Natural Killer cells, indicating generalised altered cytotoxic responses across the innate and adaptive immune system. These immunological differences likely reflect different disease pathogenesis mechanisms occurring in the two clinical groups, opening up opportunities for the development of prognostic markers and stratified treatments. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=130 SRC="FIGDIR/small/24319359v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@1e3f2e5org.highwire.dtl.DTLVardef@5fd9fborg.highwire.dtl.DTLVardef@e015eforg.highwire.dtl.DTLVardef@1c03ae1_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG

BackgroundThe importance of autotaxin, an enzyme that catalyzes lysophospholipid production, has recently been recognized in various diseases, including cancer and autoimmune diseases. Herein, we examined the role of autotaxin in systemic lupus erythematosus (SLE), utilizing data from ImmuNexUT, a comprehensive database consisting of transcriptome data and expression quantitative trait locus (eQTL) data of immune cells from patients with immune-mediated disorders. MethodsSerum autotaxin concentrations in patients with SLE and healthy controls (HCs) were compared. The transcriptome data of patients with SLE and age-and sex-matched HCs were obtained from ImmuNexUT. The expression of ENPP2, the gene encoding autotaxin, was examined in peripheral blood immune cells. Next, weighted gene correlation network analysis (WGCNA) was performed to identify genes with expression patterns similar to ENPP2. The ImmuNexUT eQTL database and public epigenomic databases were used to infer the relationship between autotaxin and pathogenesis of SLE. ResultsAutotaxin levels were elevated in the serum of patients with SLE compared to HCs. Furthermore, the expression of ENPP2 was higher in plasmacytoid dendritic cells (pDCs) than in other immune cell subsets, and its expression was elevated in pDCs of patients with SLE compared to HCs. In WGCNA, ENPP2 belonged to a module that correlated with disease activity. This module was enriched in interferon-associated genes and included genes whose expression was influenced by single-nucleotide polymorphisms associated with SLE, suggesting that it is a key module connecting genetic risk factors of SLE with disease pathogenesis. Analysis utilizing the ImmuNexUT eQTL database and public epigenomic databases suggested that the increased expression of ENPP2 in pDCs from patients with SLE may be caused by increased expression of interferon-associated genes and increased binding of STAT3 complexes to the regulatory region of ENPP2. ConclusionsAutotaxin may play a critical role in connecting genetic risk factors of SLE to disease pathogenesis in pDCs.