Epigenome-wide association study and network analysis for IgA Nephropathy from CD19+ B-cell in Chinese Population

Integrated analysis of ATAC-seq and RNA-seq reveals the chromatin accessibility and transcriptional landscape of immunoglobulin a nephropathy

BACKGROUNDS

The association between chromatin accessibility in CD4+ T cells and Immunoglobulin A nephropathy (IgAN) remains unclear.

METHODS

We performed the assay for transposase accessible chromatin with sequencing (ATAC-seq) and RNA sequencing (RNA-seq) on CD4+ T cells. ATAC-seq and RNA-seq were conducted to identify differentially accessible regions and differentially expressed genes (DEGs), respectively (P < 0.05, |log2 Fold Change| >1). QRT-PCR was utilized to validate target gene expression.

RESULTS

We identified 100,865 differentially accessible regions, of which 7225 exhibited higher accessibility in IgAN. Functional analysis revealed that these regions are enriched in T lymphocyte activation and immune pathways. ELF3, MEIS1, and NFYC were identified as key TFs associated with IgAN. QRT-PCR indicated a significant upregulation of hub genes including MEIS1 in IgAN.

CONCLUSION

We identified key TFs and genes by integrating ATAC-seq and RNA-seq, which provide novel therapeutic targets for IgAN and insights into its pathogenesis from an epigenetic perspective.

Patients With Immunoglobulin A Nephropathy Show Abnormal Frequencies of B Cell Subsets, Unconventional T Cells, and High Levels of Galactose-Deficient IgA1-Coated Gut Bacteria

Introduction

Mucosal inflammation is involved in the pathophysiology of immunoglobulin-A nephropathy (IgAN); however, peripheral immune phenotype analyses of patients with IgAN often do not include unconventional T cells, the major subset in mucosal immunity.

Methods

We measured serum total IgA, galactose-deficient IgA1 (gd-IgA1), secretory IgA (SIgA), B cell-activating factor (BAFF), and A proliferation-inducing ligand (APRIL) in 66 patients with IgAN and 30 healthy controls (HCs). We also quantified the total IgA and gd-IgA1 in stool supernatant along with the same coated on bacteria. In 35 patients and 14 controls, we performed extensive phenotyping using cytometry by Time-of-Flight (CyTOF) of circulating immune cells, including unconventional T cells (mucosal associated invariant T [MAIT] cells, γδ T, and natural killer [NK] T cells). The results were validated using RNAseq data from a larger cohort of 179 patients with IgAN, 140 patients with minimal change disease, and 91 HCs.

Results

Patients with IgAN had higher circulating levels of total IgA, gd-IgA1, and APRIL, and higher IgA and gd-IgA1-coated gut bacteria than controls, whereas serum levels of SIgA and BAFF did not differ between groups. Patients with IgAN showed more class-switched memory (CSM) and double negative (DN) B cells than controls. MAIT cells and γδ T cells were significantly lower, and CD4-CD8- NK T cells were significantly higher in patients with IgAN than in HCs. We validated the significant decrease in MAIT cells in an independent cohort of patients with IgAN.

Conclusion

The data indicate that patients with IgAN have increased circulating CSM and DN B cells associated with abnormal T cell immunity, involving defects in unconventional T cell frequency. This may suggest putative alterations at mucosal sites because of cell migration leading to altered IgA production.

Genetic association study of TERT gene variants with chronic kidney disease susceptibility in the Chinese population

The incidence and mortality of chronic kidney disease (CKD) are increasing globally. Studies have demonstrated the significance of genetic risk factors in the progression of CKD. Telomerase reverse transcriptase (TERT) may be implicated in the development of CKD. This study aimed to investigate the correlation between TERT gene variants and susceptibility to CKD in the Chinese population. A total of 507 patients with CKD and 510 healthy controls were recruited for this case-control study. Four candidate loci were identified using the MassARRAY platform. Logistic regression analysis was employed to assess the association between TERT gene variants and the risk of CKD. The false positive reporting probability (FPRP) method was utilized to evaluate the validity of statistically significant associations. The multifactorial dimensionality reduction (MDR) method was used to evaluate the interaction between SNPs and the risk of CKD. Furthermore, discrepancies in the clinical features of subjects with diverse genotypes were evaluated using one-way analysis of variance (ANOVA). Our findings revealed a correlation between rs2735940 and rs4635969 and an increased risk of CKD. Stratification analysis indicated that rs4635969 was related to an increased risk of CKD in different subgroups (age ≤ 50 years and male). MDR analysis indicated that the two-site model (rs2735940 and rs4635969) was the best prediction model. Furthermore, the rs2735940 GG genotype was found to be linked to an increased level of microalbuminuria (MAU) in patients with CKD. Our study is the first to reveal a connection between TERT gene variants and susceptibility to CKD, providing new insights into the field of nephrology.

The Genetics of IgA Nephropathy: Implications for Future Therapies

IgA nephropathy (IgAN), the most prevalent primary glomerulonephritis worldwide, carries a considerable lifetime risk of kidney failure. The etiology of IgAN, however, remains incompletely understood, and effective treatment is lacking. Although the multihit model effectively identifies key steps in IgAN development and, to date, provides the best description of IgAN pathogenesis, it remains under development to fully capture the complexity of immune system dysregulation. Large-scale genome-wide association studies have revealed clues regarding the association between IgAN and genes in both innate and adaptive immune pathways. Hence, genetic investigations may shed light on the aberrant molecular mechanisms, thereby presenting new opportunities for therapeutic advancements. This review discusses the genetic associations that have been robustly connected with IgAN, placing them within the framework of disease mechanism. Altogether, these findings highlight numerous new possibilities for the development of treatments and the road to personalized medicine.

Sinomenine Hydrochloride Protects IgA Nephropathy Through Regulating Cell Growth and Apoptosis of T and B Lymphocytes

Purpose

Sinomenine hydrochloride (SH) is used to treat chronic inflammatory diseases such as rheumatoid arthritis and may also be efficacious against Immunoglobulin A nephropathy (IgAN). However, no trial has investigated the molecular mechanism of SH on IgAN. Therefore, this study aims to investigate the effect and mechanism of SH on IgAN.

Methods

The pathological changes and IgA and C3 depositions in the kidney of an IgAN rat model were detected by periodic acid-Schiff (PAS) and direct immunofluorescence staining. After extracting T and B cells using immunomagnetic beads, we assessed their purity, cell cycle phase, and apoptosis stage through flow cytometry. Furthermore, we quantified cell cycle-related and apoptosis-associated proteins by Western blotting.

Results

SH reduced IgA and C3 depositions in stage 4 IgAN, thereby decreasing inflammatory cellular infiltration and mesangial injury in an IgAN model induced using heteroproteins. Furthermore, SH arrested the cell cycle of lymphocytes T and B from the spleen of IgAN rats. Regarding the mechanism, our results demonstrated that SH regulated the Cyclin D1 and Cyclin E1 protein levels for arresting the cell cycle and it also regulated Bax and Bcl-2 protein levels, thus increasing Cleaved caspase-3 protein levels in Jurkat T and Ramos B cells.

Conclusion

SH exerts a dual regulation on the cell cycle and apoptosis of T and B cells by controlling cell cycle-related and apoptosis-associated proteins; it also reduces inflammatory cellular infiltration and mesangial proliferation. These are the major mechanisms of SH in IgAN.

An Update on the Genetics of IgA Nephropathy

Immunoglobulin A (IgA) nephropathy (IgAN), the most common form of glomerulonephritis, is one of the leading causes of end-stage kidney disease (ESKD). It is widely believed that genetic factors play a significant role in the development of IgAN. Previous studies of IgAN have provided important insights to unravel the genetic architecture of IgAN and its potential pathogenic mechanisms. The genome-wide association studies (GWASs) together have identified over 30 risk loci for IgAN, which emphasizes the importance of IgA production and regulation in the pathogenesis of IgAN. Follow-up fine-mapping studies help to elucidate the candidate causal variant and the potential pathogenic molecular pathway and provide new potential therapeutic targets. With the rapid development of next-generation sequencing technologies, linkage studies based on whole-genome sequencing (WGS)/whole-exome sequencing (WES) also identify rare variants associated with IgAN, accounting for some of the missing heritability. The complexity of pathogenesis and phenotypic variability may be better understood by integrating genetics, epigenetics, and environment. We have compiled a review summarizing the latest advancements in genetic studies on IgAN. We similarly summarized relevant studies examining the involvement of epigenetics in the pathogenesis of IgAN. Future directions and challenges in this field are also proposed.

Detection of N‑glycoprotein associated with IgA nephropathy in urine as a potential diagnostic biomarker using glycosylated proteomic analysis

The aim of the present study was to elucidate the potential diagnostic value of urinary N-glycoprotein in patients with IgA nephropathy (IgAN) using mass spectrometry (MS). All procedures were performed between June 2021 and June 2023 at Guangan People's Hospital (Guangan, China). Fresh mid-morning fasting midstream urine samples were collected from a total of 30 patients with IgAN and 30 sex- and age-matched healthy volunteers. Data acquired from 6 participants are available through ProteomeXchange with the identifier PXD041151. By comparison between the IgAN group (n=3) and healthy controls (n=3) and selection criteria of P<0.05 and |log fold-change|>2, a total of 11 upregulated and 22 downregulated glycoproteins in patients with IgAN were identified. The results of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses suggested that glycoproteins are involved in various functions, such as the regulation of cell growth, cell adhesion, cellular component organization and protein binding, as well as multiple pathways, including p53, Notch and mTOR signaling pathways. The urine levels of afamin were further measured by ELISA in a validation cohort to assess the diagnostic performance of the single indicator model. In conclusion, MS-based proteomics of urinary glycoproteins may be an alternative option for diagnosing patients with IgAN. Biomarkers of IgAN may include, but are not limited to, CCL25, PD-L1, HLA-DRB1, IL7RD and WDR82. In addition, the levels of urinary AFM indicators are of diagnostic value for IgAN.

Deciphering prognostic value of CD22 and its contribution to suppression of proinflammatory cytokines production in patients with IgA nephropathy

BACKGROUND

CD22, mainly expressed in mature B cells, could negatively regulate the function of B cells by binding to sialic acid-positive IgG (SA-IgG). Soluble CD22 (sCD22) is generated by the cleavage of the extracellular domain of CD22 on the membrane surface. However, the role of CD22 in IgA nephropathy (IgAN) remains unknown.

METHODS

A total of 170 IgAN patients with a mean follow-up of 18 months were included in this study. The sCD22, TGF-β, IL-6 and TNF-α were detected using commercial ELISA kits. SA-IgG were purified to stimulate peripheral blood mononuclear cells (PBMCs) from IgAN patients.

RESULTS

The plasma levels of sCD22 were lower in IgAN patients in comparison with healthy control. Furthermore, CD22 mRNA levels in PBMCs from patients with IgAN were significantly lower than those of healthy controls. The plasma levels of sCD22 were positively correlated to the mRNA levels of CD22. We found that patients with higher sCD22 levels had a lower level of serum creatinine and a higher level of eGFR on the time of renal biopsy and a higher remission rate of proteinuria and a lower risk of kidney events at the end of follow-up. The logistic regression analysis showed sCD22 was associated with an increased odd of proteinuria remission after being adjusted for eGFR, proteinuria, and SBP. After adjusting for confounding variables, sCD22 was a borderline significant predictor of less kidney composite endpoint. In addition, the sCD22 levels were positively associated with SA-IgG in plasma. The experimental results in vitro showed that addition of SA-IgG enhanced the release of sCD22 in cell supernatant and the phosphorylation of CD22 in PBMCs, further inhibiting the production of IL-6, TNF-α, and TGF-β in cell supernatant in a dose-dependent manner. Pretreatment with CD22-antibody significantly increased the expression of cytokines in PBMCs.

CONCLUSIONS

This is the first study to demonstrate that lower plasma soluble CD22 in IgAN patients and high soluble CD22 levels are associated with an increased odd of proteinuria remission and a decreased odd of kidney endpoint. The interaction between CD22 and SA-IgG can inhibit proliferation and inflammation release in PBMCs from IgAN patients.