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ObjectivesLittle is known about the immunology underlying variable treatment response in rheumatoid arthritis (RA). We performed large scale transcriptome analyses of peripheral blood immune cell subsets to identify immune cells that predict treatment resistance.MethodsWe isolated 18 peripheral blood immune cell subsets of 55 pre-treatment RA patients and 39 healthy controls, and performed RNA sequencing. Transcriptome changes in RA and treatment effects were systematically characterized. Association between immune cell gene modules and treatment resistance was evaluated. We validated predictive value of identified parameters for treatment resistance using quantitative polymerase chain reaction (qPCR) and mass cytometric analysis cohorts. We also characterized the identified population by synovial single cell RNA-seq analysis.ResultsImmune cells of RA patients were characterized by enhanced interferon and IL6-JAK-STAT3 signaling that demonstrate partial normalization after treatment. A gene expression module of plasmacytoid dendritic cells (pDC) reflecting the expansion of pre-dendritic cells (pre-DC) exhibited strongest association with treatment resistance. Type I interferon signaling was negatively correlated to pre-DC gene expression. qPCR and mass cytometric analysis in independent cohorts validated that the pre-DC associated gene expression and the proportion of pre-DC were significantly higher before treatment in treatment-resistant patients. A cluster of synovial DCs showed both features of pre-DC and proinflammatory conventional DC2s.ConclusionsAn increase in pre-DC in peripheral blood predicted RA treatment resistance. Pre-DC could have pathophysiological relevance to RA treatment response.Key messagesWhat is already known about this subject?Limited information is available about the immune cells that are associated with RA treatment resistance.What does this study add?RA treatment resistance can be predicted by an increase in pre-DC in peripheral blood prior to treatment.The expression of genes reflecting an increase in pre-DC is negatively correlated to the type I interferon signature, which is associated with good therapeutic response.Synovial pre-DC-like cells are proinflammatory cDC2s.How might this impact on clinical practice or future developments?Stratified treatment of RA is possible using pre-DC as a biomarker, and it might be possible to develop new therapies for treatment-resistant RA by targeting pre-DC.

Systemic lupus erythematosus (SLE) is a complex and heterogeneous autoimmune disease involving multiple immune cells. A major hurdle to the elucidation of SLE pathogenesis is our limited understanding of dysregulated gene expression linked to various clinical statuses with a high cellular resolution. Here, we conducted a large-scale transcriptome study with 6,386 RNA sequencing data covering 27 immune cell types from 159 SLE and 89 healthy donors. We first profiled two distinct cell-type-specific transcriptomic signatures: disease-state and disease-activity signatures, reflecting disease establishment and exacerbation, respectively. We next identified candidate biological processes unique to each signature. This study suggested the clinical value of disease-activity signatures, which were associated with organ involvement and responses to therapeutic agents such as belimumab. However, disease-activity signatures were less enriched around SLE risk variants than disease-state signatures, suggesting that the genetic studies to date may not well capture clinically vital biology in SLE. Together, we identified comprehensive gene signatures of SLE, which will provide essential foundations for future genomic, genetic, and clinical studies.

Human Leukocyte Antigen (HLA) alleles regulate susceptibility to rheumatoid arthritis (RA) and immune-mediated diseases. This study aims to elucidate the impact of HLA alleles to T cell subsets.We performed genome-wide and HLA allele association analysis for T cell receptor (TCR) beta chain repertoire in 13 purified T cell subsets from the ImmuNexUT database, consisting of 407 donors with ten immune-mediated diseases and healthy controls.HLA class II alleles were associated with TRBV gene usage and the public clones of CD4 T cells, while HLA class I alleles were associated with CD8 T cells. RA-risk and immune-mediated diseases-risk HLA alleles were associated with TRBV gene usage of naive and effector CD4 T cell subsets and public clones accumulating in Th17. Clonal diversity was independent of HLA alleles and was correlated with transcriptome changes that reflect TCR signaling.This study revealed in vivo evidence that both HLA alleles and environmental factors shape naive and effector TCR repertoires in RA and immune-mediated diseases patients.

Objectives We evaluated flow-cytometric and transcriptome features of peripheral blood immune cells from early-phase (disease duration Methods Fifty Japanese patients with SSc (12 early SSc cases and 38 late SSc cases) and 50 age- and sex-matched healthy controls were enrolled. A comparison of flow-cytometric subset proportions and RNA-sequencing of 24 peripheral blood immune cell subsets was performed. We evaluated differentially expressed genes (DEGs), characterized the co-expressed gene modules, and estimated the composition of subpopulations by deconvolution based on single-cell RNA-sequencing data. As a disease control, idiopathic inflammatory myositis (IIM) patients were also evaluated. Results Analysing the data from early and late SSc, fraction II effector regulatory T cell (Fr. II eTreg) genes showed a remarkable differential gene expression, enriched for genes related to oxidative phosphorylation. Although the flow-cytometric proportion of Fr. II eTregs was not changed in early SSc, deconvolution indicated expansion of the activated subpopulation. Co-expressed gene modules of Fr. II eTregs demonstrated enrichment of the DEGs of early SSc and correlation with the proportion of the activated subpopulation. These results suggested that DEGs in Fr. II eTregs from patients with early SSc were closely associated with the increased proportion of the activated subpopulation. Similar dysregulation of Fr. II eTregs was also observed in data from patients with early IIM. Conclusions RNA-seq of immune cells indicated the dysregulation of Fr. II eTregs in early SSc with increased proportion of the activated subpopulation.

The objective of this study was to identify factors predictive of malignancy in patients with polymyositis (PM) and dermatomyositis (DM) in Japan. We conducted a retrospective study of PM and DM patients who were admitted to our hospital between January 1992 and September 2017. Among 134 patients, 29 (21.6%) were diagnosed with cancer in the 3 years prior to and 3 years after the initial diagnosis of PM or DM. According to multivariate analyses, male sex [odds ratio (OR) = 3.65, p = 0.03], old age (OR = 1.05, p = 0.02), and a past history of diabetes mellitus (OR = 10.4, p = 0.005) were associated with an increased risk of malignancy. The absence of interstitial lung disease (ILD) (OR = 0.25, p = 0.03) was also associated with an increased risk of malignancy. Diabetes mellitus was observed in 28.6% of PM and DM patients with malignancy, but in only 7.3% of those with malignancy. Survival was significantly lower in patients with malignancy than in those without malignancy (p

Systemic lupus erythematosus (SLE) is a complex autoimmune disease involving multiple immune cells. To elucidate SLE pathogenesis, it is essential to understand the dysregulated gene expression pattern linked to various clinical statuses with a high cellular resolution. Here, we conducted a large-scale transcriptome study with 6,386 RNA sequencing data covering 27 immune cell types from 136 SLE and 89 healthy donors. We profiled two distinct cell-type-specific transcriptomic signatures: disease-state and disease-activity signatures, reflecting disease establishment and exacerbation, respectively. We then identified candidate biological processes unique to each signature. This study suggested the clinical value of disease-activity signatures, which were associated with organ involvement and therapeutic responses. However, disease-activity signatures were less enriched around SLE risk variants than disease-state signatures, suggesting that current genetic studies may not well capture clinically vital biology. Together, we identified comprehensive gene signatures of SLE, which will provide essential foundations for future genomic and genetic studies.

Overlap syndrome refers to a group of conditions that have clinical features of more than one well-characterised rheumatic disease and meet the respective classification criteria. There are no typical renal histological findings in overlap syndrome. When patients with overlap syndrome develop renal dysfunction, various potential causes, including lupus nephritis (LN), renal crisis by systemic sclerosis, interstitial nephritis, and so on, need to be distinguished. Here, we report a 44-year-old woman with overlap syndrome involving systemic lupus erythematosus (SLE), diffuse cutaneous systemic scleroderma, and Sjogren’s syndrome, who was also positive for anti-mitochondrial M2 antibody. She developed glomerular haematuria, proteinuria, and increase in creatinine appeared gradually. Suspecting LN, renal biopsy was performed. However, in the interstitium, mild infiltration of lymphocytes and plasma cells and very partial fibrosis were observed. Immunofluorescence microscopy revealed predominant mesangial immunoglobulin M, C3, and λ light chain staining. Overall, LN was not diagnosed based on these findings. Renal dysfunction was normalised by glucocorticoid treatment for 3 months. This case suggests the importance of a renal diagnosis based on renal pathological findings, especially in a case of overlap syndrome including SLE.

Objective Previous gene expression analyses seeking genes specific to antineutrophil cytoplasmic antibody-associated vasculitis (AAV) have been limited due to crude cell separation and the use of microarrays. This study aims to identify AAV-specific gene expression profiles in a way that overcomes those limitations. Methods Blood samples were collected from 26 AAV patients and 28 healthy controls (HCs). Neutrophils were isolated by negative selection, whereas 19 subsets of peripheral blood mononuclear cells were sorted by fluorescence assisted cell sorting. RNA-sequencing was then conducted for each sample, and iterative weighted gene correlation network analysis (iterativeWGCNA) and random forest were consecutively applied to identify the most influential gene module in distinguishing AAV from HCs. Correlations of the identified module with clinical parameters were evaluated, and the biological role was assessed with hub gene identification and pathway analysis. Particularly, the module's association with neutrophil extracellular trap formation, NETosis, was analyzed. Finally, the module's overlap with GWAS-identified autoimmune disease genes (GADGs) was assessed for validation. Results A neutrophil module (Neu_M20) was ranked top in the random forest analysis among 255 modules created by iterativeWGCNA. Neu_M20 correlated with disease activity and neutrophil counts but not with the presence of antineutrophil cytoplasmic antibody. The module comprised pro-inflammatory genes, including those related to NETosis, supported by experimental evidence. The genes in the module significantly overlapped GADGs. Conclusion We identified the distinct group of pro-inflammatory genes in neutrophils, which characterize AAV. Further investigations are warranted to confirm our findings as they could serve as novel therapeutic targets.

Thrombotic microangiopathies (TMAs) rarely accompany polymyositis/dermatomyositis. We treated three patients with dermatomyositis combined with TMA. A literature review identified 13 previously reported cases. Exacerbation of myositis at the time of the TMA onset was observed in 62.5% of all patients, suggesting that the TMA onset may be associated with autoantibody production. We also found that cases of TMA with polymyositis/dermatomyositis often had a poor treatment response rate (37.5%). Furthermore, even if treatment was effective, the mortality rate associated with subsequent complications was high, and the survival rate was low (18.8%). Therefore, careful attention should be paid to patient management after TMA treatment.

Summary Genetic studies have revealed many variant loci that are associated with immune-mediated diseases. To elucidate the disease pathogenesis, it is essential to understand the function of these variants, especially under disease-associated conditions. Here, we performed a large-scale immune cell gene-expression analysis, together with whole-genome sequence analysis. Our dataset consists of 28 distinct immune cell subsets from 337 patients diagnosed with 10 categories of immune-mediated diseases and 79 healthy volunteers. Our dataset captured distinctive gene-expression profiles across immune cell types and diseases. Expression quantitative trait loci (eQTL) analysis revealed dynamic variations of eQTL effects in the context of immunological conditions, as well as cell types. These cell-type-specific and context-dependent eQTLs showed significant enrichment in immune disease-associated genetic variants, and they implicated the disease-relevant cell types, genes, and environment. This atlas deepens our understanding of the immunogenetic functions of disease-associated variants under in vivo disease conditions.

The effects of autoclave and microwave heating on the protein and oil in soybean seeds were investigated under low moisture conditions. The nitrogen solubility index (NSI) decreased on heating. The reduction in the NSI was accompanied by an increase in the size and deformation of the oil bodies in the cellular tissue of soybean seeds. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis revealed that lipoxygenase was susceptible to heat denaturation, but 7S and 11S globulins were only partially denatured. The partial denaturation of the proteins was confirmed by Fourier transform infrared spectroscopy measurements. The ratio of oil to protein peaks increased with increasing heating, suggesting the exudation of oil to the surface or outside of oil bodies. Microwave heating is more efficient in changing the oil distribution in soybean seeds than autoclave heating. On the other hand, the degree of protein denaturation is lower after microwave heating.

We report here on the first case, to our knowledge, of retro-odontoid pseudotumor (ROP) in a patient with an autoimmune disease other than rheumatoid arthritis (RA). It is possible that the onset of ROP was related to Sjogren syndrome (SS) with serology for systemic lupus erythematosus (SLE). A 34-year-old man presented with an ROP without RA. Three years earlier, he had sicca symptoms and many renal and splenic infarctions, and was diagnosed with SS and antiphospholipid antibody syndrome. The anti-SSA, anti-SSB, anti-dsDNA, anti-RNP, and anti-Sm antibodies and …