OBJECTIVE:Systemic lupus erythematosus (SLE) is a multiorgan disease with widespread immune dysregulation and significant unmet clinical need. Blood-based gene expression studies have advanced our understanding of SLE pathogenesis but may overlook critical tissue-specific mechanisms that drive disease heterogeneity and progression. We posited that integrated multidimensional profiling could reveal novel molecular patterns underlying distinct SLE pathologies. METHODS:Here, we integrated immune cell, protein, and transcriptome data sets with disease activity and damage indices across 87 patients with SLE to reveal three independent protein signatures corresponding to discrete organ pathologies and immune perturbations. RESULTS:Alongside type I interferon and granulocyte pathways, our multidimensional analyses identified a previously uncharacterized immune cell priming protein signature that was enriched in patients with renal involvement and was indicative of elevated risk of six-year organ damage accrual. This minimally invasive signature outperformed conventional assessments and was only found in the serum proteomics data. Collectively, the protein signatures demonstrated a combined prevalence of 94%, reflecting their broad relevance to SLE. CONCLUSION:Together, these results reveal parallel immune mechanisms in SLE and provide a framework to identify new therapeutic targets. Clinical and immune data are available for public exploration through the interactive SLE Immune Atlas.

OBJECTIVE:The efficacy of nucleic acid-based vaccines against SARS-CoV-2 varies across individuals, partly due to genetic factors influencing neutralizing antibody production. In patients with systemic autoimmune diseases (SADs), this response may be further altered by immune dysregulation. METHODS:We conducted a genome-wide association study (GWAS) to identify genetic variants associated with postvaccination anti-SARS-CoV-2 IgG antibody levels and to assess whether these associations differ between patients with SAD and healthy individuals. RESULTS:The study included 165 participants (138 with SADs, 27 healthy controls), all of whom received nucleic acid-based vaccines. Antibody levels targeting the spike protein receptor-binding domain (RBD) and nucleocapsid were measured between 1 and 12 months after vaccination. GWAS results were metaanalyzed with data from a previously published GWAS with 1076 healthy individuals. We identified a novel association near RACGAP1 (rs706785; βmeta = -0.30, P meta = 3.85 × 10-8) and replicated a known association at HLA-DRB1 position 71 (βmeta = -0.23, P meta = 1.94 × 10-11). No significant interactions were observed between genotype and disease status. CONCLUSION:This study highlights both MHC and non-MHC genetic contributions to SARS-CoV-2 vaccine responses and suggests these effects are consistent across patients with SADs and healthy individuals, supporting standard vaccination strategies for individuals with systemic autoimmune conditions.

OBJECTIVE:Systemic lupus erythematosus (SLE) increases cardiovascular disease (CVD) risk, and this is not explained by traditional risk factors. Characterization of blood immunologic signatures that associate with subclinical CVD and predict its progression has been challenging and may help identify subgroups at risk. METHODS:Patients with SLE (n = 77) and healthy controls (HCs) (n = 27) underwent assessments of arterial stiffness, vascular wall inflammation, and coronary atherosclerosis burden with cardio-ankle vascular index (CAVI); fluorodeoxyglucose-positron emission tomography/computed tomography (CT) (target-to-background ratio [TBR]); and coronary CT angiography. Whole blood bulk RNA sequencing was performed in a subset of study participants (HC n = 10, SLE n = 20). In a partially overlapping subset (HC n = 24, SLE n = 64), serum inflammatory protein biomarkers were quantified with an Olink platform. RESULTS:CAVI, TBR, and noncalcified coronary plaque burden (NCB) were increased in patients with SLE compared to HCs. When comparing patients with SLE with high CAVI scores to those with low CAVI scores or to HCs, there was a down-regulation of genes in pathways involved in the cell cycle and differentially regulated pathways related to metabolism. Distinct serum proteins associated with increased CAVI (CCL23, colony-stimulating factor 1, latency-activating peptide transforming growth factor β1, interleukin 33 [IL-33], CD8A, and IL-12B), NCB (monocyte chemotactic protein 4 and FMS-like tyrosine kinase 3 ligand [Flt3L]), and TBR (CD5, IL-1α, AXIN1, cystatin D [CST5], and tumor necrosis factor receptor superfamily 9; P < 0.05). CONCLUSION:Blood gene expression patterns and serum proteins that associate with worse vascular phenotypes suggest dysregulated immune and metabolic pathways linked to premature CVD. Cytokines and chemokines identified in associations with arterial stiffness, inflammation, and NCB in SLE may allow for characterization of new CVD biomarkers in lupus.

The Krebs cycle enzyme aconitate decarboxylase 1 (ACOD1) mediates itaconate synthesis in monocytes and macrophages. Previously, we reported that administration of 4-octyl itaconate to lupus-prone mice abrogated immune dysregulation and clinical features. In this study, we explore the role of the endogenous ACOD1/itaconate pathway in the development of TLR7-induced lupus (imiquimod [IMQ] model). We found that, in vitro, ACOD1 was induced in mouse bone marrow-derived macrophages and human monocyte-derived macrophages following TLR7 stimulation. This induction was partially dependent on type I IFN receptor signaling and on specific intracellular pathways. In the IMQ-induced mouse model of lupus, ACOD1 knockout (Acod1-/-) displayed disruptions of the splenic architecture, increased serum levels of anti-dsDNA and proinflammatory cytokines, and enhanced kidney immune complex deposition and proteinuria, when compared with the IMQ-treated wild-type mice. Consistent with these results, Acod1-/- bone marrow-derived macrophages treated in vitro with IMQ showed higher proinflammatory features. Furthermore, itaconate serum levels in systemic lupus erythematosus patients were decreased compared with healthy individuals, in association with disease activity and specific perturbed cardiometabolic parameters. These findings suggest that the ACOD1/itaconate pathway plays important immunomodulatory and vasculoprotective roles in systemic lupus erythematosus, supporting the potential therapeutic role of itaconate analogs in autoimmune diseases. The Journal of Immunology, 2024, 213: 419-434.

Communities near transportation sources can be impacted by higher concentrations of particulate matter (PM) and other air pollutants. Few studies have reported on air quality in complex urban environments with multiple transportation sources. To better understand these environments, the Kansas City Transportation and Local-Scale Air Quality Study (KC-TRAQS) was conducted in three neighborhoods in Southeast Kansas City, Kansas. This area has several emissions sources including transportation (railyards, vehicles, diesel trucks), light industry, commercial facilities, and residential areas. Stationary samples were collected for 1-year (October 24, 2017, to October 31, 2018) at six sites using traditional sampling methods and lower-cost air sensor packages. This work examines PM less than 2.5 mu m in diameter (PM2.5), black carbon (BC), and trace metals data collected during KC-TRAQS. PM2.5 filter samples showed the highest 24-h mean concentrations (9.34 mu g/m(3)) at the sites located within 20-50 m of the railyard. Mean 24-h PM2.5 concentrations, ranging from 7.96 to 9.34 mu g/m(3), at all sites were lower than that of the nearby regulatory site (9.83 mu g/m(3)). Daily maximum PM2.5 concentrations were higher at the KC-TRAQS sites (ranging from 25.31 to 43.76 mu g/m(3)) compared to the regulatory site (20.50 mu g/m(3)), suggesting short-duration impacts of localized emissions sources. Across the KC-TRAQS sites, 24-h averaged PM2.5 concentrations from the sensor package (P-POD) ranged from 3.24 to 5.69 mu g/m(3) showing that, out-of-the-box, the PM sensor underestimated the reference concentrations. KC-TRAQS was supplemented by elemental and organic carbon (EC/OC) and trace metal analysis of filter samples. The EC/OC data suggested the presence of secondary organic aerosol formation, with the highest mean concentrations observed at the site within 20 m of the railyard. Trace metals data showed daily, monthly, and seasonal variations for iron, copper, zinc, chromium, and nickel, with elevated concentrations occurring during the summer at most of the sites. Implications: This work reports on findings from a year-long air quality study in Southeast Kansas City, Kansas to understand micro-scale air quality in neighborhoods impacted by multiple emissions sources such as transportation sources (including a large railyard operation), light industry, commercial facilities, and residential areas. While dozens of studies have reported on air quality near roadways, this work will provide more information on PM2.5, black carbon, and trace metals concentrations near other transportation sources in particular railyards. This work can also inform additional field studies near railyards.

Systemic lupus erythematosus (SLE) is multiorgan disease with widespread immune dysregulation, unmet clinical need, and a growing requirement for precision medicine treatment options. Here, we overlay immune cell phenotyping, protein, and transcriptome datasets with disease activity and damage indices in a cohort of 87 patients with SLE and 48 healthy controls to reveal three independent protein signatures corresponding to discrete organ pathologies and immune perturbations. Alongside type I interferon and granulocyte pathways, our multidimensional analyses identified a previously uncharacterized immune cell priming protein signature enriched in patients with renal involvement that was predictive of disease worsening and accumulation of organ damage during longitudinal follow-up. These results revealed parallel immune mechanisms in SLE and provide a tool for treatment mapping and new treatment opportunities for untargeted pathways. In support of open science, these clinical and immune parameter data are now available for public exploration through an interactive SLE Immune Atlas.Funding Information: This support was funded by AstraZeneca in accordance with Good Publication Practice (GPP3) guidelines.Declaration of Interests: AH, CC, CG, CM, CR, DS, JH, KC, KZ, MASmith, MdIR, MS, RE, RF, RK, SR, and SW are or once were shareholders and employees of AstraZeneca; CG is a current employee of Q2 solutions; JH is a current employee of Bristol Myers Squibb; KC is a current shareholder and employee of Regeneron Pharmaceuticals; MASmith, RE and SW are current shareholders and employees of Horizon Therapeutics; MS is a current employee of Provention Bio; RK is a current employee of Spirovant Sciences; RS is a current shareholder and employee of Novartis; SR is a current employee of Sanofi; CG, JC, JH, KZ, MD, MK, MS, RF, RK, SG, SH, SR and ZM declare no competing interests.Ethics Approval Statement: De-identified peripheral human whole blood samples from 87 patients with mild to moderate SLE (NIH-SLE 2013–2014 cohort) were shipped to MedImmune in Gaithersburg, MD on a weekly basis throughout 2014 under clinical protocol NIH 94-AR-0066, approved by the NIAMS/National Institute of Diabetes and Digestive and Kidney Diseases Institutional Review Board (IRB). A total of 48 whole blood samples from healthy controls were also obtained on a weekly basis under the internal donor program, approved by the MedImmune IRB. To ensure the robustness of the protein signatures, an independent validation cohort of 43 patients with mild to moderate SLE (NIH-SLE 2016–2017 cohort) and 52 healthy controls were also collected from the NIH and MedImmune, respectively, under the same protocols. All patients gave signed informed consent.

The troponin complex regulates Ca2+ sensitivity of the myofibrillar contractile apparatus in striated muscles. This complex is comprised of three associated troponin proteins: troponin I (TNNI), T, and C. TNNI is the inhibitory subunit, TNNI1 is predominantly expressed in slow-twitch (type 1) skeletal muscle fibers and has not been conclusively established to cause skeletal myopathy. We report a family with a novel dominantly acting heterozygous TNNI1 substitution p.R174Q in three similarly affected siblings, two males (44 and 37 years) and one female (39 years). The youngest sibling was evaluated at the NIH Clinical Center. Per history, he had abnormal stiffness in his first year of life but normal motor development. Muscle cramps, myalgias, stiffness, and swallowing difficulties have been lifelong issues. Examination showed normal muscle bulk and strength without myotonia. Handheld computer myometry showed increased muscle relaxation time (mean, SD: 0.63±0.19 sec; normal reference: 0.32±0.23). Creatine kinase (CK) levels had been consistently elevated (800-1,330U/L range; normal < 200U/L). Muscle MRI was normal, while a swallowing study revealed a cricopharyngeal bar with significant esophageal narrowing, caused by an enlarged cricopharyngeal muscle, which consists of mostly type-1-slow-twitch fibers. Pulmonary function tests, an electrodiagnostic study, and echocardiography were normal. Muscle histopathology (from the patient's brother's biopsy) showed type 1 fiber hypertrophy with internalized nuclei and eosinophilic inclusions with corresponding cores on NADH staining. Single fiber contractility studies revealed increased force response of sarcomeres to submaximal Ca2+ consistent with a gain-of-function hypercontractile mechanism due to Ca2+ hypersensitivity mediated by the variant troponin I1. This case thus establishes TNNI1-associated hypercontractile muscle disease manifesting with cramping, abnormal relaxation, and swallowing difficulties. Understanding the specific disease mechanism for variants in sarcomeric proteins is essential for the consideration of potential pharmacological interventions, in this case fiber type-1 Ca2+ desensitizers. The troponin complex regulates Ca2+ sensitivity of the myofibrillar contractile apparatus in striated muscles. This complex is comprised of three associated troponin proteins: troponin I (TNNI), T, and C. TNNI is the inhibitory subunit, TNNI1 is predominantly expressed in slow-twitch (type 1) skeletal muscle fibers and has not been conclusively established to cause skeletal myopathy. We report a family with a novel dominantly acting heterozygous TNNI1 substitution p.R174Q in three similarly affected siblings, two males (44 and 37 years) and one female (39 years). The youngest sibling was evaluated at the NIH Clinical Center. Per history, he had abnormal stiffness in his first year of life but normal motor development. Muscle cramps, myalgias, stiffness, and swallowing difficulties have been lifelong issues. Examination showed normal muscle bulk and strength without myotonia. Handheld computer myometry showed increased muscle relaxation time (mean, SD: 0.63±0.19 sec; normal reference: 0.32±0.23). Creatine kinase (CK) levels had been consistently elevated (800-1,330U/L range; normal < 200U/L). Muscle MRI was normal, while a swallowing study revealed a cricopharyngeal bar with significant esophageal narrowing, caused by an enlarged cricopharyngeal muscle, which consists of mostly type-1-slow-twitch fibers. Pulmonary function tests, an electrodiagnostic study, and echocardiography were normal. Muscle histopathology (from the patient's brother's biopsy) showed type 1 fiber hypertrophy with internalized nuclei and eosinophilic inclusions with corresponding cores on NADH staining. Single fiber contractility studies revealed increased force response of sarcomeres to submaximal Ca2+ consistent with a gain-of-function hypercontractile mechanism due to Ca2+ hypersensitivity mediated by the variant troponin I1. This case thus establishes TNNI1-associated hypercontractile muscle disease manifesting with cramping, abnormal relaxation, and swallowing difficulties. Understanding the specific disease mechanism for variants in sarcomeric proteins is essential for the consideration of potential pharmacological interventions, in this case fiber type-1 Ca2+ desensitizers.

Aims Dysferlinopathy is an autosomal recessive muscular dystrophy, caused by bi-allelic variants in the gene encoding dysferlin (DYSF). Onset typically occurs in the second to third decade and is characterised by slowly progressive skeletal muscle weakness and atrophy of the proximal and/or distal muscles of the four limbs. There are rare cases of symptomatic DYSF variant carriers. Here, we report a large family with a dominantly inherited hyperCKaemia and late-onset muscular dystrophy. Methods and Results Genetic analysis identified a co-segregating novel DYSF variant [NM_003494.4:c.6207del p.(Tyr2070Metfs*4)]. No secondary variants in DYSF or other dystrophy-related genes were identified on whole genome sequencing and analysis of the proband's DNA. Skeletal muscle involvement was milder and later onset than typical dysferlinopathy presentations; these clinical signs manifested in four individuals, all between the fourth and sixth decades of life. All individuals heterozygous for the c.6207del variant had hyperCKaemia. Histological analysis of skeletal muscle biopsies across three generations showed clear dystrophic signs, including inflammatory infiltrates, regenerating myofibres, increased variability in myofibre size and internal nuclei. Muscle magnetic resonance imaging revealed fatty replacement of muscle in two individuals. Western blot and immunohistochemical analysis of muscle biopsy demonstrated consistent reduction of dysferlin staining. Allele-specific quantitative PCR analysis of DYSF mRNA from patient muscle found that the variant, localised to the extreme C-terminus of dysferlin, does not activate post-transcriptional mRNA decay. Conclusions We propose that this inheritance pattern may be underappreciated and that other late-onset muscular dystrophy cases with mono-allelic DYSF variants, particularly C-terminal premature truncation variants, may represent dominant forms of disease.

Bicyclo[1.1.1]pentanes (BCPs) are of great interest to the agrochemical, materials, and pharmaceutical industries. In particular, synthetic methods to access 1,3-dicarbosubsituted BCP-aryls have recently been developed but most protocols rely on stepwise C-C bond formation via initial manipulation of BCP core to make the BCP-electrophile or -nucleophile followed by a second step (e.g., transition-metal mediated cross-coupling step) to form the second key BCP-aryl bond. Moreover, despite prevalence of C-F bonds in bioactive compounds, one pot, multicomponent cross-coupling methods to directly functionalize BCP to the corresponding fluoroalkyl BCP-aryl scaffolds are lacking. In this work, we describe a conceptual different approach to access diverse (fluoro)alkyl BCP-aryls at low temperatures and fast reaction times enabled by an iron-catalyzed multicomponent radical cross-coupling reaction from readily available (fluoro)alkyl halides, bicyclo[1.1.1]pentane, and Grignard reagents. Further, experimental and computational mechanistic studies provide insights into mechanism and ligand effects on the nature of C-C bond formation. Finally, these studies are used to develop a new method to rapidly access synthetic versatile 1-(fluoro)alkyl,3-bromo and -iodo BCPs via bisphosphine iron catalysis.

Objective In patients with systemic lupus erythematosus (SLE), fatigue is a debilitating symptom with poorly understood pathophysiology. Cardiorespiratory dysfunction has been hypothesised as a contributor to SLE-fatigue. The purpose of this exploratory study was to examine changes in cardiorespiratory function, following an exercise training programme in women with SLE, together with patient reported outcomes and other pathophysiological measures that may underlie SLE-fatigue. Methods Sixteen women with SLE and fatigue (Fatigue Severity Scale (FSS) ≥3) were enrolled in a supervised aerobic exercise training programme of vigorous intensity. The primary outcome was time to reach anaerobic threshold (AT-Time) during a cardiopulmonary exercise test (CPET). Secondary outcomes included changes in the 10-minute walk test (10MWT), FSS scores and the Patient Reported Outcomes Measurement Information System (PROMIS-57) survey. Mitochondrial function was assessed by the oxygen consumption rate (OCR)/extracellular acidification rate (ECAR) metabolic potential ratio. Results Following 12 weeks of exercise training, AT-Time increased by 93±82 (mean±SD) s (p<0.001), 10MWT increased by 84±66 m (p<0.001) and peak oxygen uptake (VO2) increased by 1.4±2.0 mL/kg/min (p=0.013). There were improvements in FSS score (−1.4±1.0, p<0.0001) and in most of the PROMIS-57 domains. The decrease in FSS scores correlated with an increase in the OCR/ECAR ratio (Pearson’s correlation r=-0.59, p=0.03). A subset of subjects (9/15) had significant reduction in their Interferon Stimulated Genes (ISG) (p=0.007) accompanied by a significant increase in the OCR/ECAR ratio (p=0.013). Conclusions Cardiorespiratory function was improved in concomitance with reductions in fatigue following a 12-week aerobic exercise programme. The reduction in fatigue scores correlated with improvements in mitochondrial function.

Objectives Premature cardiovascular events in systemic lupus erythematosus (SLE) contribute to morbidity and mortality, with no effective preventive strategies described to date. Immune dysregulation and metabolic disturbances appear to play prominent roles in the induction of vascular disease in SLE. The peroxisome proliferator activated receptor-gamma agonist pioglitazone (PGZ suppresses vascular damage and immune dysregulation in murine lupus and improves endothelial dysfunction in other inflammatory diseases. We hypothesised that PGZ could improve vascular dysfunction and cardiometabolic parameters in SLE. Methods Eighty SLE subjects with mild to severe disease activity were randomised to a sequence of PGZ followed by placebo for 3 months, or vice versa, in a double-blind, cross-over design with a 2-month wash-out period. Primary endpoints were parameters of endothelial function and arterial inflammation, measured by multimodal assessments. Additional outcome measures of disease activity, neutrophil dysregulation, metabolic disturbances and gene expression studies were performed. Results Seventy-two subjects completed the study. PGZ was associated with a significant reduction in Cardio-Ankle Vascular Index (a measure of arterial stiffness) compared with placebo. Various metabolic parameters improved with PGZ, including insulin resistance and lipoprotein profiles. Circulating neutrophil extracellular trap levels also significantly decreased with PGZ compared with placebo. Most adverse events experienced while on PGZ were mild and resolved with reduction in PGZ dose. Conclusion PGZ was well tolerated and induced significant improvement in vascular stiffness and cardiometabolic parameters in SLE. The results suggest that PGZ should be further explored as a modulator of cardiovascular disease risk in SLE. Trial registration number NCT02338999 .

Background: Next generation sequencing studies have revealed an ever-increasing number of causes for genetic disorders of central nervous system white matter. A substantial number of disorders are identifiable from their specific pattern of biochemical and/or imaging findings for which single gene testing may be indicated. Beyond this group, the causes of genetic white matter disorders are unclear and a broader approach to genomic testing is recommended.Aim: This study aimed to identify the genetic causes for a group of individuals with unclassified white matter disorders with suspected genetic aetiology and highlight the investigations required when the initial testing is non-diagnostic.Methods: Twenty-six individuals from 22 families with unclassified white matter disorders underwent deep phenotyping and genome sequencing performed on trio, or larger, family groups. Functional studies and tran-scriptomics were used to resolve variants of uncertain significance with potential clinical relevance. Results: Causative or candidate variants were identified in 15/22 (68.2%) families. Six of the 15 implicated genes had been previously associated with white matter disease (COL4A1, NDUFV1, SLC17A5, TUBB4A, BOLA3, DARS2). Patients with variants in the latter two presented with an atypical phenotype. The other nine genes had not been specifically associated with white matter disease at the time of diagnosis and included genes associated with monogenic syndromes, developmental disorders, and developmental and epileptic encephalopathies (STAG2, LSS, FIG4, GLS, PMPCA, SPTBN1, AGO2, SCN2A, SCN8A). Consequently, only 46% of the diagnoses would have been made via a current leukodystrophy gene panel test. Discussion: These results confirm the importance of broad genomic testing for patients with white matter dis-orders. The high diagnostic yield reflects the integration of deep phenotyping, whole genome sequencing, trio analysis, functional studies, and transcriptomic analyses. Conclusions: Genetic white matter disorders are genetically and phenotypically heterogeneous. Deep phenotyping together with a range of genomic technologies underpin the identification of causes of unclassified white matter disease. A molecular diagnosis is essential for prognostication, appropriate management, and accurate repro-ductive counseling.

Increased risk of premature cardiovascular disease (CVD) is well recognized in systemic lupus erythematosus (SLE). Aberrant type I-Interferon (IFN)-neutrophil interactions contribute to this enhanced CVD risk. In lupus animal models, the Janus kinase (JAK) inhibitor tofacitinib improves clinical features, immune dysregulation and vascular dysfunction. We conducted a randomized, double-blind, placebo-controlled clinical trial of tofacitinib in SLE subjects (ClinicalTrials.gov NCT02535689). In this study, 30 subjects are randomized to tofacitinib (5 mg twice daily) or placebo in 2:1 block. The primary outcome of this study is safety and tolerability of tofacitinib. The secondary outcomes include clinical response and mechanistic studies. The tofacitinib is found to be safe in SLE meeting study’s primary endpoint. We also show that tofacitinib improves cardiometabolic and immunologic parameters associated with the premature atherosclerosis in SLE. Tofacitinib improves high-density lipoprotein cholesterol levels ( p = 0.0006, CI 95%: 4.12, 13.32) and particle number ( p = 0.0008, CI 95%: 1.58, 5.33); lecithin: cholesterol acyltransferase concentration ( p = 0.024, CI 95%: 1.1, −26.5), cholesterol efflux capacity ( p = 0.08, CI 95%: −0.01, 0.24), improvements in arterial stiffness and endothelium-dependent vasorelaxation and decrease in type I IFN gene signature, low-density granulocytes and circulating NETs. Some of these improvements are more robust in subjects with STAT4 risk allele.