IgG Immunocomplexes Sensitize Human Monocytes for Inflammatory Hyperactivity via Transcriptomic and Epigenetic Reprogramming in Rheumatoid Arthritis.

Prevalence of circulating immunocomplexes (ICs) strongly correlates with rheumatoid arthritis (RA) in humans. Deposits of IgG-ICs are abundant in affected joints of patients, yet molecular mechanisms for the pathogenic roles of such ICs are not fully understood. In this study, we present evidence that IgG-ICs precipitated from RA sera sensitized human monocytes for a long-lasting inflammatory functional state, characterized by a strong TNF-α response to cellular proteins representing damage-associated molecular patterns and microbe-derived pathogen-associated molecular patterns. Importantly, plate-coated human IgG (a mimic of deposited IC without Ag restriction) exhibited a similarly robust ability of monocyte sensitization in vitro. The plate-coated human IgG-induced functional programming is accompanied by transcriptomic and epigenetic modification of various inflammatory cytokines and negative regulator genes. Moreover, macrophages freshly isolated from synovia of patients with RA, but not sera-negative arthropathy, displayed a signature gene expression profile highly similar to that of IC-sensitized human monocytes, indicative of historical priming events by IgG-ICs in vivo. Thus, the ability of IgG-ICs to drive sustainable functional sensitization/reprogramming of monocytes and macrophages toward inflammation may render them key players in the development of RA.

Rheumatoid arthritis-associated DNA methylation sites in peripheral blood mononuclear cells.

OBJECTIVES: To identify novel DNA methylation sites significant for rheumatoid arthritis (RA) and comprehensively understand their underlying pathological mechanism. METHODS: We performed (1) genome-wide DNA methylation and mRNA expression profiling in peripheral blood mononuclear cells from RA patients and health controls; (2) correlation analysis and causal inference tests for DNA methylation and mRNA expression data; (3) differential methylation genes regulatory network construction; (4) validation tests of 10 differential methylation positions (DMPs) of interest and corresponding gene expressions; (5) correlation between PARP9 methylation and its mRNA expression level in Jurkat cells and T cells from patients with RA; (6) testing the pathological functions of PARP9 in Jurkat cells. RESULTS: A total of 1046 DNA methylation positions were associated with RA. The identified DMPs have regulatory effects on mRNA expressions. Causal inference tests identified six DNA methylation-mRNA-RA regulatory chains (eg, cg00959259-PARP9-RA). The identified DMPs and genes formed an interferon-inducible gene interaction network (eg, MX1, IFI44L, DTX3L and PARP9). Key DMPs and corresponding genes were validated their differences in additional samples. Methylation of PARP9 was correlated with mRNA level in Jurkat cells and T lymphocytes isolated from patients with RA. The PARP9 gene exerted significant effects on Jurkat cells (eg, cell cycle, cell proliferation, cell activation and expression of inflammatory factor IL-2). CONCLUSIONS: This multistage study identified an interferon-inducible gene interaction network associated with RA and highlighted the importance of PARP9 gene in RA pathogenesis. The results enhanced our understanding of the important role of DNA methylation in pathology of RA.

Identification of expression quantitative trait loci (eQTLs) in human peripheral blood mononuclear cells (PBMCs) and shared with liver and brain.

PBMCs are essential for immunity and involved in various diseases. To identify genetic variations contributing to PBMCs transcriptome-wide gene expression, we performed a genome-wide eQTL analysis by using genome-wide SNPs data and transcriptome-wide mRNA expression data. To assess whether there are common regulation patterns shared among different tissues/organs, public datasets were utilized to identify common eQTLs shared with PBMCs in lymphoblastoid, monocytes, liver, and brain. Allelic expression imbalance (AEI) assay was employed to validate representative eQTLs identified. We identified 443 cis- and 2386 trans-eSNPs (FDR <0.05), which regulated 128 and 635 target genes, respectively. A transcriptome-wide expression regulation network was constructed, highlighting the importance of 28 pleiotropic eSNPs and 18 dually (cis- and trans-) regulated genes. Three genes, that is, TIPRL, HSPB8, and EGLN3, were commonly regulated by hundreds of eSNPs and constituted a very complex interaction network. Strikingly, the missense SNP rs371513 trans- regulated 25 target genes, which were functionally related to poly(A) RNA binding. Among 8904 eQTLs (P < 0.001) identified herein in PBMCs, a minority (163) was overlapped with lymphoblastoid, monocytes, liver, and/or brain. Besides, two cis-eSNPs in PBMC were confirmed by AEI. The present results demonstrated a comprehensive expression regulation network for human PBMCs and may provide novel insights into the pathogenesis of immunological diseases related to PBMCs.

Multiple correlation analyses revealed complex relationship between DNA methylation and mRNA expression in human peripheral blood mononuclear cells.

DNA methylation is an important regulator on the mRNA expression. However, a genome-wide correlation pattern between DNA methylation and mRNA expression in human peripheral blood mononuclear cells (PBMCs) is largely unknown. The comprehensive relationship between mRNA and DNA methylation was explored by using four types of correlation analyses and a genome-wide methylation-mRNA expression quantitative trait locus (eQTL) analysis in PBMCs in 46 unrelated female subjects. An enrichment analysis was performed to detect biological function for the detected genes. Single pair correlation coefficient (r T1) between methylation level and mRNA is moderate (-0.63-0.62) in intensity, and the negative and positive correlations are nearly equal in quantity. Correlation analysis on each gene (T4) found 60.1% genes showed correlations between mRNA and gene-based methylation at P < 0.05 and more than 5.96% genes presented very strong correlation (R T4 > 0.8). Methylation sites have regulation effects on mRNA expression in eQTL analysis, with more often observations in region of transcription start site (TSS). The genes under significant methylation regulation both in correlation analysis and eQTL analysis tend to cluster to the categories (e.g., transcription, translation, regulation of transcription) that are essential for maintaining the basic life activities of cells. Our findings indicated that DNA methylation has predictive regulation effect on mRNA with a very complex pattern in PBMCs. The results increased our understanding on correlation of methylation and mRNA and also provided useful clues for future epigenetic studies in exploring biological and disease-related regulatory mechanisms in PBMC.

Integrative multi-omics analysis revealed SNP-lncRNA-mRNA (SLM) networks in human peripheral blood mononuclear cells.

Long non-coding RNAs (lncRNAs) serve as important controller of cellular functions via regulating RNA transcription, degradation and translation. However, what are the regulation patterns of lncRNAs on downstream mRNA and how the upstream genetic variants regulate lncRNAs are largely unknown. We first performed a comprehensive expression quantitative trait locus (eQTL) analysis (MatrixeQTL package, R) using genome-wide lncRNA expression and SNP genotype data from human peripheral blood mononuclear cells (PBMCs) of 43 unrelated individuals. Subsequently, multi-omics integrative network analysis was applied to construct SNP-lncRNA-mRNA (SLM) interaction networks. The causal inference test (CIT) was used to identify lncRNA-mediated (epi-) genetic regulation on mRNA expressions. Our eQTL analysis detected 707 pairs of cis-effect associations (p < 5.64E-06) and 6657 trans-effect associations (p < 3.51E-08), respectively. We also found that top significant cis-eSNPs were enriched around the lncRNA transcription start site regions, and that enrichment patterns of cis-eSNPs differs among different lncRNA sizes (small, medium and large).The constructed SLM interaction networks (1 primary networks and four small separate networks) showed various complex interaction patterns. Especially, the in-depth CIT detected 50 significant lncRNA-mediated SLM trios, and some hotspots (e.g., SNPs: rs926370, rs7716167 and rs16880521; lncRNAs: HIT000061975 and ENST00000579057.1). This study represents the first effort of dissecting the SLM interaction patterns in PBMCs by multi-omics integrative network analysis and causal inference test for clearing the regulation chain. The results provide novel insights into the regulation patterns of lncRNA, and may facilitate investigations of PBMC-related immune physiological process and immunological diseases in the future.

IgG Immunocomplexes Drive the Differentiation of a Novel Subset of Osteoclasts Independent of RANKL and Inflammatory Cytokines.

Potentiation of receptor activator of NF-κB ligand (RANKL)-induced osteoclastogenesis by IgG immunocomplexes (ICs) is generally considered an important pathway leading to cartilage and bone destruction in rheumatoid arthritis (RA). However, whether IgG ICs possess pro-osteoclastogenic potential independent of RANKL and inflammatory cytokines is unclear. Here we demonstrate that by fully cross-linking human FcγRIIa (hFcγRIIa) or co-ligating hFcγRIIa and TLR4, IgG ICs alone could drive the differentiation of human blood monocytes into nuclear factor of activated T cells cytoplasmic 1 (NFATc1-negative nonclassical osteoclasts (NOCs). Surprisingly, IgG ICs could also overrule RANKL-induced classical osteoclast (COC) differentiation in vitro. In mouse model of collagen-induced arthritis, hFcγRIIa-transgenic, but not nontransgenic control, mice suffered from cartilage/bone destruction accompanied by the presence of NFATc1- NOCs lining the eroded cartilage surface in affected joints. Our results not only identify a novel subset of IC-induced NOCs but also provide a possible explanation for the uncoupling of FcγR-mediated cartilage destruction from RANKL-related bone erosion in autoinflammatory arthritis. © 2021 American Society for Bone and Mineral Research (ASBMR)..

[Study on regulatory effect of Bushen Antai Recipe on levels of estrogen and progesterone in blastocyst implantation dysfunction mice].

OBJECTIVE: To investigate the effect and explore the mechanism of Bushen Antai Recipe (BAR) on pregnancy rate and number of implantation site in blastocyst implantation dysfunction (BID) mice induced by indomethacin. METHODS: Pregnant mice were divided into 3 groups randomly: the normal group, the model group and the BAR group. Tap water was given orally to the rats in the normal and model groups, and BAR to the rats in the BAR group from the first day of pregnancy for 5 or 8 days; on the 3rd and 4th day dissolvent was injected subcutaneously twice per day in the normal group, while indomethacin (4.33 mg/kg) was injected subcutaneously twice per day in the other two groups to establish implantation dysfunction model; serum estrogen (E) and progesterone (P4) levels were detected on the 5th and 8th day; the pregnancy rate and number of implanted site was observed and the receptors of E and P4 in endometrium of uterus were examined by immunohistochemistry on the 8th day. RESULTS: The pregnancy rate and number of implanted site was 27.3% and 5.3 +/- 0.7 respectively in the model group, significantly lower than those in the normal group (90.9%, 13.3 +/- 2.8), and the BAR group (72.7%, 10.7 +/- 2.2, P < 0.05). Serum E level was higher in the BAR group than that in the model group on the 5th and 8th day, and even higher than that in the normal group on the 8th day; serum P4 level was lower in the model and BAR groups than that in the normal group on the 5th day (P < 0.01), but higher in the BAR group than that in the model group on the 8th day. Immunohistochemical observation showed that expressions of E and P4 receptor increased remarkably in the BAR group than those in the model group. CONCLUSION: BAR increases the pregnancy rate and number of implanted site of indomethacrne induced BID mice through regulating E and P4 levels and enhancing the expressions of their receptors in the endometrium.