Expression profile of PU.1 in CD4+T cells from patients with systemic lupus erythematosus

Molecular profiling and therapeutic tailoring to address disease heterogeneity in systemic lupus erythematosus

Systemic lupus erythematosus (SLE) is a chronic, heterogeneous, systemic autoimmune disease characterized by autoantibody production, complement activation, and immune complex deposition. SLE predominantly affects young, middle-aged, and child-bearing women with episodes of flare-up and remission, although it affects males at a much lower frequency (female: male; 7:1 to 15:1). Technological and molecular advancements have helped in patient stratification and improved patient prognosis, morbidity, and treatment regimens overall, impacting quality of life. Despite several attempts to comprehend the pathogenesis of SLE, knowledge about the precise molecular mechanisms underlying this disease is still lacking. The current treatment options for SLE are pragmatic and aim to develop composite biomarkers for daily practice, which necessitates the robust development of novel treatment strategies and drugs targeting specific responsive pathways. In this communication, we review and aim to explore emerging therapeutic modalities, including multiomics-based approaches, rational drug design, and CAR-T-cell-based immunotherapy, for the management of SLE.

Immunoprofiling of cytokines, chemokines, and growth factors in female patients with systemic lupus erythematosus- a pilot study

Systemic Lupus Erythematosus (SLE) is a chronic autoimmune disease affecting different organ systems. This study aimed to determine the concentrations of 30 different human cytokines, chemokines, and growth factors in human plasma to understand the role of these markers in the pathogenicity of SLE using Luminex Multiple Analyte Profiling (xMAP) technology. Plasma samples were obtained from patients with SLE (n = 28), osteoarthritis (OA) (n = 9), and healthy individuals (n = 12) were obtained. High levels of TNF, IL-6, IFN-γ, INF-α, IL-4, IL-5, IL-13, IL-8, IP-10, MIG, MCP-1, MIP-1β, GM-CSF, G-CSF, EGF, VEGF, IL-12, IL-1RA, and IL-10 was detected in SLE patients compared with the OA and healthy control groups. xMAP analysis has been used to address the differential regulation of clinical heterogeneity and immunological phenotypes in SLE patients. In addition, complete disease phenotyping information along with cytokine immune profiles would be useful for developing personalized treatments for patients with SLE.

3D genome alterations in T cells associated with disease activity of systemic lupus erythematosus

OBJECTIVES

Three-dimensional (3D) genome alterations can dysregulate gene expression by rewiring physical interactions within chromosomes in a tissue-specific or cell-specific manner and lead to diseases. We aimed to elucidate the 3D genome structure and its role in gene expression networks dysregulated in systemic lupus erythematosus (SLE).

METHODS

We performed Hi-C experiments using CD4+ T cells from 7 patients with SLE and 5 age-matched and sex-matched healthy controls (HCs) combined with RNA sequencing analysis. Further integrative analyses, including transcription factor motif enrichment, SPI1 knockdown and histone modifications (H3K27ac, H3K4me1, H3K4me3), were performed for altered loop-associated gene loci in SLE.

RESULTS

We deciphered the 3D chromosome organisation in T cells of patients with SLE and found it was clearly distinct from that of HCs and closely associated with the disease activity of SLE. Importantly, we identified loops within chromosomes associated with the disease activity of SLE and differentially expressed genes and found some key histone modifications close to these loops. Moreover, we demonstrated the contribution of the transcription factor SPI1, whose motif is located in the altered loop in SLE, to the overexpression of interferon pathway gene. In addition, we identified the potential influences of genetic variations in 3D genome alterations in SLE.

CONCLUSIONS

Our results highlight the 3D genome structure alterations associated with SLE development and provide a foundation for future interrogation of the relationships between chromosome structure and gene expression control in SLE.

Potential biomarkers for active renal involvement in systemic lupus erythematosus patients

OBJECTIVE

This study aimed to identify the key genes related to active renal involvement in patients with systemic lupus erythematosus (SLE).

METHODS

Microarray datasets were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between SLE patients with active renal involvement and those who did not have active renal involvement were identified by R software. Hub genes were identified using protein-protein interaction networks. The relationships between the expression levels of identified hub genes and SLEDAI were subjected to linear correlation analysis. The diagnostic accuracy of the hub genes was evaluated with the area under the curve of the receiver operating characteristic curve (ROC-AUC). Transcription factors (TFs) were predicted. The expression levels of different hub genes and histopathological patterns were also examined.

RESULTS

A total of 182 DEGs were identified. Enrichment analysis indicated that DEGs were primarily enriched in neutrophil degranulation, neutrophil activation involved in immune response and neutrophil activation. The expression levels of 12 identified hub genes were verified. Ten of the 12 hub genes were positively associated with SLEDAI. The combination model of DEFA4, CTSG, RETN, CEACAM8, TOP2A, LTF, MPO, ELANE, BIRC5, and LCN2 had a certain diagnostic accuracy in detecting renal involvement with high disease activity in SLE patients. The expressions of five predicted TFs were validated by GSE65391 dataset.

CONCLUSION

This work explored the pathogenesis of renal involvement in SLE. These results may guide future experimental research and clinical transformation.

Genome-wide association study of SNP- and gene-based approaches to identify susceptibility candidates for lupus nephritis in the Han Chinese population

Background

Lupus nephritis (LN) is one of the most common and serious complications of systemic lupus erythaematosus (SLE). Genetic factors play important roles in the pathogenesis of LN and could be used to predict who might develop LN. The purpose of this study was to screen for susceptible candidates of LN across the whole genome in the Han Chinese population.

Methods

592 LN patients and 453 SLE patients without renal damage were genotyped at 492,970 single nucleotide polymorphisms (SNPs) in the genome-wide association study (GWAS). Fifty-six SNPs were selected for replication in an independent cohort of 188 LN and 171 SLE without LN patients. Further quantitative real-time (qRT) PCR was carried out in 6 LN patients and 6 healthy controls. Gene-based analysis was conducted using the versatile gene-based test for GWAS. Subsequently, enrichment and pathway analyses were performed in the DAVID database.

Results

The GWAS analysis and the following replication research identified 9 SNPs showing suggestive correlation with LN (P<10-4). The most significant SNP was rs12606116 (18p11.32), at P=8.72×10−6. The qRT-PCR results verified the mRNA levels of LINC00470 and ADCYAP1, the closest genes to rs12606116, were significantly lower in LN patients. From the gene-based analysis, 690 genes had suggestive evidence of association (P<0.05), including LINC00470. The enrichment analysis identified the involvement of transforming growth factor beta (TGF-β) signalings in the development of LN. Lower plasma level of TGF-β1 (P<0.05) in LN patients and lower expression of transforming growth factor beta receptor 2 in lupus mice kidney (P<0.05) futher indicate the involvement of TGF-β in LN.

Conclusions

Our analyses identified several promising susceptibility candidates involved in LN, and further verification of these candidates was necessary.

The role of a key transcription factor PU.1 in autoimmune diseases

PU.1, a transcription factor member of the E26 transformation-specific family, affects the function of a variety of immune cells in several physiological and pathological conditions. Previous studies studying the role of PU.1 in pathological conditions have mainly focused on immune system-related cancers, and a series of articles have confirmed that PU.1 mutation can induce a variety of immune cell-related malignancies. The underlying mechanism has also been extensively validated. However, the role of PU.1 in other major immune system-related diseases, namely, systemic autoimmune diseases, is still unclear. It was only in recent years that researchers began to gradually realize that PU.1 also played an important role in a variety of autoimmune diseases, such as rheumatoid arthritis (RA), experimental autoimmune encephalomyelitis (EAE) and systemic lupus erythematosus (SLE). This review article summarizes the findings of recent studies that investigated the role of PU.1 in various autoimmune diseases and the related underlying mechanisms. Furthermore, it presents new ideas and provides insight into the role of PU.1 as a potential treatment target for autoimmune diseases and highlights existing research problems and future research directions in related fields.